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2024

Gandhi, Rajesh T; Landovitz, Raphael J; Sax, Paul E; Smith, Davey M; Springer, Sandra A; Günthard, Huldrych F; Thompson, Melanie A; Bedimo, Roger J; Benson, Constance A; Buchbinder, Susan P; Crabtree-Ramirez, Brenda E; Del Rio, Carlos; Eaton, Ellen F; Eron, Joseph J; Hoy, Jennifer F; Lehmann, Clara; Molina, Jean-Michel; Jacobsen, Donna M; Saag, Michael S (2024). Antiretroviral Drugs for Treatment and Prevention of HIV in Adults: 2024 Recommendations of the International Antiviral Society-USA Panel. JAMA : the Journal of the American Medical Association:Epub ahead of print.

Groen, Kevin; Kuratli, Roger; Sar, Lauren; Vasou, Andri; Huber, Michael; Hughes, David J; Hale, Benjamin G (2024). Highly sensitive reporter cell line for detection of interferon types I-III and their neutralization by antibodies. European Journal of Immunology, 54(12):e2451325.

Fusco, Dahlene; Malenica, Ivana; Günthard, Huldrych F; Gupta, Samir K; Kurbegov, Dax; Balani, Bindu; Olender, Susan; Aberg, Judith A; Telep, Laura E; Tian, Yuan; Blair, Christiana; Wu, George; Haubrich, Richard; Wang, Chen-Yu; Chokkalingam, Anand P; Osinusi, Anu O; Wendtner, Clemens-Martin; Gottlieb, Robert L (2024). Remdesivir for Treatment of COVID-19 Requiring Oxygen Support: A Cross-Study Comparison from Two Large, Open-Label Studies. Clinical Infectious Diseases, 79(5):1182-1189.

Tusch, Erich; Ryom, Lene; Pelchen-Matthews, Annegret; Mocroft, Amanda; Elbirt, Daniel; Oprea, Cristiana; Günthard, Huldrych F; Staehelin, Cornelia; Zangerle, Robert; Suarez, Isabelle; Vehreschild, Jörg Janne; Wit, Ferdinand; Menozzi, Marianna; d'Arminio Monforte, Antonella; Spagnuolo, Vincenzo; Pradier, Christian; Carlander, Christina; Suanzes, Paula; Wasmuth, Jan-Christian; Carr, Andrew; Petoumenos, Kathy; Borgans, Frauke; Bonnet, Fabrice; De Wit, Stephane; El-Sadr, Wafaa; Neesgaard, Bastian; Jaschinski, Nadine; Greenberg, Lauren; Hosein, Sean R; Gallant, Joel; et al (2024). Trends in mortality in people with HIV from 1999 to 2020: a multi-cohort collaboration. Clinical Infectious Diseases, 79(5):1242-1257.

Ballif, Marie; Braun, Dominique; Calmy, Alexandra; Bernasconi, Enos; Cavassini, Matthias; Tissot, Frédéric; Stoeckle, Marcel; Schmid, Patrick; Fux, Christoph A; Van der Valk, Marc; Brinkman, Kees; Mudrikova, Tania; Bonnet, Fabrice; Leleux, Olivier; Saúde, Manuela; Hirter, Daniela; Schwab, Nathalie; Limacher, Andreas; Rintelen, Felix; Kouyos, Roger; Haerry, David; Zambrano, Sofia C; Egloff, Martina; Akre, Christina; Peytremann-Bridevaux, Isabelle; Rauch, Andri; Wandeler, Gilles; Surial, Bernard (2024). Booster-free anti-retroviral therapy for persons living with HIV and multidrug resistance (B-Free): protocol for a multicentre, multistage, randomised, controlled, non-inferiority trial. BMJ Open, 14(11):e094912.

Lanz, Caroline; Meier, Jan; Stöckle, Marcel; Furrer, Hansjakob; Calmy, Alexandra; Cavassini, Matthias; Bernasconi, Enos; Schmid, Patrick; Braun, Dominique L; Kouyos, Roger D; Loosli, Tom; Kusejko, Katharina; Günthard, Huldrych F; Swiss HIV Cohort Study (2024). HIV-1 low-level viremia predicts viral failure in participants on antiretroviral therapy in the Swiss HIV Cohort Study. Clinical Infectious Diseases:Epub ahead of print.

Thoueille, Paul; Saldanha, Susana Alves; Schaller, Fabian; Choong, Eva; Veuve, François; Munting, Aline; Cavassini, Matthias; Braun, Dominique; Günthard, Huldrych F; Duran Ramirez, Jessy J; Surial, Bernard; Furrer, Hansjakob; Rauch, Andri; Ustero, Pilar; Calmy, Alexandra; Stöckle, Marcel; Di Benedetto, Caroline; Bernasconi, Enos; Schmid, Patrick; Marzolini, Catia; Girardin, Francois R; Buclin, Thierry; Decosterd, Laurent A; Guidi, Monia (2024). Population pharmacokinetics of rilpivirine following oral administration and long-acting intramuscular injection in real-world people with HIV. Frontiers in Pharmacology, 15:1437400.

Tepekule, Burcu; Jörimann, Lisa; Schenkel, Corinne D; Opitz, Lennart; Tschumi, Jasmin; Wolfensberger, Rebekka; Neumann, Kathrin; Kusejko, Katharina; Zeeb, Marius; Boeck, Lucas; Kälin, Marisa; Notter, Julia; Furrer, Hansjakob; Hoffmann, Matthias; Hirsch, Hans H; Calmy, Alexandra; Cavassini, Matthias; Labhardt, Niklaus D; Bernasconi, Enos; Oesch, Gabriela; Metzner, Karin J; Braun, Dominique L; Günthard, Huldrych F; Kouyos, Roger D; Duffy, Fergal; Nemeth, Johannes (2024). Transcriptional profile of Mycobacterium tuberculosis infection in people living with HIV. iScience, 27(11):111228.

Glas, Irina. Inactivation of Influenza and Coronaviruses at Acidic pH Encountered in Respiratory Aerosols. 2024, University of Zurich, Faculty of Science.

Jackson-Perry, David; Cart-Richter, Ellen; Haerry, David; Ahmeti, Lindrit; Bieri, Annatina; Calmy, Alexandra; Ballif, Marie; Pasin, Chloé; Notter, Julia; Amstutz, Alain; Swiss HIV Cohort Study Young Researchers’ Group, and the Swiss H (2024). Patient and public involvement in HIV research: a mapping review and development of an online evidence map. Journal of the International Aids Society, 27(11):e26385.

Marinosci, Annalisa; Sculier, Delphine; Wandeler, Gilles; Yerly, Sabine; Stoeckle, Marcel; Bernasconi, Enos; Braun, Dominique L; Vernazza, Pietro; Cavassini, Matthias; Decosterd, Laurent; Günthard, Huldrych F; Schmid, Patrick; Limacher, Andreas; Branca, Mattia; Calmy, Alexandra; Swiss HIV Cohort Study; et al; Metzner, Karin J (2024). Efficacy and Safety of Dolutegravir Plus Emtricitabine vs Combined Antiretroviral Therapy for the Maintenance of HIV Suppression: Results Through Week 144 of the SIMPL’HIV Trial. Open Forum Infectious Diseases, 11(11):ofae618.

Schaub, Aline; Luo, Beiping; David, Shannon C; Glas, Irina; Klein, Liviana K; Costa, Laura; Terrettaz, Céline; Bluvshtein, Nir; Motos, Ghislain; Violaki, Kalliopi; Pohl, Marie O; Hugentobler, Walter; Nenes, Athanasios; Stertz, Silke; Krieger, Ulrich K; Peter, Thomas; Kohn, Tamar (2024). Salt Supersaturation as an Accelerator of Influenza A Virus Inactivation in 1 μL Droplets. Environmental Science & Technology, 58(42):18856-18869.

Amstutz, Alain; Chammartin, Frédérique; Audigé, Annette; Eichenberger, Anna L; Braun, Dominique L; Amico, Patrizia; Stoeckle, Marcel P; Hasse, Barbara; Papadimitriou-Olivgeris, Matthaios; Manuel, Oriol; Bongard, Cédric; Schuurmans, Macé M; Hage, René; Damm, Dominik; Tamm, Michael; Mueller, Nicolas J; Rauch, Andri; Günthard, Huldrych F; Koller, Michael T; Schönenberger, Christof M; Griessbach, Alexandra; Labhardt, Niklaus D; Kouyos, Roger D; Trkola, Alexandra; Kusejko, Katharina; Bucher, Heiner C; Abela, Irene A; Briel, Matthias; Speich, Benjamin; et al (2024). Antibody and T-Cell Response to Bivalent Booster SARS-CoV-2 Vaccines in People With Compromised Immune Function: COVERALL-3 Study. Journal of Infectious Diseases, 230(4):e847-e859.

Begré, Lorin; Boyd, Anders; Plissonnier, Marie-Laure; Testoni, Barbara; Salazar-Vizcaya, Luisa; Suter-Riniker, Franziska; Scholtès, Caroline; Béguelin, Charles; Rockstroh, Jürgen K; Günthard, Huldrych F; Calmy, Alexandra; Cavassini, Matthias; Hirsch, Hans H; Schmid, Patrick; Bernasconi, Enos; Levrero, Massimo; Wandeler, Gilles; Zoulim, Fabien; Rauch, Andri; Swiss HIV Cohort Study (2024). Circulating HBV RNA and Hepatitis B Core–Related Antigen Trajectories in Persons With HIV/HBV Coinfection and Hepatitis B Surface Antigen Loss During Tenofovir Therapy. Journal of Infectious Diseases, 230(4):e954-e963.

Motos, Ghislain; Schaub, Aline; David, Shannon C; Costa, Laura; Terrettaz, Céline; Kaltsonoudis, Christos; Glas, Irina; Klein, Liviana K; Bluvshtein, Nir; Luo, Beiping; Violaki, Kalliopi; Pohl, Marie O; Hugentobler, Walter; Krieger, Ulrich K; Pandis, Spyros N; Stertz, Silke; Peter, Thomas; Kohn, Tamar; Nenes, Athanasios (2024). Dependence of aerosol-borne influenza A virus infectivity on relative humidity and aerosol composition. Frontiers in Microbiology, 15:1484992.

Kusejko, Katharina; Kouyos, Roger D; Bernasconi, Enos; Boggian, Katia; Braun, Dominique L; Calmy, Alexandra; Cavassini, Matthias; van Delden, Christian; Furrer, Hansjakob; Garzoni, Christian; Hirsch, Hans H; Hirzel, Cédric; Manuel, Oriol; Schmid, Patrick; Khanna, Nina; Haidar, Fadi; Bonani, Marco; Golshayan, Dela; Dickenmann, Michael; Sidler, Daniel; Schnyder, Aurelia; Mueller, Nicolas J; Günthard, Huldrych F; Schreiber, Peter W (2024). Infectious disease events in people with HIV receiving kidney transplantation: Analysis of the Swiss HIV Cohort Study and the Swiss Transplant Cohort Study. BMC Infectious Diseases, 24(1):1143.

Siedentop, Berit; Losa Mediavilla, Carlota; Kouyos, Roger D; Bonhoeffer, Sebastian; Chabas, Hélène (2024). Assessing the role of bacterial innate and adaptive immunity as barriers to conjugative plasmids. Molecular Biology and Evolution, 41(10):msae207.

Pasin, Chloé; Nuñez, David Garcia; Kusejko, Katharina; Hachfeld, Anna; Buvelot, Hélène; Cavassini, Matthias; Damonti, Lauro; Fux, Christoph; de Tejada, Begoña Martinez; Notter, Julia; Trkola, Alexandra; Günthard, Huldrych F; Aebi-Popp, Karoline; Kouyos, Roger D; Abela, Irene A (2024). Impact of hormonal therapy on HIV‐1 immune markers in cis women and gender minorities. HIV Medicine, 25(10):1112-1124.

Baxter, James; Villabona-Arenas, Ch Julián; Thompson, Robin N; Hué, Stéphane; Regoes, Roland R; Kouyos, Roger D; Günthard, Huldrych F; Albert, Jan; Leigh Brown, Andrew; Atkins, Katherine E (2024). Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4$^{+}$ decline. Journal of the Royal Society Interface, 21(219):20240255.

Vetter, Viola Katharina; Haberecker, Martina; Huber, Florian Alexander; Pauli, Chantal (2024). Aberrant positivity for BCOR immunohistochemistry in merkel cell carcinoma - a potential diagnostic pitfall. Diagnostic Pathology, 19(1):130.

Zeeb, Marius; Frischknecht, Paul; Huber, Michael; Schenkel, Corinne D; Neumann, Kathrin; Leeman, Christine; Notter, Julia; Rauch, Andri; Stöckle, Marcel; Cavassini, Matthias; Bernasconi, Enos; Braun, Dominique L; Günthard, Huldrych F; Metzner, Karin J; Kouyos, Roger D (2024). Genetic diversity from proviral DNA as a proxy for time since HIV-1 infection. Journal of Infectious Diseases, 230(3):e631-e636.

Schwarzmüller, Magdalena; Trkola, Alexandra (2024). ART-DEX: A novel strategy to monitor broadly neutralizing antibody activity during antiretroviral therapy of HIV-1. STAR Protocols, 5(3):103056.

Zhang, Yuepeng; Otte, Fabian; Stoeckle, Marcel; Thielen, Alexander; Däumer, Martin; Kaiser, Rolf; Kusejko, Katharina; Metzner, Karin J; Klimkait, Thomas (2024). HIV-1 diversity in viral reservoirs obtained from circulating T-cell subsets during early ART and beyond. PLoS Pathogens, 20(9):e1012526.

Fernbach, Sonja; Mair, Nina K; Abela, Irene A; Groen, Kevin; Kuratli, Roger; Lork, Marie; Thorball, Christian W; Bernasconi, Enos; Filippidis, Paraskevas; Leuzinger, Karoline; Notter, Julia; Rauch, Andri; Hirsch, Hans H; Huber, Michael; Günthard, Huldrych F; Fellay, Jacques; Kouyos, Roger D; Hale, Benjamin G; Swiss HIV Cohort Study (2024). Loss of tolerance precedes triggering and lifelong persistence of pathogenic type I interferon autoantibodies. Journal of Experimental Medicine, 221(9):e20240365.

Paioni, Paolo; Capaul, Murezi; Brunner, Anja; Traytel, Anna; Aebi-Popp, Karoline; Crisinel, Pierre-Alex; Duppenthaler, Andrea; Günthard, Huldrych; Martinez de Tejada, Begoña; Kottanattu, Lisa; Stöckle, Marcel; Rauch, Andri; Wagner, Noémie; Hösli, Irene; Rudin, Christoph; Scherrer, Alexandra; Kusejko, Katharina; Kahlert, Christian R; Swiss HIV Cohort Study (SHCS); Swiss Mother and Child HIV Cohort Study (MoCHiV) (2024). Cohort profile: the Swiss Mother and Child HIV Cohort Study (MoCHiV). BMJ Open, 14(9):e086543.

Schwarzmüller, Magdalena; Lozano, Cristina; Schanz, Merle; Abela, Irene A; Grosse-Holz, Silvan; Epp, Selina; Curcio, Martina; Greshake, Jule; Rusert, Peter; Huber, Michael; Kouyos, Roger D; Günthard, Huldrych F; Trkola, Alexandra; Swiss HIV Cohort Study (2024). Decoupling HIV-1 antiretroviral drug inhibition from plasma antibody activity to evaluate broadly neutralizing antibody therapeutics and vaccines. Cell Reports Medicine, 5(9):101702.

Abela, Irene A; Chammartin, Frédérique; Amstutz, Alain; Surial, Bernard; Ballif, Marie; Marzolini, Catia; Aebi-Popp, Karoline; Notter, Julia; Segeral, Olivier; Stoeckle, Marcel; Cavassini, Matthias; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D; Pasin, Chloé; Swiss HIV Cohort Study (2024). Gender Disparities in Statin Prescriptions in People With HIV With Low/Moderate to High Cardiovascular Risk. Open Forum Infectious Diseases, 11(9):ofae502.

Riebensahm, Carlotta; Brocker, Julia; Berzigotti, Annalisa; Günthard, Huldrych F; Tarr, Philip E; Furrer, Hansjakob; Rauch, Andri; Wandeler, Gilles; Surial, Bernard; Swiss HIV Cohort Study (2024). External Validation of Serologic Scores for the Detection of Liver Steatosis Among People With HIV. Open Forum Infectious Diseases, 11(9):ofae411.

Egger, Matthias; Sauermann, Mamatha; Loosli, Tom; Hossmann, Stefanie; Riedo, Selma; Beerenwinkel, Niko; Jaquet, Antoine; Minga, Albert; Ross, Jeremy; Giandhari, Jennifer; Kouyos, Roger D; Lessells, Richard (2024). HIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre study (DTG RESIST). BMJ Open, 14(8):e085819.

Abela, Irene A; Hauser, Anthony; Schwarzmüller, Magdalena; Pasin, Chloé; Kusejko, Katharina; Epp, Selina; Cavassini, Matthias; Battegay, Manuel; Rauch, Andri; Calmy, Alexandra; Notter, Julia; Bernasconi, Enos; Fux, Christoph A; Leuzinger, Karoline; Perreau, Matthieu; Ramette, Alban; Gottschalk, Jochen; Schindler, Eméry; Wepf, Alexander; Marconato, Maddalena; Manz, Markus G; Frey, Beat M; Braun, Dominique L; Huber, Michael; Günthard, Huldrych F; Trkola, Alexandra; Kouyos, Roger D; Swiss HIV Cohort Study (2024). Deciphering factors linked with reduced SARS-CoV-2 susceptibility in the Swiss HIV Cohort Study. Journal of Infectious Diseases, 230(2):e292-e304.

Neuner-Jehle, Nadia; Zeeb, Marius; Thorball, Christian W; Fellay, Jacques; Metzner, Karin J; Frischknecht, Paul; Neumann, Kathrin; Leeman, Christine; Rauch, Andri; Stöckle, Marcel; Huber, Michael; Perreau, Matthieu; Bernasconi, Enos; Notter, Julia; Hoffmann, Matthias; Leuzinger, Karoline; Günthard, Huldrych F; Pasin, Chloé; Kouyos, Roger D; Swiss HIV Cohort Study (SHCS) (2024). Using viral diversity to identify HIV-1 variants under HLA-dependent selection in a systematic viral genome-wide screen. PLoS Pathogens, 20(8):e1012385.

Hofer, Kevin D; Wolfensberger, Nathan; Bachofner, Adrian; Schneidawind, Corina; Stühler, Claudia; Bühler, Marco M; Abela, Irene A; Müller, Nicolas J; Zenz, Thorsten; Manz, Markus G; Rösler, Wiebke; Khanna, Nina; Schneidawind, Dominik (2024). B‐cell maturation antigen‐directed bispecific antibodies in plasmablastic lymphoma. British Journal of Haematology, 205(2):722-725.

Zeeb, Marius. Using Complex Data in Observational Cohorts to Identify the Mechanisms and Drivers of Comorbidities in People with HIV. 2024, University of Zurich, Faculty of Science.

Weber, M S R; Duran Ramirez, J J; Hentzien, M; Cavassini, M; Bernasconi, E; Hofmann, E; Furrer, H; Kovari, H; Stöckle, M; Schmid, P; Haerry, D; Braun, D L; Günthard, H F; Kusejko, K; Swiss HIV Cohort Study; Aebi-Popp, K; Anagnostopoulos, A; Battegay, M; Bernasconi, E; Braun, D L; Bucher, H C; Calmy, A; Cavassini, M; Ciuffi, A; Dollenmaier, G; Egger, M; Elzi, L; Fehr, J; Fellay, J; Furrer, H; et al (2024). Time Trends in Causes of Death in People With Human Immunodeficiency Virus: Insights From the Swiss HIV Cohort Study. Clinical Infectious Diseases, 79(1):177-188.

Karakus, Umut; Mena, Ignacio; Kottur, Jithesh; El Zahed, Sara S; Seoane, Rocío; Yildiz, Soner; Chen, Leanne; Plancarte, Magdalena; Lindsay, LeAnn; Halpin, Rebecca; Stockwell, Timothy B; Wentworth, David E; Boons, Geert-Jan; Krammer, Florian; Stertz, Silke; Boyce, Walter; de Vries, Robert P; Aggarwal, Aneel K; García-Sastre, Adolfo (2024). H19 influenza A virus exhibits species-specific MHC class II receptor usage. Cell Host & Microbe, 32(7):1089-1102.e10.

Mills, Dominic Christopher; Huder, Jon Barduot; Bloemberg, Guido Vincent; Huber, Michael (2024). Comparison of three cartridge-based platforms for syndromic testing for respiratory viruses. Diagnostic Microbiology and Infectious Disease, 109(3):116308.

Roen, Ashley O; Peters, Lars; Wandeler, Gilles; van der Valk, Marc; Zangerle, Robert; Günthard, Huldrych F; Wit, Ferdinand; Mussini, Cristina; De Wit, Stephane; d’Arminio Monforte, Antonella; Vehreschild, Jörg Janne; Castagna, Antonella; Jaschinski, Nadine; Vannappagari, Vani; Chen, Linda; Tallada, Joan; C’mar, John; Mocroft, Amanda; Ryom, Lene (2024). Chronic Liver Enzyme Elevation and Use of Contemporary ARVs Among People With HIV. Open Forum Infectious Diseases, 11(6):ofae308.

Skrivankova, Veronika Whitesell; Huwa, Jacqueline; Muula, Guy; Chiwaya, Geldert D; Banda, Esau; Buleya, Shameem; Chihota, Belinda; Chintedza, Joseph; Bolton, Carolyn; Tweya, Hannock; Kalua, Thokozani; Hossmann, Stefanie; Kouyos, Roger; Wandeler, Gilles; Egger, Matthias; Lessells, Richard J (2024). Virologic Failure and Drug Resistance After Programmatic Switching to Dolutegravir-based First-line Antiretroviral Therapy in Malawi and Zambia. Clinical Infectious Diseases:Epub ahead of print.

Thoueille, Paul; Saldanha, Susana Alves; Schaller, Fabian; Choong, Eva; Veuve, François; Munting, Aline; Cavassini, Matthias; Braun, Dominique; Günthard, Huldrych F; Duran Ramirez, Jessy J; Surial, Bernard; Furrer, Hansjakob; Rauch, Andri; Ustero, Pilar; Calmy, Alexandra; Stöckle, Marcel; Di Benedetto, Caroline; Bernasconi, Enos; Schmid, Patrick; Marzolini, Catia; Girardin, François R; Buclin, Thierry; Decosterd, Laurent A; Guidi, Monia (2024). Population Pharmacokinetics of Cabotegravir Following Oral Administration and Long‐Acting Intramuscular Injection in Real‐World People with HIV. Clinical Pharmacology and Therapeutics, 115(6):1450-1459.

Zeeb, Marius; Pasin, Chloé; Cavassini, Matthias; Bieler-Aeschlimann, Mélanie; Frischknecht, Paul; Kusejko, Katharina; Fellay, Jacques; Blanquart, François; Metzner, Karin J; Neumann, Kathrin; Jörimann, Lisa; Tschumi, Jasmin; Bernasconi, Enos; Huber, Michael; Kovari, Helen; Leuzinger, Karoline; Notter, Julia; Perreau, Matthieu; Rauch, Andri; Ramette, Alban; Stöckle, Marcel; Yerly, Sabine; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study; Abela, Irene; Anagnostopoulos, Alexia; Battegay, Manuel; Bernasconi, Enos; Braun, Dominique L; et al (2024). Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study. Brain Communications, 6(4):fcae188.

van Ackeren, Vanessa; Schmutz, Stefan; Pichler, Ian; Ziltener, Gabriela; Zaheri, Maryam; Kufner, Verena; Huber, Michael (2024). Retrospective Genotyping of Enteroviruses Using a Diagnostic Nanopore Sequencing Workflow. Pathogens, 13(5):390.

Wegner, Fanny; Cabrera-Gil, Blanca; Tanguy, Araud; Beckmann, Christiane; Beerenwinkel, Niko; Bertelli, Claire; Carrara, Matteo; Cerutti, Lorenzo; Chen, Chaoran; Cordey, Samuel; Dumoulin, Alexis; du Plessis, Louis; Friedli, Marc; Gerth, Yannick; Greub, Gilbert; Härri, Adrian; Hirsch, Hans; Howald, Cedric; Huber, Michael; Imhof, Alexander; Kaiser, Laurent; Kufner, Verena; Leib, Stephen L; Leuzinger, Karoline; Lleshi, Etleva; Martinetti, Gladys; Mäusezahl, Mirjam; Neher, Richard; Trkola, Alexandra; Egli, Adrian; et al; SPSP consortium (2024). How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort. Microbiology Spectrum, 12(5):e0362823.

Turk, Teja; Labarile, Marco; Braun, Dominique L; Rauch, Andri; Stöckle, Marcel; Cavassini, Matthias; Hoffmann, Matthias; Calmy, Alexandra; Bernasconi, Enos; Notter, Julia; Pasin, Chloé; Günthard, Huldrych F; Kouyos, Roger D (2024). Characterization And Determinants Of Long-term Immune Recovery Under Suppressive Antiretroviral Therapy. Journal of Acquired Immune Deficiency Syndromes, 96(1):68-76.

Trepl, Julia; Pasin, Chloé; Schneidawind, Dominik; Mueller, Nicolas J; Manz, Markus G; Bankova, Andriyana K; Abela, Irene A (2024). Evaluating tixagevimab/cilgavimab prophylaxis in allogeneic haematopoietic cell transplantation recipients for COVID‐19 prevention. British Journal of Haematology, 204(5):1908-1912.

Marinosci, Annalisa; Sculier, Delphine; Wandeler, Gilles; Yerly, Sabine; Stoeckle, Marcel; Bernasconi, Enos; Braun, Dominique L; Vernazza, Pietro; Cavassini, Matthias; Buzzi, Marta; Metzner, Karin J; Decosterd, Laurent; Günthard, Huldrych F; Schmid, Patrick; Limacher, Andreas; Branca, Mattia; Calmy, Alexandra (2024). Costs and acceptability of simplified monitoring in HIV-suppressed patients switching to dual therapy: the SIMPL’HIV open-label, factorial randomised controlled trial. Swiss Medical Weekly, 154(4):3762.

Kufner, Verena; Frey, Andrea C; Burkhard, Sara H; Schmutz, Stefan; Ziltener, Gabriela; Zaheri, Maryam; Wiedmer, Caroline V; Plate, Andreas; Trkola, Alexandra; Huber, Michael; Mueller, Nicolas J (2024). Exploring viral aetiology in upper respiratory tract infections: insights from metagenomic next-generation sequencing in Swiss outpatients before and during the SARS-CoV-2 pandemic. Schweizerische Medizinische Wochenschrift, 154(4):3797.

Künzler-Heule, Patrizia; Schmidt, Axel J; Fierz, Katharina; Battegay, Manuel; Engberg, Sandra; Kouyos, Roger D; Nöstlinger, Christiana; Stöckle, Marcel; Béguelin, Charles; Delaloye, Julie; Schmid, Patrick; Rougemont, Mathieu; Braun, Dominique L; Fehr, Jan S; Nicca, Dunja (2024). Exploring group differences in the response to a sexual risk reduction intervention to prevent hepatitis C virus reinfection in HIV-infected MSM: a mixed-methods study. AIDS Care, 36(4):442-451.

Trkola, Alexandra; Moore, Penny L (2024). Vaccinating people living with HIV: a fast track to preventive and therapeutic HIV vaccines. Lancet Infectious Diseases, 24(4):e252-e255.

Hedskog, Charlotte; Spinner, Christoph D; Protzer, Ulrike; Hoffmann, Dieter; Ko, Chunkyu; Gottlieb, Robert L; Askar, Medhat; Roestenberg, Meta; de Vries, Jutte J C; Carbo, Ellen C; Martin, Ross; Li, Jiani; Han, Dong; Rodriguez, Lauren; Parvangada, Aiyappa; Perry, Jason K; Ferrer, Ricard; Antón, Andrés; Andrés, Cristina; Casares, Vanessa; Günthard, Huldrych F; Huber, Michael; McComsey, Grace A; Sadri, Navid; Aberg, Judith A; van Bakel, Harm; Porter, Danielle P (2024). No Remdesivir Resistance Observed in the Phase 3 Severe and Moderate COVID-19 SIMPLE Trials. Viruses, 16(4):546.

Foulkes, Caio. HIV-1 Envelope Plasticity and Its Interplay with Broad Neutralizing Antibody Activity. 2024, University of Zurich, Faculty of Science.

Schiefer, Samira Nadine. Analysis of Human Interferon Signaling and its Regulation. 2024, University of Zurich, Faculty of Science.

Mocroft, Amanda; Pelchen-Matthews, Annegret; Hoy, Jennifer; Llibre, Josep M; Neesgaard, Bastian; Jaschinski, Nadine; Domingo, Pere; Rasmussen, Line Dahlerup; Günthard, Huldrych F; Surial, Bernard; Öllinger, Angela; Knappik, Michael; De Wit, Stephan; Wit, Ferdinand; Mussini, Cristina; Vehreschild, Joerg; Monforte, Antonella d'Arminio; Sönnerborg, Anders; Castagna, Antonella; Anne, Alain Volny; Vannappagari, Vani; Cohen, Cal; Greaves, Wayne; Wasmuth, Jan C; Spagnuolo, Vincenzo; Ryom, Lene; RESPOND, cohort collaboration (2024). Heavy arv exposure and exhausted/limited arv options: predictors and clinical outcomes. AIDS, 38(4):497-508.

Kusejko, Katharina; Neofytos, Dionysios; van Delden, Christian; Hirsch, Hans H; Meylan, Pascal; Boggian, Katia; Hirzel, Cédric; Garzoni, Christian; Sidler, Daniel; Schnyder, Aurelia; Schaub, Stefan; Golshayan, Déla; Haidar, Fadi; Bonani, Marco; Kouyos, Roger D; Mueller, Nicolas J; Schreiber, Peter W; Swiss Transplant Cohort Study; et al (2024). Do Infectious Diseases After Kidney Retransplantation Differ From Those After First Kidney Transplantation? Open Forum Infectious Diseases, 11(3):ofae055.

Trickey, Adam; McGinnis, Kathleen; Gill, M John; Abgrall, Sophie; Berenguer, Juan; Wyen, Christoph; Hessamfar, Mojgan; Reiss, Peter; Kusejko, Katharina; Silverberg, Michael J; Imaz, Arkaitz; Teira, Ramon; d'Arminio Monforte, Antonella; Zangerle, Robert; Guest, Jodie L; Papastamopoulos, Vasileios; Crane, Heidi; Sterling, Timothy R; Grabar, Sophie; Ingle, Suzanne M; Sterne, Jonathan A C (2024). Longitudinal trends in causes of death among adults with HIV on antiretroviral therapy in Europe and North America from 1996 to 2020: a collaboration of cohort studies. The Lancet : HIV, 11(3):e176-e185.

Klinnert, Sarah; Schenkel, Corinne D; Freitag, Patrick C; Günthard, Huldrych F; Plückthun, Andreas; Metzner, Karin J (2024). Targeted shock-and-kill HIV-1 gene therapy approach combining CRISPR activation, suicide gene tBid and retargeted adenovirus delivery. Gene Therapy, 31(3-4):74-84.

Manuel, Oriol; Laager, Mirjam; Hirzel, Cédric; Neofytos, Dionysios; Walti, Laura N; Hoenger, Gideon; Binet, Isabelle; Schnyder, Aurelia; Stampf, Susanne; Koller, Michael; Mombelli, Matteo; Kim, Min Jeong; Hoffmann, Matthias; Koenig, Katrin; Hess, Christoph; Burgener, Anne-Valérie; Cippà, Pietro E; Hübel, Kerstin; Mueller, Thomas F; Sidler, Daniel; Dahdal, Suzan; Suter-Riniker, Franziska; Villard, Jean; Zbinden, Andrea; Pantaleo, Giuseppe; Semmo, Nasser; Hadaya, Karine; Enríquez, Natalia; Meylan, Pascal R; Froissart, Marc; et al; Mueller, Nicolas J (2024). Immune monitoring-guided vs fixed duration of antiviral prophylaxis against cytomegalovirus in solid-organ transplant recipients. A Multicenter, Randomized Clinical Trial. Clinical Infectious Diseases, 78(2):312-323.

Chammartin, Frédérique; Griessbach, Alexandra N; Kusejko, Katharina; Audigé, Annette; Epp, Selina; Stoeckle, Marcel P; Eichenberger, Anna L; Amstutz, Alain; Schoenenberger, Christof M; Hasse, Barbara; Braun, Dominique L; Rauch, Andri; Trkola, Alexandra; Briel, Matthias; Bucher, Heiner C; Günthard, Huldrych F; Speich, Benjamin; Abela, Irene A; Swiss HIV Cohort Study (2024). Bridging the Gap: identifying factors impacting mRNA SARS-CoV-2 vaccine booster response in people living with HIV-1. AIDS, 38(2):217-222.

Riebensahm, Carlotta; Berzigotti, Annalisa; Surial, Bernard; Haerry, David; Günthard, Huldrych F; Tarr, Philip E; Furrer, Hansjakob; Rauch, Andri; Wandeler, Gilles; Swiss HIV Cohort Study (2024). Decreased Physical Activity and Prolonged Sitting Time Are Associated With Liver Steatosis in People With HIV. Journal of Acquired Immune Deficiency Syndromes, 95(2):179-184.

Begré, Lorin; Boyd, Anders; Salazar-Vizcaya, Luisa; Suter-Riniker, Franziska; Béguelin, Charles; Rockstroh, Jürgen K; Günthard, Huldrych F; Calmy, Alexandra; Cavassini, Matthias; Stöckle, Marcel; Schmid, Patrick; Bernasconi, Enos; Levrero, Massimo; Zoulim, Fabien; Wandeler, Gilles; Rauch, Andri; Swiss HIV Cohort Study (SHCS) (2024). Long-term quantitative hepatitis B surface antigen (HBsAg) trajectories in persons with and without HBsAg loss on tenofovir-containing antiretroviral therapy. HIV Medicine, 25(2):291-298.

Freind, Matt C; Tallón de Lara, Carmen; Kouyos, Roger D; Wimmersberger, David; Kuster, Hebert; Aceto, Leonardo; Kovari, Helen; Flepp, Markus; Schibli, Adrian; Hampel, Benjamin; Grube, Christina; Braun, Dominique L; Günthard, Huldrych F (2024). Cohort Profile: The Zurich Primary HIV Infection Study. Microorganisms, 12(2):302.

Abela, Irene A; Schwarzmüller, Magdalena; Ulyte, Agne; Radtke, Thomas; Haile, Sarah R; Ammann, Priska; Raineri, Alessia; Rueegg, Sonja; Epp, Selina; Berger, Christoph; Böni, Jürg; Manrique, Amapola; Audigé, Annette; Huber, Michael; Schreiber, Peter W; Scheier, Thomas; Fehr, Jan; Weber, Jacqueline; Rusert, Peter; Günthard, Huldrych F; Kouyos, Roger D; Puhan, Milo A; Kriemler, Susi; Trkola, Alexandra; Pasin, Chloé (2024). Cross-protective HCoV immunity reduces symptom development during SARS-CoV-2 infection. mBio, 15(2):e0272223.

Hentzien, Maxime; Frossard, Jaromil; Kouyos, Roger; Prendki, Virginie; Damas, José; Hofmann, Eveline; Braun, Dominique; Schmid, Patrick; Bernasconi, Enos; Ragozzino, Silvio; Efthimiou, Orestis; Delpierre, Cyrille; Allavena, Clotilde; Bani-Sadr, Firouzé; Calmy, Alexandra (2024). External validation of the Dat'AIDS score: A risk score for predicting 5-year overall mortality in people living with HIV aged 60 years or older. HIV Medicine, 25(1):72-82.

Hovaguimian, Frédérique; Kouyos, Roger D; Kusejko, Katharina; Schmidt, Axel J; Tarr, Philip E; Bernasconi, Enos; Braun, Dominique L; Calmy, Alexandra; Notter, Julia; Stoeckle, Marcel; Surial, Bernard; Christinet, Vanessa; Darling, Katharine E A; Depmeier, Carsten; Läuchli, Severin; Reinacher, Matthias; Rasi, Manuela; Nicca, Dunja; Bruggmann, Philip; Haerry, David; Bize, Raphaël; Low, Nicola; Vock, Florian; El Amari, Emmanuelle Boffi; Böni, Jürg; Bosshard, Philipp P; Fehr, Jan S; Hampel, Benjamin; SwissPrEPared Cohort Study (2024). Incidence of sexually transmitted infections and association with behavioural factors: Time-to-event analysis of a large pre-exposure prophylaxis (PrEP) cohort. HIV Medicine, 25(1):117-128.

Baumann, Lukas; Braun, Dominique L; Cavassini, Matthias; Stoeckle, Marcel; Bernasconi, Enos; Schmid, Patrick; Calmy, Alexandra; Haerry, David; Béguelin, Charles; Fux, Christoph A; Wandeler, Gilles; Surial, Bernard; Rauch, Andri (2024). Long-term trends in hepatitis C prevalence, treatment uptake and liver-related events in the Swiss HIV Cohort Study. Liver International, 44(1):169-179.

Achleitner, Martin; Mair, Nina K; Dänhardt, Juliane; Kardashi, Romina; Puhan, Milo A; Abela, Irene A; Toepfner, Nicole; de With, Katja; Kanczkowski, Waldemar; Jarzebska, Natalia; Rodionov, Roman N; Wolf, Christine; Lee-Kirsch, Min Ae; Steenblock, Charlotte; Hale, Benjamin G; Bornstein, Stefan R (2024). Absence of Type I Interferon Autoantibodies or Significant Interferon Signature Alterations in Adults With Post-COVID-19 Syndrome. Open Forum Infectious Diseases, 11(1):ofad641.

Thoueille, Paul; Saldanha, Susana Alves; Schaller, Fabian; Choong, Eva; Munting, Aline; Cavassini, Matthias; Braun, Dominique; Günthard, Huldrych F; Kusejko, Katharina; Surial, Bernard; Furrer, Hansjakob; Rauch, Andri; Rougemont, Mathieu; Ustero, Pilar; Calmy, Alexandra; Stöckle, Marcel; Marzolini, Catia; Di Benedetto, Caroline; Bernasconi, Enos; Schmid, Patrick; Piso, Rein Jan; Andre, Pascal; Girardin, François R; Guidi, Monia; Buclin, Thierry; Decosterd, Laurent A; Swiss HIV Cohort Study (2024). Real-world trough concentrations and effectiveness of long-acting cabotegravir and rilpivirine: a multicenter prospective observational study in Switzerland. The Lancet Regional Health : Europe, 36:100793.

2023

Perrig, Lisa; Abela, Irene A; Banholzer, Nicolas; Audigé, Annette; Epp, Selina; Mugglin, Catrina; Zürcher, Kathrin; Egger, Matthias; Trkola, Alexandra; Fenner, Lukas (2023). Long-term course of neutralising antibodies against SARS-CoV-2 in vaccinated and unvaccinated staff and residents in a Swiss nursing home: a cohort study 2021–2022. Swiss Medical Weekly, 153(12):3502.

Meissner, Ramona; Wixler, Viktor; Wulfert, Franziska Paulina; Jacob, Jasmin Carina; Hale, Benjamin G; Robeck, Thomas; Masemann, Dörthe; Boergeling, Yvonne; Ludwig, Stephan (2023). Replication-incompetent influenza A viruses armed with IFN-γ effectively mediate immune modulation and tumor destruction in mice harboring lung cancer. Molecular Therapy : Oncolytics, 31:100741.

Glas, Irina; David, Shannon C (2023). A new chapter of healthy indoor air: antiviral air treatments. EMBO Molecular Medicine, 15(12):e18710.

Zeeb, Marius; Tepekule, Burcu; Kusejko, Katharina; Reiber, Claudine; Kälin, Marisa; Bartl, Lena; Notter, Julia; Furrer, Hansjakob; Hoffmann, Matthias; Hirsch, Hans H; Calmy, Alexandra; Cavassini, Matthias; Labhardt, Niklaus D; Bernasconi, Enos; Braun, Dominique L; Günthard, Huldrych F; Kouyos, Roger D; Nemeth, Johannes; Swiss HIV Cohort Study (2023). Understanding the decline of incident, active tuberculosis in people with HIV in Switzerland. Clinical Infectious Diseases, 77(9):1303-1311.

Loosli, Tom; Hossmann, Stefanie; Ingle, Suzanne M; Okhai, Hajra; Kusejko, Katharina; Mouton, Johannes; Bellecave, Pantxika; van Sighem, Ard; Stecher, Melanie; d'Arminio Monforte, Antonella; Gill, M John; Sabin, Caroline A; Maartens, Gary; Günthard, Huldrych F; Sterne, Jonathan A C; Lessells, Richard; Egger, Matthias; Kouyos, Roger D (2023). HIV-1 drug resistance in people on dolutegravir-based antiretroviral therapy: a collaborative cohort analysis. The Lancet : HIV, 10(11):e733-e741.

Griessbach, Alexandra; Chammartin, Frédérique; Abela, Irene A; Amico, Patrizia; Stoeckle, Marcel P; Eichenberger, Anna L; Hasse, Barbara; Braun, Dominique L; Schuurmans, Macé M; Müller, Thomas F; Tamm, Michael; Audigé, Annette; Mueller, Nicolas J; Rauch, Andri; Günthard, Huldrych F; Koller, Michael T; Trkola, Alexandra; Epp, Selina; Amstutz, Alain; Schönenberger, Christof M; Taji Heravi, Ala; Papadimitriou-Olivgeris, Matthaios; Casutt, Alessio; Manuel, Oriol; Kusejko, Katharina; Bucher, Heiner C; Briel, Matthias; Speich, Benjamin; Swiss HIV Cohort Study and the Swiss Transplant Cohort Study (2023). Antibody Response After the Third SARS-CoV-2 Vaccine in Solid Organ Transplant Recipients and People Living With HIV (COVERALL-2). Open Forum Infectious Diseases, 10(11):ofad536.

Iseli, Alena N; Pohl, Marie O; Glas, Irina; Gaggioli, Elisabeth; Martínez-Barragán, Patricia; David, Shannon C; Schaub, Aline; Luo, Beiping; Klein, Liviana K; Bluvshtein, Nir; Violaki, Kalliopi; Motos, Ghislain; Hugentobler, Walter; Nenes, Athanasios; Krieger, Ulrich K; Peter, Thomas; Kohn, Tamar; Stertz, Silke (2023). The neuraminidase activity of influenza A virus determines the strain-specific sensitivity to neutralization by respiratory mucus. Journal of Virology, 97(10):e0127123.

David, Shannon C; Vadas, Oscar; Glas, Irina; Schaub, Aline; Luo, Beiping; D'angelo, Giovanni; Montoya, Jonathan Paz; Bluvshtein, Nir; Hugentobler, Walter; Klein, Liviana K; Motos, Ghislain; Pohl, Marie; Violaki, Kalliopi; Nenes, Athanasios; Krieger, Ulrich K; Stertz, Silke; Peter, Thomas; Kohn, Tamar (2023). Inactivation mechanisms of influenza A virus under pH conditions encountered in aerosol particles as revealed by whole-virus HDX-MS. mSphere, 8(5):e0022623.

Caraballo Cortés, Kamila; Osuch, Sylwia; Perlejewski, Karol; Radkowski, Marek; Janiak, Maciej; Berak, Hanna; Rauch, Andri; Fehr, Jan S; Hoffmann, Matthias; Günthard, Huldrych F; Metzner, Karin J (2023). T-Cell Exhaustion in HIV-1/Hepatitis C Virus Coinfection Is Reduced After Successful Treatment of Chronic Hepatitis C. Open Forum Infectious Diseases, 10(11):ofad514.

Brown, Jennifer A; Hauser, Anthony; Abela, Irene A; Pasin, Chloé; Epp, Selina; Mohloanyane, Tsepang; Nsakala, Bienvenu L; Trkola, Alexandra; Labhardt, Niklaus D; Kouyos, Roger D; Günthard, Huldrych F (2023). Seroprofiling of Antibodies Against Endemic Human Coronaviruses and Severe Acute Respiratory Syndrome Coronavirus 2 in a Human Immunodeficiency Virus Cohort in Lesotho: Correlates of Antibody Response and Seropositivity. Journal of Infectious Diseases, 228(8):1042-1054.

West, Emily; Zeeb, Marius; Grube, Christina; Kuster, Herbert; Wanner, Katrin; Scheier, Thomas; Neumann, Kathrin; Jörimann, Lisa; Hampel, Benjamin; Metzner, Karin J; Kouyos, Roger D; Braun, Dominique L; Günthard, Huldrych F (2023). Sustained Viral Suppression With Dolutegravir Monotherapy Over 192 Weeks in Patients Starting Combination Antiretroviral Therapy During Primary Human Immunodeficiency Virus Infection (EARLY-SIMPLIFIED): A Randomized, Controlled, Multi-site, Noninferiority Trial. Clinical Infectious Diseases, 77(7):1012-1020.

Jörimann, Lisa; Tschumi, Jasmin; Zeeb, Marius; Leemann, Christine; Schenkel, Corinne D; Neumann, Kathrin; Chaudron, Sandra E; Zaheri, Maryam; Frischknecht, Paul; Neuner-Jehle, Nadia; Kuster, Herbert; Braun, Dominique L; Grube, Christina; Kouyos, Roger; Metzner, Karin J; Günthard, Huldrych F; Swiss HIV Cohort Study (SHCS) (2023). Absence of Proviral Human Immunodeficiency Virus (HIV) Type 1 Evolution in Early-Treated Individuals With HIV Switching to Dolutegravir Monotherapy During 48 Weeks. Journal of Infectious Diseases, 228(7):907-918.

Pichler, Ian; Schmutz, Stefan; Ziltener, Gabriela; Zaheri, Maryam; Kufner, Verena; Trkola, Alexandra; Huber, Michael (2023). Rapid and sensitive single-sample viral metagenomics using Nanopore Flongle sequencing. Journal of Virological Methods, 320:114784.

Maliqi, Liridona; Friedrich, Nikolas; Glögl, Matthias; Schmutz, Stefan; Schmidt, Daniel; Rusert, Peter; Schanz, Merle; Zaheri, Maryam; Pasin, Chloé; Niklaus, Cyrille; Foulkes, Caio; Reinberg, Thomas; Dreier, Birgit; Abela, Irene; Peterhoff, David; Hauser, Alexandra; Kouyos, Roger D; Günthard, Huldrych F; van Gils, Marit J; Sanders, Rogier W; Wagner, Ralf; Plückthun, Andreas; Trkola, Alexandra (2023). Assessing immunogenicity barriers of the HIV-1 envelope trimer. NPJ vaccines, 8(1):148.

Schwenke, Johannes M; Thorball, Christian W; Schoepf, Isabella C; Ryom, Lene; Hasse, Barbara; Lamy, Olivier; Calmy, Alexandra; Wandeler, Gilles; Marzolini, Catia; Kahlert, Christian R; Bernasconi, Enos; Kouyos, Roger D; Günthard, Huldrych F; Ledergerber, Bruno; Fellay, Jacques; Burkhalter, Felix; Tarr, Philip E; Swiss HIV Cohort Study (2023). Association of a Polygenic Risk Score With Osteoporosis in People Living With HIV: The Swiss HIV Cohort Study. Journal of Infectious Diseases, 228(6):742-750.

Surial, Bernard; Chammartin, Frédérique; Damas, José; Calmy, Alexandra; Haerry, David; Stöckle, Marcel; Schmid, Patrick; Bernasconi, Enos; Fux, Christoph A; Tarr, Philip E; Günthard, Huldrych F; Wandeler, Gilles; Rauch, Andri; Swiss HIV Cohort Study (2023). Impact of Integrase Inhibitors on Cardiovascular Disease Events in People With Human Immunodeficiency Virus Starting Antiretroviral Therapy. Clinical Infectious Diseases, 77(5):729-737.

Jaha, Bashkim; Schenkel, Corinne D; Jörimann, Lisa; Huber, Michael; Zaheri, Maryam; Neumann, Kathrin; Leemann, Christine; Calmy, Alexandra; Cavassini, Matthias; Kouyos, Roger D; Günthard, Huldrych F; Metzner, Karin J; Swiss HIV Cohort Study (2023). Prevalence of HIV-1 drug resistance mutations in proviral DNA in the Swiss HIV Cohort Study, a retrospective study from 1995 to 2018. Journal of Antimicrobial Chemotherapy, 78(9):2323-2334.

Perakakis, Nikolaos; Harb, Hani; Hale, Benjamin G; Varga, Zsuzsanna; Steenblock, Charlotte; Kanczkowski, Waldemar; Alexaki, Vasileia Ismini; Ludwig, Barbara; Mirtschink, Peter; Solimena, Michele; Toepfner, Nicole; Zeissig, Sebastian; Gado, Manuel; Abela, Irene Alma; Beuschlein, Felix; Spinas, Giatgen A; Cavelti-Weder, Claudia; Gerber, Philipp A; Huber, Michael; Trkola, Alexandra; Puhan, Milo A; Wong, Wendy Wei-Lynn; Linkermann, Andreas; Mohan, Viswanathan; Lehnert, Hendrik; Nawroth, Peter; Chavakis, Triantafyllos; Mingrone, Geltrude; Wolfrum, Christian; Zinkernagel, Annelies S; et al (2023). Mechanisms and clinical relevance of the bidirectional relationship of viral infections with metabolic diseases. The Lancet. Diabetes & Endocrinology, 11(9):675-693.

Hovaguimian, Frédérique; Beeler, Patrick E; Müllhaupt, Beat; Günthard, Huldrych F; Maeschli, Bettina; Bruggmann, Philip; Fehr, Jan S; Kouyos, Roger D (2023). Mortality and morbidity related to hepatitis C virus infection in hospitalized adults-A propensity score matched analysis. Journal of Viral Hepatitis, 30(9):765-774.

Inzaule, Seth C; Siedner, Mark J; Little, Susan J; Avila-Rios, Santiago; Ayitewala, Alisen; Bosch, Ronald J; Calvez, Vincent; Ceccherini-Silberstein, Francesca; Charpentier, Charlotte; Descamps, Diane; Eshleman, Susan H; Fokam, Joseph; Frenkel, Lisa M; Gupta, Ravindra K; Ioannidis, John P A; Kaleebu, Pontiano; Kantor, Rami; Kassaye, Seble G; Kosakovsky Pond, Sergei L; Kouamou, Vinie; Kouyos, Roger D; Kuritzkes, Daniel R; Lessells, Richard; Marcelin, Anne-Genevieve; Mbuagbaw, Lawrence; Minalga, Brian; Ndembi, Nicaise; Neher, Richard A; Paredes, Roger; Pillay, Deenan; et al; Gunthard, Huldrych F; et al (2023). Recommendations on data sharing in HIV drug resistance research. PLoS Medicine, 20(9):e1004293.

Estill, Janne; Venkova-Marchevska, Plamenna; Günthard, Huldrych F; Botero-Mesa, Sara; Thiabaud, Amaury; Roelens, Maroussia; Vancauwenberghe, Laure; Damonti, Lauro; Heininger, Ulrich; Iten, Anne; Schreiber, Peter W; Sommerstein, Rami; Tschudin-Sutter, Sarah; Troillet, Nicolas; Vuichard-Gysin, Danielle; Widmer, Andreas; Hothorn, Torsten; Keiser, Olivia (2023). Treatment effect of remdesivir on the mortality of hospitalised COVID-19 patients in Switzerland across different patient groups: a tree-based model analysis. Swiss Medical Weekly, 153:40095.

Zürcher, Kathrin; Abela, Irene A; Stange, Madlen; Dupont, Carole; Mugglin, Catrina; Egli, Adrian; Trkola, Alexandra; Egger, Matthias; Fenner, Lukas (2023). Alpha variant coronavirus outbreak in a nursing home despite high vaccination coverage: molecular, epidemiological and immunological studies. Clinical Infectious Diseases, 77(4):537-546.

Álvarez, Hortensia; Mocroft, Amanda; Ryom, Lene; Neesgaard, Bastian; Edwards, Simon; Svedhem, Veronica; Günthard, Huldrych F; Zangerle, Robert; Smith, Colette; Castagna, Antonella; d'Arminio Monforte, Antonella; Wit, Ferdinand; Stecher, Melanie; Lehman, Clara; Mussini, Cristina; Fontas, Eric; González, Eva; Wasmuth, Jan-Christian; Sönnerborg, Anders; De Wit, Stéphane; Chkhartishvili, Nikoloz; Stephan, Christoph; Petoumenos, Kathy; Jaschinski, Nadine; Vannappagari, Vani; Gallant, Joel; Young, Lital; Volny Anne, Alain; Greenberg, Lauren; Martín-Iguacel, Raquel; et al (2023). Plasma Human Immunodeficiency Virus 1 RNA and CD4$^{+}$ T-Cell Counts Are Determinants of Virological Nonsuppression Outcomes With Initial Integrase Inhibitor-Based Regimens: A Prospective RESPOND Cohort Study. Clinical Infectious Diseases, 77(4):593-605.

Glögl, Matthias; Friedrich, Nikolas; Cerutti, Gabriele; Lemmin, Thomas; Kwon, Young D; Gorman, Jason; Maliqi, Liridona; Mittl, Peer R E; Hesselman, Maria C; Schmidt, Daniel; Weber, Jacqueline; Foulkes, Caio; Dingens, Adam S; Bylund, Tatsiana; Olia, Adam S; Verardi, Raffaello; Reinberg, Thomas; Baumann, Nicolas S; Rusert, Peter; Dreier, Birgit; Shapiro, Lawrence; Kwong, Peter D; Plückthun, Andreas; Trkola, Alexandra (2023). Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nature Structural & Molecular Biology, 30(9):1323-1336.

Mugglin, Catrina; Hamusonde, Kalongo; Salazar-Vizcaya, Luisa; Kusejko, Katharina; Nicca, Dunja; Haerry, David; Braun, Dominique L; Stoeckle, Marcel; Kouyos, Roger; Calmy, Alexandra; Cavassini, Matthias; Cipriani, Michela; Bernasconi, Enos; Rauch, Andri; Hachfeld, Anna; Swiss HIV Cohort Study (SHCS) (2023). Sexual Behaviour and STI Incidence in Sexually Active MSM Living With HIV in Times of COVID-19. Open Forum Infectious Diseases, 10(8):ofad399.

McLaren, Paul J; Porreca, Immacolata; Iaconis, Gennaro; Mok, Hoi Ping; Mukhopadhyay, Subhankar; Karakoc, Emre; Cristinelli, Sara; Pomilla, Cristina; Bartha, István; Thorball, Christian W; Tough, Riley H; Angelino, Paolo; Kiar, Cher S; Carstensen, Tommy; Fatumo, Segun; Porter, Tarryn; Jarvis, Isobel; Skarnes, William C; Bassett, Andrew; DeGorter, Marianne K; Sathya Moorthy, Mohana Prasad; Tuff, Jeffrey F; Kim, Eun-Young; Walter, Miriam; Simons, Lacy M; Bashirova, Arman; Buchbinder, Susan; Carrington, Mary; Cossarizza, Andrea; De Luca, Andrea; et al; Trkola, Alexandra (2023). Africa-specific human genetic variation near CHD1L associates with HIV-1 load. Nature, 620(7976):1025-1030.

Kristen-Burmann, Claudia; Rogger, Peter; Veiga, Inês Berenguer; Riebesehl, Stefanie; Rappe, Julie; Ebert, Nadine; Sautter, Carmen A; Kelly, Jenna N; Stalder, Hanspeter; Ehmann, Rosina; Huber, Michael; Posthaus, Horst; Ruggli, Nicolas; Thiel, Volker; Tekes, Gergely (2023). Reverse Genetic Assessment of the Roles Played by the Spike Protein and ORF3 in Porcine Epidemic Diarrhea Virus Pathogenicity. Journal of Virology, 97(7):e0196422.

Pasin, Chloé; Consiglio, Camila R; Huisman, Jana S; de Lange, Ann-Marie G; Peckham, Hannah; Vallejo-Yagüe, Enriqueta; Abela, Irene A; Islander, Ulrika; Neuner-Jehle, Nadia; Pujantell, Maria; Roth, Olivia; Schirmer, Melanie; Tepekule, Burcu; Zeeb, Marius; Hachfeld, Anna; Aebi-Popp, Karoline; Kouyos, Roger D; Bonhoeffer, Sebastian (2023). Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications. Royal Society Open Science, 10(7):221628.

Otte, Fabian; Zhang, Yuepeng; Spagnuolo, Julian; Thielen, Alexander; Däumer, Martin; Wiethe, Carsten; Stoeckle, Marcel; Kusejko, Katharina; Klein, Florian; Metzner, Karin J; Klimkait, Thomas; Swiss HIV Cohort Study (2023). Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods. Cell Reports Methods, 3(6):100485.

Avery, Emma F; Kleynhans, Julia N; Ledergerber, Bruno; Schoepf, Isabella C; Thorball, Christian W; Kootstra, Neeltje A; Reiss, Peter; Ryom, Lene; Braun, Dominique L; Thurnheer, Maria Christine; Marzolini, Catia; Seneghini, Marco; Bernasconi, Enos; Cavassini, Matthias; Buvelot, Hélène; Kouyos, Roger D; Fellay, Jacques; Günthard, Huldrych F; Tarr, Philip E; Swiss HIV Cohort Study (2023). Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study. Clinical Infectious Diseases, 76(11):1969-1979.

Thoueille, Paul; Alves Saldanha, Susana; Desfontaine, Vincent; Kusejko, Katharina; Courlet, Perrine; André, Pascal; Cavassini, Matthias; Decosterd, Laurent A; Buclin, Thierry; Guidi, Monia; Swiss HIV Cohort Study (2023). Population pharmacokinetic modelling to characterize the effect of chronic kidney disease on tenofovir exposure after tenofovir alafenamide administration. Journal of Antimicrobial Chemotherapy, 78(6):1433-1443.

Kusejko, Katharina; Smith, Daniel; Scherrer, Alexandra; Paioni, Paolo; Kohns Vasconcelos, Malte; Aebi-Popp, Karoline; Kouyos, Roger D; Günthard, Huldrych F; Kahlert, Christian R; Swiss HIV Cohort Study and the Swiss Mother and Child HIV Cohort (2023). Migrating a Well-Established Longitudinal Cohort Database From Oracle SQL to Research Electronic Data Entry (REDCap): Data Management Research and Design Study. JMIR Formative Research, 7:e44567.

Belavgeni, Alexia; Maremonti, Francesca; Tonnus, Wulf; Stadtmüller, Marlena; Gavali, Shubhangi; Mallais, Melodie; Flade, Karolin; Brucker, Anne; Becker, Jorunn Naila; Beer, Kristina; Tmava, Mirela; Stumpf, Julian; Gembardt, Florian; Hugo, Christian; Giacca, Mauro; Hale, Benjamin G; Perakakis, Nikolaos; Sha, Wei; Pratt, Derek A; Schally, Andrew V; Bornstein, Stefan R; Linkermann, Andreas (2023). vPIF-1 is an insulin-like antiferroptotic viral peptide. Proceedings of the National Academy of Sciences of the United States of America, 120(21):e2300320120.

Schreiber, Peter W; Scheier, Thomas; Wolfensberger, Aline; Saleschus, Dirk; Vazquez, Miriam; Kouyos, Roger; Zingg, Walter (2023). Parallel dynamics in the yield of universal SARS-CoV-2 admission screening and population incidence. Scientific Reports, 13(1):7296.

Schoepf, Isabella C; Esteban-Cantos, Andrés; Thorball, Christian W; Rodés, Berta; Reiss, Peter; Rodríguez-Centeno, Javier; Riebensahm, Carlotta; Braun, Dominique L; Marzolini, Catia; Seneghini, Marco; Bernasconi, Enos; Cavassini, Matthias; Buvelot, Hélène; Thurnheer, Maria Christine; Kouyos, Roger D; Fellay, Jacques; Günthard, Huldrych F; Arribas, José R; Ledergerber, Bruno; Tarr, Philip E; Swiss HIV Cohort Study (2023). Epigenetic ageing accelerates before antiretroviral therapy and decelerates after viral suppression in people with HIV in Switzerland: a longitudinal study over 17 years. The Lancet Healthy Longevity, 4(5):e211-e218.

Surial, Bernard; Ramírez Mena, Adrià; Roumet, Marie; Limacher, Andreas; Smit, Colette; Leleux, Olivier; Mocroft, Amanda; van der Valk, Marc; Bonnet, Fabrice; Peters, Lars; Rockstroh, Jürgen K; Günthard, Huldrych F; Berzigotti, Annalisa; Rauch, Andri; Wandeler, Gilles (2023). External validation of the PAGE-B score for HCC risk prediction in people living with HIV/HBV coinfection. Journal of Hepatology, 78(5):947-957.

Neves, Aitana; Walther, Daniel; Martin-Campos, Trinidad; Barbie, Valerie; Bertelli, Claire; Blanc, Dominique; Bouchet, Gérard; Erard, Frédéric; Greub, Gilbert; Hirsch, Hans H; Huber, Michael; Kaiser, Laurent; Leib, Stephen L; Leuzinger, Karoline; Lazarevic, Vladimir; Mäusezahl, Mirjam; Molina, Jorge; Neher, Richard A; Perreten, Vincent; Ramette, Alban; Roloff, Tim; Schrenzel, Jacques; Seth-Smith, Helena M B; Stephan, Roger; Terumalai, Dillenn; Wegner, Fanny; Egli, Adrian (2023). The Swiss Pathogen Surveillance Platform - towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata. Microbial Genomics, 9(5):mgen001001.

Hale, Benjamin G (2023). Autoantibodies targeting type I interferons: Prevalence, mechanisms of induction, and association with viral disease susceptibility. European Journal of Immunology, 53(6):e2250164.

Griessbach, Alexandra; Chammartin, Frédérique; Abela, Irene A; Amico, Patrizia; Stoeckle, Marcel P; Eichenberger, Anna L; Hasse, Barbara; Braun, Dominique L; Schuurmans, Macé Matthew; Müller, Thomas F; Tamm, Michael; Audigé, Annette; Mueller, Nicolas J; Rauch, Andri; Günthard, Huldrych F; Koller, Michael T; Trkola, Alexandra; Epp, Selina; Amstutz, Alain; Schönenberger, Christof M; Taji Heravi, Ala; Kusejko, Katharina; Bucher, Heiner C; Briel, Matthias; Speich, Benjamin; Swiss HIV Cohort Study and the Swiss Transplant Cohort Study (2023). Antibody Response After Third Vaccination With mRNA-1273 or BNT162b2: Extension of a Randomized Controlled SARS-CoV-2 Noninferiority Vaccine Trial in Patients With Different Levels of Immunosuppression (COVERALL-2). Open Forum Infectious Diseases, 10(4):ofad150.

Bankova, Andriyana K; Pasin, Chloé; Huang, Alice; Cicin-Sain, Caroline; Epp, Selina; Audigé, Annette; Mueller, Nicolas J; Nilsson, Jakob; Vilinovszki, Oliver; Nair, Gayathri; Wolfensberger, Nathan; Hockl, Philipp; Schanz, Urs; Trkola, Alexandra; Kouyos, Roger; Hasse, Barbara; Zinkernagel, Annelies S; Manz, Markus G; Abela, Irene A; Müller, Antonia M S (2023). Antibody response to a third SARS-CoV-2 vaccine dose in recipients of an allogeneic haematopoietic cell transplantation. British Journal of Haematology, 201(1):58-63.

Balakrishna, Suraj; Loosli, Tom; Zaheri, Maryam; Frischknecht, Paul; Huber, Michael; Kusejko, Katharina; Yerly, Sabine; Leuzinger, Karoline; Perreau, Matthieu; Ramette, Alban; Wymant, Chris; Fraser, Christophe; Kellam, Paul; Gall, Astrid; Hirsch, Hans H; Stoeckle, Marcel; Rauch, Andri; Cavassini, Matthias; Bernasconi, Enos; Notter, Julia; Calmy, Alexandra; Günthard, Huldrych F; Metzner, Karin J; Kouyos, Roger D (2023). Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1. Journal of Antimicrobial Chemotherapy, 78(3):656-664.

Hofmann, Eveline; Surial, Bernard; Boillat-Blanco, Noémie; Günthard, Huldrych F; Stöckle, Marcel; Bernasconi, Enos; Schmid, Patrick; Calmy, Alexandra; Suter-Riniker, Franziska; Rauch, Andri; Wandeler, Gilles; Béguelin, Charles; SHCS (2023). HBV replication during tenofovir therapy is frequent in HIV/HBV-coinfection. Clinical Infectious Diseases, 76(4):730-733.

Labarile, Marco; Loosli, Tom; Zeeb, Marius; Kusejko, Katharina; Huber, Michael; Hirsch, Hans H; Perreau, Matthieu; Ramette, Alban; Yerly, Sabine; Cavassini, Matthias; Battegay, Manuel; Rauch, Andri; Calmy, Alexandra; Notter, Julia; Bernasconi, Enos; Fux, Christoph; Günthard, Huldrych F; Pasin, Chloé; Kouyos, Roger D; Swiss HIV Cohort Study (2023). Quantifying and predicting ongoing Human Immunodeficiency Virus Type 1 (HIV-1) transmission dynamics in Switzerland using a distance-based clustering approach. Journal of Infectious Diseases, 227(4):554-564.

Hamusonde, Kalongo; Nicca, Dunja; Günthard, Huldrych F; Stöckle, Marcel; Darling, Katharine Ea; Calmy, Alexandra; Bernasconi, Enos; Haerry, David; Schmid, Patrick; Kouyos, Roger D; Rauch, Andri; Salazar-Vizcaya, Luisa; Swiss HIV Cohort Study (2023). Triggers of change in sexual behavior among people with HIV: The Swiss U = U statement and Covid-19 compared. Journal of Infectious Diseases, 227(3):407-411.

Mauri, Fabio; Cottler-Casanova, Sara; Cavassini, Matthias; Stoeckle, Marcel; Wandeler, Gilles; Schmid, Patrick; Braun, Dominique L; Scherrer, Alexandra; Bernasconi, Enos; Calmy, Alexandra; Abdulcadir, Jasmine (2023). Female Genital Mutilation/Cutting in the Swiss HIV Cohort Study: A Cross-Sectional Study. Journal of Immigrant and Minority Health, 25(1):136-141.

Nadeau, Sarah A; Vaughan, Timothy G; Beckmann, Christiane; Topolsky, Ivan; Chen, Chaoran; Hodcroft, Emma; Schär, Tobias; Nissen, Ina; Santacroce, Natascha; Burcklen, Elodie; Ferreira, Pedro; Jablonski, Kim Philipp; Posada-Céspedes, Susana; Capece, Vincenzo; Seidel, Sophie; Santamaria de Souza, Noemi; Martinez-Gomez, Julia M; Cheng, Phil; Bosshard, Philipp P; Levesque, Mitchell P; Kufner, Verena; Schmutz, Stefan; Zaheri, Maryam; Huber, Michael; Trkola, Alexandra; Cordey, Samuel; Laubscher, Florian; Gonçalves, Ana Rita; Aeby, Sébastien; Pillonel, Trestan; et al (2023). Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Science Translational Medicine, 15(680):eabn7979.

Luo, Beiping; Schaub, Aline; Glas, Irina; Klein, Liviana K; David, Shannon C; Bluvshtein, Nir; Violaki, Kalliopi; Motos, Ghislain; Pohl, Marie O; Hugentobler, Walter; Nenes, Athanasios; Krieger, Ulrich K; Stertz, Silke; Peter, Thomas; Kohn, Tamar (2023). Expiratory Aerosol pH: The Overlooked Driver of Airborne Virus Inactivation. Environmental Science & Technology, 57(1):486-497.

Béguelin, Charles; Atkinson, Andrew; Boyd, Anders; Falconer, Karolin; Kirkby, Nikolai; Suter-Riniker, Franziska; Günthard, Huldrych F; Rockstroh, Jürgen K; Mocroft, Amanda; Rauch, Andri; Peters, Lars; Wandeler, Gilles (2023). Hepatitis delta infection among persons living with HIV in Europe. Liver International, 43(4):819-828.

Braendli, Tobias; Schindler, Valeria; Braun, Dominique Laurent; Murray, Fritz Ruprecht; Hente, Juliane Marie; Pohl, Daniel (2023). Clarithromycin-based Helicobacter pylori eradication therapy is not associated with higher treatment failure compared with non-clarithromycin-based regimens in a tertiary referral hospital in Switzerland. Swiss Medical Weekly, 153(1):40024.

Gandhi, Rajesh T; Bedimo, Roger; Hoy, Jennifer F; Landovitz, Raphael J; Smith, Davey M; Eaton, Ellen F; Lehmann, Clara; Springer, Sandra A; Sax, Paul E; Thompson, Melanie A; Benson, Constance A; Buchbinder, Susan P; del Rio, Carlos; Eron, Joseph J; Günthard, Huldrych F; Molina, Jean-Michel; Jacobsen, Donna M; Saag, Michael S (2023). Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2022 Recommendations of the International Antiviral Society-USA Panel. JAMA : the Journal of the American Medical Association, 329(1):63-84.

Jaschinski, Nadine; Greenberg, Lauren; Neesgaard, Bastian; et al; Günthard, Huldrych F (2023). Recent abacavir use and incident cardiovascular disease in contemporary treated people living with HIV. AIDS, 37(3):467-475.

2022

Chammartin, Frédérique; Darling, Katharine; Abela, Irene A; Battegay, Manuel; Furrer, Hansjakob; Calmy, Alexandra; Bernasconi, Enos; Schmid, Patrick; Hoffmann, Matthias; Bucher, Heiner C (2022). CD4:CD8 Ratio and CD8 Cell Count and Their Prognostic Relevance for Coronary Heart Disease Events and Stroke in Antiretroviral Treated Individuals: The Swiss HIV Cohort Study. Journal of Acquired Immune Deficiency Syndromes, 91(5):508-515.

Bick, Alexander G; Popadin, Konstantin; Thorball, Christian W; Uddin, Md Mesbah; Zanni, Markella V; Yu, Bing; Cavassini, Matthias; Rauch, Andri; Tarr, Philip; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F; et al (2022). Author Correction: Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV. Scientific Reports, 12(1):11638.

Kusejko, Katharina; Salazar-Vizcaya, Luisa; Shah, Cyril; Stöckle, Marcel; Béguelin, Charles; Schmid, Patrick; Ongaro, Marie; Darling, Katherine; Bernasconi, Enos; Rauch, Andri; Kouyos, Roger D; Gunthard, Huldrych F; Böni, Jürg; Fehr, Jan S; Braun, Dominique L; Swiss HIV Cohort Study (2022). Sustained Effect on Hepatitis C Elimination Among Men Who Have Sex With Men in the Swiss HIV Cohort Study: A Systematic Re-Screening for Hepatitis C RNA Two Years Following a Nation-Wide Elimination Program. Clinical Infectious Diseases, 75(10):1723-1731.

Riebensahm, Carlotta; Berzigotti, Annalisa; Surial, Bernard; Günthard, Huldrych F; Tarr, Philip E; Furrer, Hansjakob; Rauch, Andri; Wandeler, Gilles; Swiss HIV Cohort Study (2022). Factors Associated With Liver Steatosis in People With Human Immunodeficiency Virus on Contemporary Antiretroviral Therapy. Open Forum Infectious Diseases, 9(11):ofac538.

Andresen, Sara; Balakrishna, Suraj; Mugglin, Catrina; Schmidt, Axel J; Braun, Dominique L; Marzel, Alex; Doco Lecompte, Thanh; Darling, Katharine Ea; Roth, Jan A; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F; Rauch, Andri; Kouyos, Roger D; Salazar-Vizcaya, Luisa; Swiss HIV Cohort Study (2022). Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men. PLoS Computational Biology, 18(10):e1010559.

Schmiedeberg, Kristin; Abela, Irene A; Pikor, Natalia Barbara; Vuilleumier, Nicolas; Schwarzmueller, Magdalena; Epp, Selina; Pagano, Sabrina; Grabherr, Sarah; Patterson, Angelica Brooke; Nussberger, Madalina; Trkola, Alexandra; Ludewig, Burkhard; von Kempis, Johannes; Rubbert-Roth, Andrea (2022). Postvaccination anti-S IgG levels predict anti-SARS-CoV-2 neutralising activity over 24 weeks in patients with RA. RMD Open, 8(2):e002575.

Isfordink, Cas; Boyd, Anders; Mocroft, Amanda; Kusejko, Katharina; Smit, Colette; de Wit, Stephane; Mahungu, Tabitha; Falconer, Karolin; Wandeler, Gilles; Cavassini, Matthias; Stöckle, Marcel; Schinkel, Janke; Rauch, Andri; Peters, Lars; van der Valk, Marc (2022). Low Risk of Failing Direct-Acting Antivirals in People With Human Immunodeficiency Virus/Hepatitis C Virus From Sub-Saharan Africa or Southeastern Asia: A European Cross-Sectional Study. Open Forum Infectious Diseases, 9(10):ofac508.

Wensing, Annemarie M; Calvez, Vincent; Ceccherini-Silberstein, Francesca; Charpentier, Charlotte; Günthard, Huldrych F; Paredes, Roger; Shafer, Robert W; Richman, Douglas D (2022). 2022 update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine, 30(4):559-574.

Chaudron, Sandra E; Leemann, Christine; Kusejko, Katharina; Nguyen, Huyen; Tschumi, Nadine; Marzel, Alex; Huber, Michael; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Ramette, Alban; Hirsch, Hans H; Rauch, Andri; Calmy, Alexandra; Vernazza, Pietro; Bernasconi, Enos; Cavassini, Matthias; Metzner, Karin J; Kouyos, Roger D; Günthard, Huldrych F (2022). A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study. Journal of Infectious Diseases, 226(7):1256-1266.

Klein, Liviana K; Luo, Beiping; Bluvshtein, Nir; Krieger, Ulrich K; Schaub, Aline; Glas, Irina; David, Shannon C; Violaki, Kalliopi; Motos, Ghislain; Pohl, Marie O; Hugentobler, Walter; Nenes, Athanasios; Stertz, Silke; Peter, Thomas; Kohn, Tamar (2022). Expiratory aerosol pH is determined by indoor room trace gases and particle size. Proceedings of the National Academy of Sciences of the United States of America, 119(39):e2212140119.

Byonanebye, Dathan M; Polizzotto, Mark N; Neesgaard, Bastian; Sarcletti, Mario; Matulionyte, Raimonda; Braun, Dominique L; et al (2022). Incidence of hypertension in people with HIV who are treated with integrase inhibitors versus other antiretroviral regimens in the RESPOND cohort consortium. HIV Medicine, 23(8):895-910.

Rindler, Audrey E; Kusejko, Katharina; Kuster, Herbert; Neumann, Kathrin; Leemann, Christine; Zeeb, Marius; Chaudron, Sandra E; Braun, Dominique L; Kouyos, Roger D; Metzner, Karin J; Günthard, Huldrych F (2022). The Interplay Between Replication Capacity of HIV-1 and Surrogate Markers of Disease. Journal of Infectious Diseases, 226(6):1057-1068.

Hepprich, Matthias; Mudry, Jonathan M; Gregoriano, Claudia; Jornayvaz, Francois R; Carballo, Sebastian; Wojtusciszyn, Anne; Bart, Pierre-Alexandre; Chiche, Jean-Daniel; Fischli, Stefan; Baumgartner, Thomas; Cavelti-Weder, Claudia; Braun, Dominique L; Günthard, Huldrych F; Beuschlein, Felix; Conen, Anna; West, Emily; Isenring, Egon; Zechmann, Stefan; Bucklar, Gabriela; Aubry, Yoann; Dey, Ludovic; Müller, Beat; Hunziker, Patrick; Schütz, Philipp; Cattaneo, Marco; Donath, Marc Y (2022). Canakinumab in patients with COVID-19 and type 2 diabetes - A multicentre, randomised, double-blind, placebo-controlled trial. eClinicalMedicine, 53:101649.

Begré, Lorin; Béguelin, Charles; Boyd, Anders; Peters, Lars; Rockstroh, Jürgen; Günthard, Huldrych F; Bernasconi, Enos; Cavassini, Matthias; Lacombe, Karine; Mocroft, Amanda; Wandeler, Gilles; Rauch, Andri (2022). Long-term trends of alanine aminotransferase levels among persons living with human immunodeficiency virus/hepatitis B virus with and without hepatitis delta coinfection. Frontiers in Medicine, 9:988356.

Mair, Nina K; Hale, Benjamin G (2022). Ultra-Rare BRD9 Loss-of-Function Variants Limit the Antiviral Action of Interferon. Scientific Reports, 12(1):15360.

Inderbitzin, Anne; Loosli, Tom; Kouyos, Roger D; Metzner, Karin J (2022). Quantification of transgene expression in GSH AAVS1 with a novel CRISPR/Cas9-based approach reveals high transcriptional variation. Molecular Therapy - Methods & Clinical Development, 26:107-118.

Jakeman, Bernadette; Scherrer, Alexandra U; Darling, Katharine E A; Damas, Jose; Bieler-Aeschlimann, Melanie; Hasse, Barbara; Schlosser, Ladina; Hachfeld, Anna; Gutbrod, Klemens; Tarr, Philip E; Calmy, Alexandra; Assal, Frederic; Kunze, Ursula; Stoeckle, Marcel; Schmid, Patrick; Toller, Gianina; Rossi, Stefania; di Benedetto, Caroline; du Pasquier, Renaud; Cavassini, Matthias; Marzolini, Catia (2022). Anticholinergic and Sedative Medications Are Associated With Neurocognitive Performance of Well Treated People With Human Immunodeficiency Virus. Open Forum Infectious Diseases, 9(9):ofac457.

ACTIV-3/TICO Study Group; et al; Braun, Dominique L; Günthard, Huldrych F; Legenne, Philippe (2022). Efficacy and Safety of Ensovibep for Adults Hospitalized With COVID-19 : A Randomized Controlled Trial. Annals of Internal Medicine, 175(9):1266-1274.

Fernbach, Sonja; Hale, Benjamin G (2022). SARS-CoV-2 takes the bait: Exosomes as endogenous decoys. PLoS Biology, 20(9):e3001787.

Günther, Sira C; Martínez-Romero, Carles; Sempere Borau, Milagros; Pham, Christine T N; García-Sastre, Adolfo; Stertz, Silke (2022). Proteomic Identification of Potential Target Proteins of Cathepsin W for Its Development as a Drug Target for Influenza. Microbiology Spectrum, 10(4):e0092122.

Inderbitzin, Anne; Loosli, Tom; Opitz, Lennart; Rusert, Peter; Metzner, Karin J (2022). Transcriptome profiles of latently- and reactivated HIV-1 infected primary CD4+ T cells: A pooled data-analysis. Frontiers in Immunology, 13:915805.

Speich, Benjamin; Chammartin, Frédérique; Abela, Irene A; Amico, Patrizia; Stoeckle, Marcel P; Eichenberger, Anna L; Hasse, Barbara; Braun, Dominique L; Schuurmans, Macé M; Müller, Thomas F; Tamm, Michael; Audigé, Annette; Mueller, Nicolas J; Rauch, Andri; Günthard, Huldrych F; Koller, Michael T; Trkola, Alexandra; Briel, Matthias; Kusejko, Katharina; Bucher, Heiner C; et al; Schanz, Urs (2022). Antibody Response in Immunocompromised Patients After the Administration of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Vaccine BNT162b2 or mRNA-1273: A Randomized Controlled Trial. Clinical Infectious Diseases, 75(1):e585-e593.

Mylonakis, Eleftherios; Lutaakome, Joseph; Jain, Mamta K; et al; Braun, Dominique (2022). Lessons from an international trial evaluating vaccination strategies for recovered inpatients with COVID-19 (VATICO). Med, 3(8):531-537.

Andermatt, Rea; Bloemberg, Guido V; Ganter, Christoph C; Mueller, Nicolas J; Mueller, Antonia M S; Muellhaupt, Beat; Kielstein, Jan T; David, Sascha (2022). Elimination of Herpes Simplex Virus-2 and Epstein-Barr Virus With Seraph 100 Microbind Affinity Blood Filter and Therapeutic Plasma Exchange: An Explorative Study in a Patient With Acute Liver Failure. Critical Care Explorations, 4(8):e0745.

Nadeau, Sarah; Thorball, Christian W; Kouyos, Roger; Günthard, Huldrych F; Böni, Jürg; Yerly, Sabine; Perreau, Matthieu; Klimkait, Thomas; Rauch, Andri; Hirsch, Hans H; Cavassini, Matthias; Vernazza, Pietro; Bernasconi, Enos; Fellay, Jacques; Mitov, Venelin; Stadler, Tanja; Swiss HIV Cohort Study (SHCS) (2022). A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits. Molecular Biology and Evolution, 39(8):msac163.

Kusejko, Katharina; Tschumi, Nadine; Chaudron, Sandra E; Nguyen, Huyen; Battegay, Manuel; Bernasconi, Enos; Böni, Jürg; Huber, Michael; Calmy, Alexandra; Cavassini, Matthias; Egle, Alexander; Grabmeier-Pfistershammer, Katharina; Haas, Bernhard; Hirsch, Hans H; Klimkait, Thomas; Öllinger, Angela; Perreau, Matthieu; Ramette, Alban; Flury, Baharak Babouee; Sarcletti, Mario; Scherrer, Alexandra; Schmid, Patrick; Yerly, Sabine; Zangerle, Robert; Günthard, Huldrych F; Kouyos, Roger D (2022). Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics. Journal of Acquired Immune Deficiency Syndromes, 90(4):e4-e12.

Hauser, Anthony; Goldstein, Fardo; Reichmuth, Martina L; Kouyos, Roger D; Wandeler, Gilles; Egger, Matthias; Riou, Julien (2022). Acquired HIV drug resistance mutations on first-line antiretroviral therapy in Southern Africa: Systematic review and Bayesian evidence synthesis. Journal of Clinical Epidemiology, 148:135-145.

Thoueille, Paul; Alves Saldanha, Susana; Schaller, Fabian; Munting, Aline; Cavassini, Matthias; Braun, Dominique; Günthard, Huldrych F; Kusejko, Katharina; Surial, Bernard; Furrer, Hansjakob; Rauch, Andri; Ustero, Pilar; Calmy, Alexandra; Stoeckle, Marcel; Battegay, Manuel; Marzolini, Catia; Andre, Pascal; Guidi, Monia; Buclin, Thierry; Decosterd, Laurent A; Swiss HIV Cohort Study (2022). Real-Life Therapeutic Concentration Monitoring of Long-Acting Cabotegravir and Rilpivirine: Preliminary Results of an Ongoing Prospective Observational Study in Switzerland. Pharmaceutics, 14(8):1588.

Kusejko, Katharina; Chammartin, Frédérique; Smith, Daniel; Odermatt, Marcel; Schuhmacher, Julian; Koller, Michael; Günthard, Huldrych F; Briel, Matthias; Bucher, Heiner C; Speich, Benjamin (2022). Developing and testing a Corona VaccinE tRiAL pLatform (COVERALL) to study Covid-19 vaccine response in immunocompromised patients. BMC Infectious Diseases, 22:654.

Hufsky, Franziska; Abecasis, Ana; Agudelo-Romero, Patricia; Bletsa, Magda; Brown, Katherine; Claus, Claudia; Deinhardt-Emmer, Stefanie; Deng, Li; Friedel, Caroline C; Gismondi, María Inés; Kostaki, Evangelia Georgia; Kühnert, Denise; Kulkarni-Kale, Urmila; Metzner, Karin J; Meyer, Irmtraud M; Miozzi, Laura; Nishimura, Luca; Paraskevopoulou, Sofia; Pérez-Cataluña, Alba; Rahlff, Janina; Thomson, Emma; Tumescheit, Charlotte; van der Hoek, Lia; Van Espen, Lore; Vandamme, Anne-Mieke; Zaheri, Maryam; Zuckerman, Neta; Marz, Manja (2022). Women in the European Virus Bioinformatics Center. Viruses, 14(7):1522.

Neesgaard, Bastian; Greenberg, Lauren; Miró, Jose M; et al; Günthard, Huldrych F (2022). Associations between integrase strand-transfer inhibitors and cardiovascular disease in people living with HIV: a multicentre prospective study from the RESPOND cohort consortium. The Lancet : HIV, 9(7):e474-e485.

Chammartin, Frédérique; Kusejko, Katharina; Pasin, Chloé; Trkola, Alexandra; Briel, Matthias; Amico, Patrizia; Stoekle, Marcel P; Eichenberger, Anna L; Hasse, Barbara; Braun, Dominique L; Schuurmans, Macé M; Müller, Thomas F; Tamm, Michael; Mueller, Nicolas J; Rauch, Andri; Koller, Michael T; Günthard, Huldrych F; Bucher, Heiner C; Speich, Benjamin; Abela, Irene A; Swiss HIV Cohort Study (2022). Determinants of antibody response to severe acute respiratory syndrome coronavirus 2 mRNA vaccines in people with HIV. AIDS, 36(10):1465-1468.

Pohl, Marie O; Martin-Sancho, Laura; Ratnayake, Ranjala; White, Kris M; Riva, Laura; Chen, Qi-Yin; Lieber, Gauthier; Busnadiego, Idoia; Yin, Xin; Lin, Samuel; Pu, Yuan; Pache, Lars; Rosales, Romel; Déjosez, Marion; Qin, Yiren; De Jesus, Paul D; Beall, Anne; Yoh, Sunnie; Hale, Benjamin G; Zwaka, Thomas P; Matsunaga, Naoko; García-Sastre, Adolfo; Stertz, Silke; Chanda, Sumit K; Luesch, Hendrik (2022). Sec61 Inhibitor Apratoxin S4 Potently Inhibits SARS-CoV-2 and Exhibits Broad-Spectrum Antiviral Activity. ACS Infectious Diseases, 8(7):1265-1279.

Nguyen, Huyen; Hampel, Benjamin; Nuñez, David Garcia; Battegay, Manuel; Hachfeld, Anna; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Vernazza, Pietro; Fellay, Jacques; Rudolph, Hannes; Huber, Michael; Leuzinger, Karoline; Perreau, Matthieu; Scherrer, Alexandra; Ramette, Alban Nicolas; Yerly, Sabine; Günthard, Huldrych F; Kouyos, Roger D; Kusejko, Katharina (2022). Correction to: Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group. Clinical Infectious Diseases, 74(12):2266.

Busnadiego, Idoia; Abela, Irene A; Frey, Pascal M; Hofmaenner, Daniel A; Scheier, Thomas C; Schuepbach, Reto A; Buehler, Philipp Karl; Brugger, Silvio D; Hale, Benjamin G (2022). Critically ill COVID-19 patients with neutralizing autoantibodies against type I interferons have increased risk of herpesvirus disease. PLoS Biology, 20(7):e3001709.

Metzner, Karin J (2022). Technologies for HIV-1 drug resistance testing: inventory and needs. Current opinion in HIV and AIDS, 17(4):222-228.

Winter, Babette L; Hovaguimian, Frédérique; Kouyos, Roger D; Schmidt, Axel Jeremias; Bernasconi, Enos; Braun, Dominique L; Calmy, Alexandra; Notter, Julia; Stoeckle, Marcel; Surial, Bernard; Christinet, Vanessa; Cavassini, Matthias; Depmeier, Carsten; Läuchli, Severin; Boffi El Amari, Emmanuelle; Reinacher, Matthias; Rasi, Manuela; Bruggmann, Philip; Haerry, David; Bize, Raphaël; Low, Nicola; Lehner, Andreas; Quednow, Boris B; Fehr, Jan S; Hampel, Benjamin (2022). Changes in mental and sexual health among MSM using HIV pre-exposure prophylaxis during the SARS-CoV-2 pandemic: longitudinal analysis of the SwissPrEPared cohort study. Swiss Medical Weekly, 152(25-26):w30192.

Marconato, Maddalena; Abela, Irene A; Hauser, Anthony; Schwarzmüller, Magdalena; Katzensteiner, Rheliana; Braun, Dominique L; Epp, Selina; Audigé, Annette; Weber, Jacqueline; Rusert, Peter; Schindler, Eméry; Pasin, Chloé; West, Emily; Böni, Jürg; Kufner, Verena; Huber, Michael; Zaheri, Maryam; Schmutz, Stefan; Frey, Beat M; Kouyos, Roger D; Günthard, Huldrych F; Manz, Markus G; Trkola, Alexandra (2022). Antibodies from convalescent plasma promote SARS-CoV-2 clearance in individuals with and without endogenous antibody response. Journal of Clinical Investigation, 132(12):e158190.

Tepekule, Burcu; Kusejko, Katharina; Zeeb, Marius; Tarr, Philip E; Calmy, Alexandra; Battegay, Manuel; Furrer, Hansjakob; Cavassini, Matthias; Bernasconi, Enos; Notter, Julia; Günthard, Huldrych F; Nemeth, Johannes; Kouyos, Roger D (2022). Impact of Latent Tuberculosis on Diabetes. Journal of Infectious Diseases, 225(12):2229-2234.

Klinnert, Sarah; Chemnitzer, Alex; Rusert, Peter; Metzner, Karin J (2022). Systematic HIV-1 promoter targeting with CRISPR/dCas9-VPR reveals optimal region for activation of the latent provirus. Journal of General Virology, 103(6):jgv.0.001754.

Salazar-Vizcaya, Luisa; Atkinson, Andrew; Kronenberg, Andreas; Plüss-Suard, Catherine; Kouyos, Roger D; Kachalov, Viacheslav; Troillet, Nicolas; Marschall, Jonas; Sommerstein, Rami (2022). The impact of public health interventions on the future prevalence of ESBL-producing Klebsiella pneumoniae: a population based mathematical modelling study. BMC Infectious Diseases, 22:487.

Balakrishna, Suraj; Wolfensberger, Aline; Kachalov, Viacheslav; Roth, Jan A; Kusejko, Katharina; Scherrer, Alexandra U; Furrer, Hansjakob; Hauser, Christoph; Calmy, Alexandra; Cavassini, Matthias; Schmid, Patrick; Bernasconi, Enos; Battegay, Manuel; Günthard, Huldrych F; Kouyos, Roger D (2022). Decreasing incidence and determinants of Bacterial Pneumonia in people with HIV: The Swiss HIV Cohort Study. Journal of Infectious Diseases, 225(9):1592-1600.

Schoepf, Isabella C; Thorball, Christian W; Ledergerber, Bruno; Kootstra, Neeltje A; Reiss, Peter; Raffenberg, Marieke; Engel, Tanja; Braun, Dominique L; Hasse, Barbara; Thurnheer, Christine; Marzolini, Catia; Seneghini, Marco; Bernasconi, Enos; Cavassini, Matthias; Buvelot, Hélène; Arribas, José R; Kouyos, Roger D; Fellay, Jacques; Günthard, Huldrych F; Tarr, Philip E; Swiss HIV Cohort Study (2022). Telomere Length Declines In Persons Living With HIV Before Antiretroviral Therapy Start But Not After Viral Suppression: A Longitudinal Study Over >17 Years. Journal of Infectious Diseases, 225(9):1581-1591.

Nguyen, Huyen; Hampel, Benjamin; Nuñez, David Garcia; Battegay, Manuel; Hachfeld, Anna; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Vernazza, Pietro; Fellay, Jacques; Rudolph, Hannes; Huber, Michael; Leuzinger, Karoline; Perreau, Matthieu; Scherrer, Alexandra; Ramette, Alban Nicolas; Yerly, Sabine; Günthard, Huldrych F; Kouyos, Roger D; Kusejko, Katharina; Swiss HIV Cohort Study (2022). Identifying and Characterizing Trans women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group. Clinical Infectious Diseases, 74(8):1468-1475.

Salazar-Vizcaya, Luisa; Kusejko, Katharina; Günthard, Huldrych F; Böni, Jürg; Metzner, Karin J; Braun, Dominique L; Nicca, Dunja; Bernasconi, Enos; Calmy, Alexandra; Darling, Katharine E A; Wandeler, Gilles; Kouyos, Roger D; Rauch, Andri; Swiss HIV Cohort Study (2022). An Approach to Quantifying the Interaction between Behavioral and Transmission Clusters. Viruses, 14(4):784.

Gao, Sihaoyu; Wu, Lang; Yu, Tingting; Kouyos, Roger; Günthard, Huldrych F; Wang, Rui (2022). Nonlinear mixed-effects models for HIV viral load trajectories before and after antiretroviral therapy interruption, incorporating left censoring. Statistical Communications in Infectious Diseases, 14(1):20210001.

Huang, Alice; Cicin-Sain, Caroline; Pasin, Chloé; Epp, Selina; Audigé, Annette; Müller, Nicolas J; Nilsson, Jakob; Bankova, Andriyana; Wolfensberger, Nathan; Vilinovszki, Oliver; Nair, Gayathri; Hockl, Philipp; Schanz, Urs; Kouyos, Roger D; Hasse, Barbara; Zinkernagel, Annelies S; Trkola, Alexandra; Manz, Markus G; Abela, Irene A; Müller, Antonia M S (2022). Antibody Response to SARS-CoV-2 Vaccination in Patients following Allogeneic Hematopoietic Cell Transplantation. Transplantation and Cellular Therapy, 28(4):214.e1-214.e11.

Fernbach, Sonja; Spieler, Eva E; Busnadiego, Idoia; Karakus, Umut; Lkharrazi, Anouk; Stertz, Silke; Hale, Benjamin G (2022). Restriction factor screening identifies RABGAP1L-mediated disruption of endocytosis as a host antiviral defense. Cell Reports, 38(12):110549.

Hunziker, Annika; Stertz, Silke (2022). Unraveling virus-induced cellular signaling cascades by label-free quantitative phosphoproteomics. STAR Protocols, 3(1):101089.

Tao, Yile; Yue, Yang; Qiu, Guangyu; Ji, Zheng; Spillman, Martin; Gai, Zhibo; Chen, Qingfa; Bielecki, Michel; Huber, Michael; Trkola, Alexandra; Wang, Qiyuan; Cao, Junji; Wang, Jing (2022). Comparison of analytical sensitivity and efficiency for SARS-CoV-2 primer sets by TaqMan-based and SYBR Green-based RT-qPCR. Applied Microbiology and Biotechnology, 106(5-6):2207-2218.

Tamò, Raphaël; Turk, Teja; Böni, Jürg; Kouyos, Roger D; Schmutz, Stefan; Huber, Michael; Shah, Cyril; Bischoff-Ferrari, Heike A; Distler, Oliver; Battegay, Edouard; Giovanoli, Pietro; Guckenberger, Matthias; Kohler, Malcolm; Müller, Rouven; Petry, Heidi; Ruschitzka, Frank; McGeer, Allison; Sax, Hugo; Weber, Rainer; Trkola, Alexandra; Kuster, Stefan P (2022). Secondary attack rates from asymptomatic and symptomatic influenza virus shedders in hospitals: Results from the TransFLUas influenza transmission study. Infection Control and Hospital Epidemiology, 43(3):312-318.

van Dorsten, Rebecca T; Reh, Lucia; Trkola, Alexandra; Morris, Lynn; Moore, Penny L (2022). Single-Chain Variable Fragments of Broadly Neutralizing Antibodies Prevent HIV Cell-Cell Transmission. Journal of Virology, 96(4):e0193421.

Scherrer, Alexandra U; Traytel, Anna; Braun, Dominique L; Calmy, Alexandra; Battegay, Manuel; Cavassini, Matthias; Furrer, Hansjakob; Schmid, Patrick; Bernasconi, Enos; Stoeckle, Marcel; Kahlert, Christian; Trkola, Alexandra; Kouyos, Roger D; Tarr, Philip; Marzolini, Catia; Wandeler, Gilles; Fellay, Jacques; Bucher, Heiner; Yerly, Sabine; Suter, Franziska; Hirsch, Hans; Huber, Michael; Dollenmaier, Günter; Perreau, Matthieu; Martinetti, Gladys; Rauch, Andri; Günthard, Huldrych F; Swiss HIV Cohort Study (2022). Cohort Profile Update: The Swiss HIV Cohort Study (SHCS). International Journal of Epidemiology, 51(1):33-34j.

Seifert, David; Joos, Beda; Braun, Dominique L; Oberle, Corinna S; Schenkel, Corinne D; Kuster, Herbert; Grube, Christina; Böni, Jürg; Yerly, Sabine; Aubert, Vincent; Klimkait, Thomas; Günthard, Huldrych F; Beerenwinkel, Niko; Metzner, Karin J; Swiss HIV Cohort Study (2022). Detecting Selection in the HIV-1 Genome during Sexual Transmission Events. Viruses, 14(2):406.

Wymant, Chris; Bezemer, Daniela; Blanquart, François; Ferretti, Luca; et al; Günthard, Huldrych F; Kouyos, Roger D (2022). A highly virulent variant of HIV-1 circulating in the Netherlands. Science, 375(6580):540-545.

Jakeman, Bernadette; Scherrer, Alexandra; Battegay, Manuel; Gunthard, Huldrych F; Hachfeld, Anna; Calmy, Alexandra; Schmid, Patrick; Bernasconi, Enos; Cavassini, Matthias; Marzolini, Catia (2022). Anticholinergic medication use in elderly people living with HIV and self-reported neurocognitive impairment: a prospective cohort study. Journal of Antimicrobial Chemotherapy, 77(2):492-499.

Moldt, Brian; Günthard, Huldrych F; Workowski, Kimberly A; Little, Susan J; Eron, Joseph J; Overton, Edgar T; Lehmann, Clara; Rokx, Casper; Kozal, Michael J; Gandhi, Rajesh T; Braun, Dominique L; Parvangada, Aiyappa; Li, Jiani; Martin, Ross; Selzer, Lisa; Cox, Stephanie; Margot, Nicolas; Liu, Hui; Slamowitz, Debbie; Makadzange, Tariro; Collins, Sean E; Geleziunas, Romas; Callebaut, Christian (2022). Evaluation of HIV-1 reservoir size and broadly neutralizing antibody susceptibility in acute antiretroviral therapy-treated individuals. AIDS, 36(2):205-214.

Hale, Benjamin G (2022). Antiviral immunity triggered by infection-induced host transposable elements. Current Opinion in Virology, 52:211-216.

Hovaguimian, Frédérique; Martin, Eileen Christiane; Reinacher, M; Rasi, M; Schmidt, A J; Bernasconi, E; Boffi El Amari, E; Braun, D L; Calmy, A; Darling, K; Christinet, V; Depmeier, C; Hauser, C; Läuchli, S; Notter, J; Stoeckle, M; Surial, B; Vernazza, P; Bruggmann, P; Tarr, P; Haerry, D; Bize, R; Low, N; Lehner, A; Böni, J; Kouyos, R D; Fehr, J S; Hampel, B (2022). Participation, retention and uptake in a multicentre pre-exposure prophylaxis cohort using online, smartphone-compatible data collection. HIV Medicine, 23(2):146-158.

Fehr, Thomas; Hübel, Kerstin; de Rougemont, Olivier; Abela, Irene; Gaspert, Ariana; Güngör, Tayfun; Hauri, Mathias; Helmchen, Birgit; Linsenmeier, Claudia; Müller, Thomas; Nilsson, Jakob; Riesterer, Oliver; Scandling, John D; Schanz, Urs; Cippà, Pietro E (2022). Successful Induction of Specific Immunological Tolerance by Combined Kidney and Hematopoietic Stem Cell Transplantation in HLA-Identical Siblings. Frontiers in Immunology, 13:796456.

Hunziker, Annika; Glas, Irina; Pohl, Marie O; Stertz, Silke (2022). Phosphoproteomic profiling of influenza virus entry reveals infection-triggered filopodia induction counteracted by dynamic cortactin phosphorylation. Cell Reports, 38(4):110306.

Wegner, Fanny; Roloff, Tim; Huber, Michael; et al; Schmutz, Stefan; Kufner, Verena; Zaheri, Maryam; Trkola, Alexandra (2022). External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories. Journal of Clinical Microbiology, 60(1):e0169821.

Greenberg, Lauren; Ryom, Lene; Neesgaard, Bastian; et al; Günthard, Huldrych F; Kusejko, Katharina (2022). Integrase Strand Transfer Inhibitor Use and Cancer Incidence in a Large Cohort Setting. Open Forum Infectious Diseases, 9(3):ofac029.

Duran Ramirez, Jessy J; Ballouz, Tala; Nguyen, Huyen; Kusejko, Katharina; Chaudron, Sandra E; Huber, Michael; Hirsch, Hans H; Perreau, Matthieu; Ramette, Alban; Yerly, Sabine; Cavassini, Matthias; Stöckle, Marcel; Furrer, Hansjakob; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2022). Increasing Frequency and Transmission of HIV-1 Non-B Subtypes among Men Who Have Sex with Men in the Swiss HIV Cohort Study. Journal of Infectious Diseases, 225(2):306-316.

Bick, Alexander G; Popadin, Konstantin; Thorball, Christian W; Uddin, Md Mesbah; Zanni, Markella V; Yu, Bing; Cavassini, Matthias; Rauch, Andri; Tarr, Philip; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F; et al (2022). Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV. Scientific Reports, 12(1):577.

2021

Gabrielaite, Migle; Bennedbæk, Marc; Zucco, Adrian G; Ekenberg, Christina; Murray, Daniel D; Kan, Virginia L; Touloumi, Giota; Vandekerckhove, Linos; Turner, Dan; Neaton, James; Lane, H Clifford; Safo, Sandra; Arenas-Pinto, Alejandro; Polizzotto, Mark N; Günthard, Huldrych F; Lundgren, Jens D; Marvig, Rasmus L (2021). Human immunotypes impose selection on viral genotypes through viral epitope specificity. Journal of Infectious Diseases, 224(12):2053-2063.

Abela, Irene A; Pasin, Chloé; Schwarzmüller, Magdalena; Epp, Selina; Sickmann, Michèle E; Schanz, Merle M; Rusert, Peter; Weber, Jacqueline; Schmutz, Stefan; Audigé, Annette; Maliqi, Liridona; Hunziker, Annika; Hesselman, Maria C; Niklaus, Cyrille R; Gottschalk, Jochen; Schindler, Eméry; Wepf, Alexander; Karrer, Urs; Wolfensberger, Aline; Rampini, Silvana K; Meyer Sauteur, Patrick M; Berger, Christoph; Huber, Michael; Böni, Jürg; Braun, Dominique L; Marconato, Maddalena; Manz, Markus G; Frey, Beat M; Günthard, Huldrych F; Kouyos, Roger D; et al (2021). Multifactorial seroprofiling dissects the contribution of pre-existing human coronaviruses responses to SARS-CoV-2 immunity. Nature Communications, 12:6703.

Raffenberg, Marieke; Engel, Tanja; Schoepf, Isabella C; Kootstra, Neeltje A; Reiss, Peter; Braun, Dominique L; Thorball, Christian W; Fellay, Jacques; Kouyos, Roger D; Ledergerber, Bruno; Günthard, Huldrych F; Tarr, Philip E; Zurich Primary HIV Infection Study; Swiss HIV Cohort Study (2021). Impact of Delaying Antiretroviral Treatment during Primary HIV Infection on Telomere Length. Journal of Infectious Diseases, 224(10):1775-1784.

Friedrich, Nikolas; Stiegeler, Emanuel; Glögl, Matthias; Lemmin, Thomas; Hansen, Simon; Kadelka, Claus; Wu, Yufan; Ernst, Patrick; Maliqi, Liridona; Foulkes, Caio; Morin, Mylène; Eroglu, Mustafa; Liechti, Thomas; Ivan, Branislav; Reinberg, Thomas; Schaefer, Jonas V; Karakus, Umut; Ursprung, Stephan; Mann, Axel; Rusert, Peter; Kouyos, Roger D; Robinson, John A; Günthard, Huldrych F; Plückthun, Andreas; Trkola, Alexandra (2021). Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization. Nature Communications, 12:6705.

Ulyte, Agne; Radtke, Thomas; Abela, Irene A; Haile, Sarah R; Ammann, Priska; Berger, Christoph; Trkola, Alexandra; Fehr, Jan; Puhan, Milo A; Kriemler, Susi (2021). Evolution of SARS-CoV-2 seroprevalence and clusters in school children from June 2020 to April 2021: prospective cohort study Ciao Corona. Swiss Medical Weekly, 151:w30092.

Schoepf, Isabella C; Thorball, Christian W; Ledergerber, Bruno; Engel, Tanja; Raffenberg, Marieke; Kootstra, Neeltje A; Reiss, Peter; Hasse, Barbara; Marzolini, Catia; Thurnheer, Christine; Seneghini, Marco; Bernasconi, Enos; Cavassini, Matthias; Buvelot, Hélène; Kouyos, Roger; Günthard, Huldrych F; Fellay, Jacques; Tarr, Philip E; Swiss HIV Cohort Study (2021). Coronary Artery Disease-associated and Longevity-associated Polygenic Risk Scores for Prediction of Coronary Artery Disease Events in Persons Living with HIV: The Swiss HIV Cohort Study. Clinical Infectious Diseases, 73(9):1597-1604.

Courlet, Perrine; Barbieux, Charlotte; Sculier, Delphine; Wandeler, Gilles; Stoeckle, Marcel; Bernasconi, Enos; Braun, Dominique; Vernazza, Pietro; Cavassini, Matthias; Marinosci, Annalisa; Smit, Mikaela; Günthard, Huldrych F; Schmid, Patrick; Limacher, Andreas; Guidi, Monia; Alves Saldanha, Susana; Decosterd, Laurent Arthur; Calmy, Alexandra (2021). Pharmacokinetic parameters and weight change in HIV patients newly switched to dolutegravir-based regimens in SIMPL'HIV clinical trial. British Journal of Clinical Pharmacology, 87(11):4455-4460.

Stertz, Silke; Hale, Benjamin G (2021). Interferon system deficiencies exacerbating severe pandemic virus infections. Trends in Microbiology, 29(11):973-982.

Balakrishna, Suraj; Salazar-Vizcaya, Luisa; Schmidt, Axel J; Kachalov, Viacheslav; Kusejko, Katharina; Thurnheer, Maria Christine; Roth, Jan A; Nicca, Dunja; Cavassini, Matthias; Battegay, Manuel; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F; Rauch, Andri; Kouyos, Roger D; Swiss HIV Cohort Study (2021). Assessing the drivers of syphilis among men who have sex with men in Switzerland reveals a key impact of screening frequency: A modelling study. PLoS Computational Biology, 17(10):e1009529.

Riou, Julien; Dupont, Carole; Bertagnolio, Silvia; Gupta, Ravindra K; Kouyos, Roger D; Egger, Matthias; Althaus, Christian L (2021). Correction to: Drivers of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTIs) in nine southern African countries: a modelling study. BMC Infectious Diseases, 21:1098.

Speich, Benjamin; Chammartin, Frédérique; Smith, Daniel; Stoeckle, Marcel P; Amico, Patrizia; Eichenberger, Anna L; Hasse, Barbara; Schuurmans, Macé M; Müller, Thomas; Tamm, Michael; Dickenmann, Michael; Abela, Irene A; Trkola, Alexandra; Hirsch, Hans H; Manuel, Oriol; Cavassini, Matthias; Hemkens, Lars G; Briel, Matthias; Mueller, Nicolas J; Rauch, Andri; Günthard, Huldrych F; Koller, Michael T; Bucher, Heiner C; Kusejko, Katharina (2021). A trial platform to assess approved SARS-CoV-2 vaccines in immunocompromised patients: first sub-protocol for a pilot trial comparing the mRNA vaccines Comirnaty® and COVID-19 mRNA Vaccine Moderna®. Trials, 22:724.

Roth, Jan A; Radevski, Gorjan; Marzolini, Catia; Rauch, Andri; Günthard, Huldrych F; Kouyos, Roger D; Fux, Christoph A; Scherrer, Alexandra U; Calmy, Alexandra; Cavassini, Matthias; Kahlert, Christian R; Bernasconi, Enos; Bogojeska, Jasmina; Battegay, Manuel (2021). Cohort-derived machine learning models for individual prediction of chronic kidney disease in people living with HIV: a prospective multicentre cohort study. Journal of Infectious Diseases, 224(7):1198-1208.

Riou, Julien; Dupont, Carole; Bertagnolio, Silvia; Gupta, Ravindra K; Kouyos, Roger D; Egger, Matthias; Althaus, Christian L (2021). Drivers of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTIs) in nine southern African countries: a modelling study. BMC Infectious Diseases, 21:1042.

Braun, Dominique L; Hampel, Benjamin; Ledergerber, Bruno; Grube, Christina; Nguyen, Huyen; Künzler-Heule, Patrizia; Shah, Cyril; Salazar-Vizcaya, Luisa; Conen, Anna; Flepp, Markus; Stöckle, Marcel; Béguelin, Charles; Schmid, Patrick; Rougemont, Mathieu; Delaloye, Julie; Bernasconi, Enos; Nicca, Dunja; Böni, Jürg; Rauch, Andri; Kouyos, Roger D; Günthard, Huldrych F; Fehr, Jan S (2021). A treatment as prevention trial to eliminate hepatitis C among men who have sex with men living with HIV in the Swiss HIV Cohort Study. Clinical Infectious Diseases, 73(7):e2194-e2202.

Börold, Jacob; Eletto, Davide; Busnadiego, Idoia; Mair, Nina K; Moritz, Eva; Schiefer, Samira; Schmidt, Nora; Petric, Philipp P; Wong, W Wei-Lynn; Schwemmle, Martin; Hale, Benjamin G (2021). BRD9 is a druggable component of interferon-stimulated gene expression and antiviral activity. EMBO Reports, 22(10):e52823.

Greenberg, Lauren; Ryom, Lene; Neesgaard, Bastian; Wandeler, Gilles; Staub, Therese; Gisinger, Martin; Skoll, Michael; Günthard, Huldrych F; et al (2021). Clinical outcomes of two-drug regimens vs. three-drug regimens in antiretroviral treatment-experienced people living with HIV. Clinical Infectious Diseases, 73(7):e2323-e2333.

Pyngottu, Ashima; Scherrer, Alexandra U; Kouyos, Roger; Huber, Michael; Hirsch, Hans; Perreau, Matthieu; Yerly, Sabine; Calmy, Alexandra; Cavassini, Matthias; Stöckle, Marcel; Furrer, Hansjakob; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F; Swiss HIV Cohort Study (2021). Predictors of virological failure and time to viral suppression of first line integrase inhibitor based antiretroviral treatment. Clinical Infectious Diseases, 73(7):e2134-e2141.

Deutschmann, Elisabeth; Bucher, Heiner C; Jaeckel, Steffen; Gibbons, Sara; McAllister, Katie; Scherrer, Alexandra U; Braun, Dominique L; Cavassini, Matthias; Hachfeld, Anna; Calmy, Alexandra; Battegay, Manuel; Cipriani, Michela; Elzi, Luigia; Young, James; Lopez-Centeno, Beatriz; Berenguer, Juan; Khoo, Saye; Moffa, Giusi; Marzolini, Catia; Swiss HIV Cohort Study (2021). Prevalence of potential drug-drug interactions in patients of the Swiss HIV Cohort Study in the era of HIV integrase inhibitors. Clinical Infectious Diseases, 73(7):e2145-e2152.

Engel, Tanja; Raffenberg, Marieke; Schoepf, Isabella C; Kootstra, Neeltje A; Reiss, Peter; Thorball, Christian W; Hasse, Barbara; Hirzel, Cédric; Wissel, Kerstin; Roth, Jan A; Bernasconi, Enos; Darling, Katharine E A; Calmy, Alexandra; Fellay, Jacques; Kouyos, Roger D; Günthard, Huldrych F; Ledergerber, Bruno; Tarr, Philip E (2021). Telomere Length, Traditional Risk Factors, HIV-related Factors and Coronary Artery Disease Events in Swiss Persons Living with HIV. Clinical Infectious Diseases, 73(7):e2070-e2076.

Wolters, Femke; Grünberg, Maria; Huber, Michael; Kessler, Harald H; Prüller, Florian; Saleh, Lanja; Fébreau, Christine; Rahamat-Langendoen, Janette; Thibault, Vincent; Melchers, Willem J G (2021). European multicenter evaluation of Xpert® Xpress SARS-CoV-2/Flu/RSV test. Journal of Medical Virology, 93(10):5798-5804.

Posada-Céspedes, Susana; Van Zyl, Gert; Montazeri, Hesam; Kuipers, Jack; Rhee, Soo-Yon; Kouyos, Roger; Günthard, Huldrych F; Beerenwinkel, Niko (2021). Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS Computational Biology, 17(9):e1008363.

Mazel-Sanchez, Beryl; Iwaszkiewicz, Justyna; Bonifacio, Joao P P; Silva, Filo; Niu, Chengyue; Strohmeier, Shirin; Eletto, Davide; Krammer, Florian; Tan, Gene; Zoete, Vincent; Hale, Benjamin G; Schmolke, Mirco (2021). Influenza A viruses balance ER stress with host protein synthesis shutoff. Proceedings of the National Academy of Sciences of the United States of America, 118(36):e2024681118.

Moldt, Brian; Parvangada, Aiyappa; Martin, Ross; Pace, Craig; Balakrishnan, Mini; Thomsen, Nathan D; E Collins, Sean; Kuster, Herbert; Braun, Dominique L; Günthard, Huldrych F; Geleziunas, Romas; Callebaut, Christian (2021). Evaluation of Broadly Neutralizing Antibody Sensitivity by Genotyping and Phenotyping for Qualifying Participants to HIV Clinical Trials. Journal of Acquired Immune Deficiency Syndromes, 88(1):61-69.

Kusejko, Katharina; Neofytos, Dionysios; Hirsch, Hans H; Meylan, Pascal; Boggian, Katia; Hirzel, Cedric; Garzoni, Christian; Kouyos, Roger D; Mueller, Nicolas J; Schreiber, Peter W; Swiss Transplant Cohort Study (2021). Differences Between Infectious Disease Events in First Liver Transplant Versus Retransplantation in the Swiss Transplant Cohort Study. Liver Transplantation, 27(9):1283-1290.

Steiner, Fiona; Schmutz, Stefan; Gosert, Rainer; Huder, Jon B; Redli, Patrick M; Capaul, Riccarda; Hirsch, Hans H; Böni, Jürg; Zbinden, Andrea (2021). Usefulness of the GenMark ePlex RPP assay for the detection of respiratory viruses compared to the FTD21 multiplex RT-PCR. Diagnostic Microbiology and Infectious Disease, 101:115424.

Audigé, Annette; Böni, Jürg; Schreiber, Peter W; Scheier, Thomas; Buonomano, Roberto; Rudiger, Alain; Braun, Dominique L; Eich, Gerhard; Keller, Dagmar I; Hasse, Barbara; Berger, Christoph; Günthard, Huldrych F; Manrique, Amapola; Trkola, Alexandra; Huber, Michael (2021). Reduced Relative Sensitivity of the Elecsys SARS-CoV-2 Antigen Assay in Saliva Compared to Nasopharyngeal Swabs. Microorganisms, 9(8):1700.

Thorball, Christian W; Oudot-Mellakh, Tiphaine; Ehsan, Nava; Hammer, Christian; Santoni, Federico A; Niay, Jonathan; Costagliola, Dominique; Goujard, Cécile; Meyer, Laurence; Wang, Sophia S; Hussain, Shehnaz K; Theodorou, Ioannis; Cavassini, Matthias; Rauch, Andri; Battegay, Manuel; Hoffmann, Matthias; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F; Mohammadi, Pejman; McLaren, Paul J; Rabkin, Charles S; Besson, Caroline; Fellay, Jacques (2021). Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma. Haematologica, 106(8):2233-2241.

Vavassori, Stefano; Chou, Janet; Faletti, Laura Eva; Haunerdinger, Veronika; Opitz, Lennart; Joset, Pascal; Fraser, Christopher J; Prader, Seraina; Gao, Xianfei; Schuch, Luise A; Wagner, Matias; Hoefele, Julia; Maccari, Maria Elena; Zhu, Ying; Elakis, George; Gabbett, Michael T; Forstner, Maria; Omran, Heymut; Kaiser, Thomas; Kessler, Christina; Olbrich, Heike; Frosk, Patrick; Almutairi, Abduarahman; Platt, Craig D; Elkins, Megan; Weeks, Sabrina; Rubin, Tamar; Planas, Raquel; Marchetti, Tommaso; Koovely, Danil; Brotschi, Barbara; Laube, Guido; Güngör, Tayfun; Kottke, Raimund; Weber, Achim; Griese, Matthias; Pachlopnik Schmid, Jana; et al (2021). Multisystem Inflammation and Susceptibility to Viral infections in Human ZNFX1 Deficiency. Journal of Allergy and Clinical Immunology, 148(2):381-393.

Palika, Archana; Armanious, Antonius; Rahimi, Akram; Medaglia, Chiara; Gasbarri, Matteo; Handschin, Stephan; Rossi, Antonella; Pohl, Marie O; Busnadiego, Idoia; Gübeli, Christian; Anjanappa, Ravi B; Bolisetty, Sreenath; Peydayesh, Mohammad; Stertz, Silke; Hale, Benjamin G; Tapparel, Caroline; Stellacci, Francesco; Mezzenga, Raffaele (2021). An antiviral trap made of protein nanofibrils and iron oxyhydroxide nanoparticles. Nature Nanotechnology, 16(8):918-925.

Ulyte, Agne; Radtke, Thomas; Abela, Irene Alma; Haile, Sarah R; Blankenberger, Jacob; Jung, Ruedi; Capelli, Celine; Berger, Christoph; Frei, Anja; Huber, Michael; Schanz, Merle; Schwarzmueller, Magdalena; Trkola, Alexandra; Fehr, Jan; Puhan, Milo Alan; Kriemler, Susi (2021). Variation in SARS-CoV-2 seroprevalence across districts, schools and classes: baseline measurements from a cohort of primary and secondary school children in Switzerland. BMJ Open, 11(7):e047483.

Hirschi, Stephan; Kalbermatter, David; Ucurum, Zöhre; Lemmin, Thomas; Fotiadis, Dimitrios (2021). Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin. Nature Communications, 12:4107.

Pohl, Marie O; Busnadiego, Idoia; Marrafino, Francesco; Wiedmer, Lars; Hunziker, Annika; Fernbach, Sonja; Glas, Irina; Moroz-Omori, Elena V; Hale, Benjamin G; Caflisch, Amedeo; Stertz, Silke (2021). Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir. Journal of General Virology, 102(7):001625.

Bachmann, Nadine; Kusejko, Katharina; Nguyen, Huyen; Chaudron, Sandra E; Kadelka, Claus; Turk, Teja; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Battegay, Manuel; Rauch, Andri; Ramette, Alban; Vernazza, Pietro; Bernasconi, Enos; Cavassini, Matthias; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2021). Phylogenetic cluster analysis identifies virological and behavioral drivers of HIV transmission in MSM. Clinical Infectious Diseases, 72(12):2175-2183.

Achermann, Yvonne; Kusejko, Katharina; Auñón, Álvaro; Clauss, Martin; Corvec, Stéphane; Esteban, Jaime; Fernandez-Sampedro, Marta; Ferrari, Matteo Carlo; Gassmann, Natalie; Jent, Philipp; Jost, Bernhard; Kouyos, Roger D; Kramer, Tobias Siegfried; Lora-Tamayo, Jaime; Morand, Philippe C; Benito, Natividad; Pablo-Marcos, Daniel; Patel, Robin; Scanferla, Giulia; Sendi, Parham; Slama, Dorsaf; Stadelmann, Vincent A; Strahm, Carol; Thurnheer, Christine; Trebše, Rihard; Uckay, Ilker; Vijayvargiya, Prakhar; Waldmann, Isabelle; Wouthuyzen-Bakker, Marjan (2021). The impact of surgical strategy and rifampin on treatment outcome in Cutibacterium periprosthetic joint infections. Clinical Infectious Diseases, 72(12):e1064-e1073.

Deng, Yun; Chatterjee, Bithi; Zens, Kyra; Zdimerova, Hana; Müller, Anne; Schuhmachers, Patrick; Ligeon, Laure-Anne; Bongiovanni, Antonino; Capaul, Riccarda; Zbinden, Andrea; Holler, Angelika; Stauss, Hans; Hammerschmidt, Wolfgang; Münz, Christian (2021). CD27 is required for protective lytic EBV antigen-specific CD8+ T-cell expansion. Blood, 137(23):3225-3236.

Lanz, Caroline; Schotsaert, Michael; Magnus, Carsten; Karakus, Umut; Hunziker, Annika; Sempere Borau, Milagros; Martínez-Romero, Carles; Spieler, Eva E; Günther, Sira C; Moritz, Eva; Hale, Benjamin G; Trkola, Alexandra; García-Sastre, Adolfo; Stertz, Silke (2021). IFITM3 incorporation sensitizes influenza A virus to antibody-mediated neutralization. Journal of Experimental Medicine, 218(6):e20200303.

Nguyen, Huyen; Thorball, Christian Wandell; Fellay, Jacques; Böni, Jürg; Yerly, Sabine; Perreau, Matthieu; Hirsch, Hans H; Kusejko, Katharina; Thurnheer, Maria Christine; Battegay, Manuel; Cavassini, Matthias; Kahlert, Christian R; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2021). Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link. eLife, 10:e67388.

Sempere Borau, Milagros; Stertz, Silke (2021). Entry of influenza A virus into host cells - recent progress and remaining challenges. Current Opinion in Virology, 48:23-29.

Echavarría-Consuegra, Liliana; Cook, Georgia M; Busnadiego, Idoia; Lefèvre, Charlotte; Keep, Sarah; Brown, Katherine; Doyle, Nicole; Dowgier, Giulia; Franaszek, Krzysztof; Moore, Nathan A; Siddell, Stuart G; Bickerton, Erica; Hale, Benjamin G; Firth, Andrew E; Brierley, Ian; Irigoyen, Nerea (2021). Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection. PLoS Pathogens, 17(6):e1009644.

Hale, Benjamin G (2021). Avoiding culture shock with the SARS-CoV-2 spike protein. eLife, 10:e69496.

Kok, Yik Lim; Vongrad, Valentina; Chaudron, Sandra E; Shilaih, Mohaned; Leemann, Christine; Neumann, Kathrin; Kusejko, Katharina; Di Giallonardo, Francesca; Kuster, Herbert; Braun, Dominique L; Kouyos, Roger D; Günthard, Huldrych F; Metzner, Karin J (2021). HIV-1 integration sites in CD4+ T cells during primary, chronic, and late presentation of HIV-1 infection. Journal of Clinical Investigation Insight, 6(9):e143940.

de Vries, Jutte J C; Brown, Julianne R; Couto, Natacha; Beer, Martin; Le Mercier, Philippe; Sidorov, Igor; Papa, Anna; Fischer, Nicole; Oude Munnink, Bas B; Rodriquez, Christophe; Zaheri, Maryam; Sayiner, Arzu; Hönemann, Mario; Pérez-Cataluña, Alba; Carbo, Ellen C; Bachofen, Claudia; Kubacki, Jakub; et al (2021). Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting. Journal of Clinical Virology, 138:104812.

Hunziker, Annika. Phosphorylation Events in Early Steps of Human and Avian Influenza A Virus Infection. 2021, University of Zurich, Faculty of Medicine.

Reichmuth, M L; Chaudron, S E; Bachmann, N; Nguyen, H; Böni, J; Metzner, K J; Perreau, M; Klimkait, T; Yerly, S; Hirsch, H H; Hauser, C; Ramette, A; Vernazza, P; Cavassini, M; Bernasconi, E; Günthard, H F; Kusejko, K; Kouyos, R D; Swiss HIV Cohort Study (2021). Using longitudinally sampled viral nucleotide sequences to characterize the drivers of HIV-1 transmission. HIV Medicine, 22(5):346-359.

Glass, Tracy R; Günthard, Huldrych; Calmy, Alexandra; Bernasconi, Enos; Scherrer, Alexandra U; Battegay, Manuel; Steffen, Ana; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Cavassini, Matthias; Furrer, Hansjakob; Swiss HIV Cohort Study (2021). The role of HIV asymptomatic status when starting ART on adherence and treatment outcomes and implications for test and treat: the Swiss HIV Cohort Study. Clinical Infectious Diseases, 72(8):1413-1421.

Caillat, Christophe; Guilligay, Delphine; Torralba, Johana; Friedrich, Nikolas; Nieva, Jose L; Trkola, Alexandra; Chipot, Christophe J; Dehez, François L; Weissenhorn, Winfried (2021). Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies. eLife, 10:e65005.

Muller, Christina K S; Spagnuolo, Julian; Audigé, Annette; Chancellor, Andrew; Russenberger, Doris; Scherrer, Alexandra U; Hoffmann, Matthias; Kouyos, Roger; Battegay, Manuel; De Libero, Gennaro; Speck, Roberto F; Swiss HIV Cohort Study (2021). Immunophenotypic characterization of TCR γδ T cells and MAIT cells in HIV-infected individuals developing Hodgkin's lymphoma. Infectious Agents and Cancer, 16:24.

Künzler-Heule, Patrizia; Fierz, Katharina; Schmidt, Axel Jeremias; Rasi, Manuela; Bogdanovic, Jasmina; Kocher, Agnes; Engberg, Sandra; Battegay, Manuel; Nöstlinger, Christiana; Lehner, Andreas; Kouyos, Roger; Schmid, Patrick; Braun, Dominique Laurent; Fehr, Jan; Nicca, Dunja (2021). Response to a sexual risk reduction intervention provided in combination with hepatitis C treatment by HIV/HCV co-infected men who have sex with men: a reflexive thematic analysis. BMC Infectious Diseases, 21:319.

Goncalves Cabecinhas, Ana Rita; Roloff, Tim; Stange, Madlen; Bertelli, Claire; Huber, Michael; Ramette, Alban; Chen, Chaoran; Nadeau, Sarah; Gerth, Yannick; Yerly, Sabine; Opota, Onya; Pillonel, Trestan; Schuster, Tobias; Metzger, Cesar M J A; Sieber, Jonas; Bel, Michael; Wohlwend, Nadia; Baumann, Christian; Koch, Michel C; Bittel, Pascal; Leuzinger, Karoline; Brunner, Myrta; Suter-Riniker, Franziska; Berlinger, Livia; Søgaard, Kirstine K; Beckmann, Christiane; Noppen, Christoph; Redondo, Maurice; Steffen, Ingrid; Seth-Smith, Helena M B; et al (2021). SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms, 9(4):677.

Werner, Jana; Reichen, Ina; Huber, Michael; Abela, Irene A; Weller, Michael; Jelcic, Ilijas (2021). Subacute cerebellar ataxia following respiratory symptoms of COVID-19: a case report. BMC Infectious Diseases, 21:298.

Lork, Marie; Lieber, Gauthier; Hale, Benjamin G (2021). Proteomic Approaches to Dissect Host SUMOylation during Innate Antiviral Immune Responses. Viruses, 13(3):528.

Huber, Michael; Schreiber, Peter Werner; Scheier, Thomas; Audigé, Annette; Buonomano, Roberto; Rudiger, Alain; Braun, Dominique L; Eich, Gerhard; Keller, Dagmar I; Hasse, Barbara; Böni, Jürg; Berger, Christoph; Günthard, Huldrych F; Manrique, Amapola; Trkola, Alexandra (2021). High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children. Microorganisms, 9(3):642.

Ulyte, Agne; Radtke, Thomas; Abela, Irene A; Haile, Sarah R; Berger, Christoph; Huber, Michael; Schanz, Merle; Schwarzmueller, Magdalena; Trkola, Alexandra; Fehr, Jan; Puhan, Milo A; Kriemler, Susi (2021). Clustering and longitudinal change in SARS-CoV-2 seroprevalence in school children in the canton of Zurich, Switzerland: prospective cohort study of 55 schools. BMJ : British medical journal, 372:n616.

Scheier, Thomas; Shah, Cyril; Huber, Michael; Sax, Hugo; Hasse, Barbara; Günthard, Huldrych F; Trkola, Alexandra; Schreiber, Peter W (2021). Do we cause false positives? An experimental series on droplet or airborne SARS-CoV-2 contamination of sampling tubes during swab collection in a test center. Antimicrobial Resistance and Infection Control, 10:51.

Rindler, Audrey E; Kuster, Herbert; Neumann, Kathrin; Leemann, Christine; Braun, Dominique L; Metzner, Karin J; Günthard, Huldrych F (2021). A Novel High Throughput, Parallel Infection Assay for Determining the Replication Capacities of 346 Primary HIV-1 Isolates of the Zurich Primary HIV-1 Infection Study in Primary Cells. Viruses, 13(3):404.

Kuster, Stefan P; Böni, Jürg; Kouyos, Roger D; Huber, Michael; Schmutz, Stefan; Shah, Cyril; Bischoff-Ferrari, Heike A; Distler, Oliver; Battegay, Edouard; Giovanoli, Pietro; Guckenberger, Matthias; Kohler, Malcolm; Müller, Rouven; Petry, Heidi; Ruschitzka, Frank; McGeer, Allison; Coleman, Brenda L; Sax, Hugo; Weber, Rainer; Trkola, Alexandra (2021). Absenteeism and presenteeism in healthcare workers due to respiratory illness. Infection Control and Hospital Epidemiology, 42(3):268-273.

Pohl, Marie O; Busnadiego, Idoia; Kufner, Verena; Glas, Irina; Karakus, Umut; Schmutz, Stefan; Zaheri, Maryam; Abela, Irene; Trkola, Alexandra; Huber, Michael; Stertz, Silke; Hale, Benjamin G (2021). SARS-CoV-2 variants reveal features critical for replication in primary human cells. PLoS Biology, 19(3):e3001006.

Hovaguimian, Frédérique; Günthard, Huldrych F; Hauser, Christoph; Conen, Anna; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Seneghini, Marco; Marzel, Alex; Heinrich, Henriette; Scherrer, Alexandra; Riou, Julien; Spoerri, Adrian; Schmidlin, Kurt; Balakrishna, Suraj; Braun, Dominique L; Rampini, Silvana K; Fehr, Jan S; Kouyos, Roger D; Swiss HIV Cohort Study (2021). Data linkage to evaluate the long-term risk of HIV infection in individuals seeking post-exposure prophylaxis. Nature Communications, 12:1219.

Brown, Jennifer A; Mbunkah, Herbert A; Lejone, Thabo I; Ringera, Isaac; Cheleboi, Molisana; Klimkait, Thomas; Metzner, Karin J; Günthard, Huldrych F; Labhardt, Niklaus D; Kouyos, Roger D; Tschumi, Nadine (2021). Emergence of Human Immunodeficiency Virus-1 Drug Resistance During the 3-Month World Health Organization-Recommended Enhanced Adherence Counseling Period in the CART-1 Cohort Study. Open Forum Infectious Diseases, 8(5):ofab046.

Tepekule, Burcu; Hauser, Anthony; Kachalov, Viacheslav N; Andresen, Sara; Scheier, Thomas; Schreiber, Peter W; Günthard, Huldrych F; Kouyos, Roger D (2021). Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19. PLoS Computational Biology, 17:e1008609.

Kachalov, Viacheslav N; Nguyen, Huyen; Balakrishna, Suraj; Salazar-Vizcaya, Luisa; Sommerstein, Rami; Kuster, Stefan P; Hauser, Anthony; Abel Zur Wiesch, Pia; Klein, Eili; Kouyos, Roger D (2021). Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level. PLoS Computational Biology, 17:e1008446.

Börold, Jacob. A Genome-Wide CRISPR/Cas Screen to Uncover Host Factors Regulating the Interferon Response and Virus Infection. 2021, University of Zurich, Faculty of Medicine.

Castillo-Mancilla, Jose R; Cavassini, Matthias; Schneider, Marie Paule; Furrer, Hansjakob; Calmy, Alexandra; Battegay, Manuel; Scanferla, Giulia; Bernasconi, Enos; Günthard, Huldrych F; Glass, Tracy R; Swiss HIV Cohort Study (2021). Association of Incomplete Adherence to Antiretroviral Therapy With Cardiovascular Events and Mortality in Virologically Suppressed Persons With HIV: The Swiss HIV Cohort Study. Open Forum Infectious Diseases, 8(2):ofab032.

Posada-Céspedes, Susana; Seifert, David; Topolsky, Ivan; Jablonski, Kim Philipp; Metzner, Karin J; Beerenwinkel, Niko (2021). V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. Bioinformatics, 37(12):1673-1680.

Benet, Susana; Gálvez, Cristina; Drobniewski, Francis; et al; Günthard, Huldrych F (2021). Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles. Journal of Extracellular Vesicles, 10(3):e12046.

Surial, Bernard; Bertholet, Nicolas; Daeppen, Jean-Bernard; Darling, Katharine E A; Calmy, Alexandra; Günthard, Huldrych F; Stöckle, Marcel; Bernasconi, Enos; Schmid, Patrick; Rauch, Andri; Furrer, Hansjakob; Wandeler, Gilles; Swiss HIV Cohort Study (2021). The Impact of Binge Drinking on Mortality and Liver Disease in the Swiss HIV Cohort Study. Journal of Clinical Medicine, 10(2):295.

Hofmaenner, Daniel Andrea; Wendel Garcia, Pedro David; Duvnjak, Branko; Chakrakodi, Bhavya; Maier, Julian David; Huber, Michael; Huder, Jon; Wolfensberger, Aline; Schreiber, Peter Werner; Schuepbach, Reto A; Zinkernagel, Annelies Sophie; Buehler, Philipp Karl; Brugger, Silvio Daniel (2021). Bacterial but no SARS-CoV-2 contamination after terminal disinfection of tertiary care intensive care units treating COVID-19 patients. Antimicrobial Resistance and Infection Control, 10:11.

Zdimerova, Hana; Murer, Anita; Engelmann, Christine; Raykova, Ana; Deng, Yun; Gujer, Cornelia; Rühl, Julia; McHugh, Donal; Caduff, Nicole; Naghavian, Reza; Pezzino, Gaetana; Capaul, Riccarda; Zbinden, Andrea; Ferlazzo, Guido; Lünemann, Jan D; Martin, Roland; Chatterjee, Bithi; Münz, Christian (2021). Attenuated immune control of Epstein-Barr virus in humanized mice is associated with the multiple sclerosis risk factor HLA-DR15. European Journal of Immunology, 51(1):64-75.

Romito, Marianna; Juillerat, Alexandre; Kok, Yik Lim; Hildenbeutel, Markus; Rhiel, Manuel; Andrieux, Geoffroy; Geiger, Johannes; Rudolph, Carsten; Mussolino, Claudio; Duclert, Aymeric; Metzner, Karin J; Duchateau, Philippe; Cathomen, Toni; Cornu, Tatjana I (2021). Preclinical Evaluation of a Novel TALEN Targeting CCR5 Confirms Efficacy and Safety in Conferring Resistance to HIV-1 Infection. Biotechnology Journal, 16(1):2000023.

Wenk, Benjamin M; Mbunkah, Herbert A; Nsanwe, Ndi N; Mbu, Eyongetah T; Besong, Lydia M; Sama, Bella A; Orock, Emmanuel; Leemann, Christine; Metzner, Karin J (2021). Prevalence of integrase strand transfer inhibitor resistance mutations in antiretroviral-naive HIV-1-infected individuals in Cameroon. Journal of Antimicrobial Chemotherapy, 76(1):124-129.

López-Labrador, F Xavier; Brown, Julianne R; Fischer, Nicole; Harvala, Heli; Van Boheemen, Sander; Cinek, Ondrej; Sayiner, Arzu; Madsen, Tina Vasehus; Auvinen, Eeva; Kufner, Verena; Huber, Michael; Rodriguez, Christophe; Jonges, Marcel; Hönemann, Mario; Susi, Petri; Sousa, Hugo; Klapper, Paul E; Pérez-Cataluňa, Alba; Hernandez, Marta; Molenkamp, Richard; van der Hoek, Lia; Schuurman, Rob; Couto, Natacha; Leuzinger, Karoline; Simmonds, Peter; Beer, Martin; Höper, Dirk; Kamminga, Sergio; Feltkamp, Mariet C W; Rodríguez-Díaz, Jesús; et al (2021). Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. Journal of Clinical Virology, 134:104691.

Glögl, Matthias. DARPins Targeting the HIV-1 Envelope: From Novel Tools to Novel Therapeutics. 2021, University of Zurich, Faculty of Medicine.

Günther, Sira Carolin. Determining the Proviral Function of the Host Cell Protease Cathepsin W in Influenza A Virus Entry. 2021, University of Zurich, Faculty of Medicine.

Fernbach, Sonja. Interferon-Mediated Regulation of RNA Virus Infection. 2021, University of Zurich, Faculty of Medicine.

Ryser-Degiorgis, Marie-Pierre; Marti, Iris; Pisano, Simone R R; Pewsner, Mirjam; Wehrle, Martin; Breitenmoser-Würsten, Christine; Origgi, Francesco C; Kübber-Heiss, Anna; Knauer, Felix; Posautz, Annika; Eberspächer-Schweda, Matthias; Huder, Jon B; Böni, Jürg; Kubacki, Jakub; Bachofen, Claudia; Riond, Barbara; Hofmann-Lehmann, Regina; Meli, Marina L (2021). Management of Suspected Cases of Feline Immunodeficiency Virus Infection in Eurasian Lynx (Lynx lynx) During an International Translocation Program. Frontiers in Veterinary Science, 8:730874.

Müller, Dominik A. MxA Inhibits Semliki Forest Virus at the Level of RNA Synthesis by Targeting its Replicase Complex. 2021, University of Zurich, Faculty of Medicine.

2020

Weissberg, Dana; Böni, Jürg; Rampini, Silvana K; Kufner, Verena; Zaheri, Maryam; Schreiber, Peter W; Abela, Irene A; Huber, Michael; Sax, Hugo; Wolfensberger, Aline (2020). Does respiratory co-infection facilitate dispersal of SARS-CoV-2? investigation of a super-spreading event in an open-space office. Antimicrobial Resistance and Infection Control, 9:191.

Keller, Emanuela; Brandi, Giovanna; Winklhofer, Sebastian; Imbach, Lukas L; Kirschenbaum, Daniel; Frontzek, Karl; Steiger, Peter; Dietler, Sabeth; Haeberlin, Marcellina; Willms, Jan; Porta, Francesca; Waeckerlin, Adrian; Huber, Michael; Abela, Irene A; Lutterotti, Andreas; Stippich, Christoph; Globas, Christoph; Varga, Zsuzsanna; Jelčić, Ilijas (2020). Large and small cerebral vessel involvement in severe COVID-19: detailed clinical workup of a case series. Stroke, 51(12):3719-3722.

Ulyte, Agne; Radtke, Thomas; Abela, Irène A; Haile, Sarah R; Braun, Julia; Jung, Ruedi; Berger, Christoph; Trkola, Alexandra; Fehr, Jan; Puhan, Milo A; Kriemler, Susi (2020). Seroprevalence and immunity of SARS-CoV-2 infection in children and adolescents in schools in Switzerland: design for a longitudinal, school-based prospective cohort study. International Journal of Public Health, 65(9):1549-1557.

Schorer, Michelle; Rakebrandt, Nikolas; Lambert, Katharina; Hunziker, Annika; Pallmer, Katharina; Oxenius, Annette; Kipar, Anja; Stertz, Silke; Joller, Nicole (2020). TIGIT limits immune pathology during viral infections. Nature Communications, 11(1):1288.

Kusejko, Katharina; Günthard, Huldrych F; Olson, Gregory S; Zens, Kyra; Darling, Katharine; Khanna, Nina; Furrer, Hansjakob; Vetter, Pauline; Bernasconi, Enos; Vernazza, Pietro; Hoffmann, Matthias; Kouyos, Roger D; Nemeth, Johannes (2020). Diagnosis of latent tuberculosis infection is associated with reduced HIV viral load and lower risk for opportunistic infections in people living with HIV. PLoS Biology, 18(12):e3000963.

Hauser, Anthony; Kusejko, Katharina; Johnson, Leigh F; Günthard, Huldrych F; Riou, Julien; Wandeler, Gilles; Egger, Matthias; Kouyos, Roger D (2020). Impact of scaling up dolutegravir on antiretroviral resistance in South Africa: A modeling study. PLoS Medicine, 17(12):e1003397.

Bons, Eva; Leemann, Christine; Metzner, Karin J; Regoes, Roland R (2020). Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history. PLoS Biology, 18(12):e3001010.

Braun, Dominique L; Scheier, Thomas; Ledermann, Ulrich; Flepp, Markus; Metzner, Karin J; Böni, Jürg; Günthard, Huldrych F (2020). Emergence of resistance to integrase strand transfer inhibitors during Dolutegravir containing triple-therapy in a treatment-experienced patient with pre-existing M184V/I mutation. Viruses, 12(11):1330.

Sculier, Delphine; Wandeler, Gilles; Yerly, Sabine; Marinosci, Annalisa; Stoeckle, Marcel; Bernasconi, Enos; Braun, Dominique L; Vernazza, Pietro; Cavassini, Matthias; Buzzi, Marta; Metzner, Karin J; Decosterd, Laurent A; Günthard, Huldrych F; Schmid, Patrick; Limacher, Andreas; Egger, Matthias; Calmy, Alexandra (2020). Efficacy and safety of dolutegravir plus emtricitabine versus standard ART for the maintenance of HIV-1 suppression: 48-week results of the factorial, randomized, non-inferiority SIMPL'HIV trial. PLoS Medicine, 17(11):e1003421.

Wan, Chenjie; Bachmann, Nadine; Mitov, Venelin; Blanquart, François; Céspedes, Susana Posada; Turk, Teja; Neumann, Kathrin; Beerenwinkel, Niko; Bogojeska, Jasmina; Fellay, Jacques; Roth, Volker; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Battegay, Manuel; Walti, Laura; Calmy, Alexandra; Vernazza, Pietro; Bernasconi, Enos; Cavassini, Matthias; Metzner, Karin J; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2020). Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART. Nature Communications, 11(1):5542.

Chimukangara, Benjamin; Giandhari, Jennifer; Lessells, Richard; Yende-Zuma, Nonhlanhla; Sartorius, Benn; Samuel, Reshmi; Khanyile, Khulekani S; Stray-Pedersen, Babill; Moodley, Pravi; Metzner, Karin J; Padayatchi, Nesri; Naidoo, Kogieleum; De Oliveira, Tulio (2020). Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals. Journal of Antimicrobial Chemotherapy, 75(11):3319-3326.

Carlisle, Louisa A; Turk, Teja; Metzner, Karin J; Mbunkah, Herbert A; Shah, Cyril; Böni, Jürg; Huber, Michael; Braun, Dominique L; Fehr, Jan; Salazar-Vizcaya, Luisa; Rauch, Andri; Yerly, Sabine; Nguyen, Aude; Cavassini, Matthias; Stoeckle, Marcel; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D (2020). HCV genetic diversity can be used to infer infection recency and time since Iifection. Viruses, 12(11):1241.

Saag, Michael S; Gandhi, Rajesh T; Hoy, Jennifer F; Landovitz, Raphael J; Thompson, Melanie A; Sax, Paul E; Smith, Davey M; Benson, Constance A; Buchbinder, Susan P; Del Rio, Carlos; Eron, Joseph J; Fätkenheuer, Gerd; Günthard, Huldrych F; Molina, Jean-Michel; Jacobsen, Donna M; Volberding, Paul A (2020). Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2020 Recommendations of the International Antiviral Society-USA Panel. JAMA : the Journal of the American Medical Association, 324(16):1651-1669.

Steiner, Fiona; Pavlovic, Jovan (2020). Subcellular Localization of MxB Determines Its Antiviral Potential against Influenza A Virus. Journal of Virology, 94(22):e00125-20.

Meyer Sauteur, Patrick M; Krautter, Selina; Ambroggio, Lilliam; Seiler, Michelle; Paioni, Paolo; Relly, Christa; Capaul, Riccarda; Kellenberger, Christian J; Haas, Thorsten; Gysin, Claudine; Bachmann, Lucas M; van Rossum, Annemarie M C; Berger, Christoph (2020). Improved diagnostics help to identify clinical features and biomarkers that predict Mycoplasma pneumoniae community-acquired pneumonia in children. Clinical Infectious Diseases, 71(7):1645-1654.

Surial, Bernard; Béguelin, Charles; Chave, Jean-Philippe; Stöckle, Marcel; Boillat-Blanco, Noémie; Doco-Lecompte, Thanh; Bernasconi, Enos; Fehr, Jan; Günthard, Huldrych F; Schmid, Patrick; Walti, Laura N; Furrer, Hansjakob; Rauch, Andri; Wandeler, Gilles; Swiss HIV Cohort Study (2020). Brief Report: Switching From TDF to TAF in HIV/HBV-Coinfected Individuals With Renal Dysfunction-A Prospective Cohort Study. Journal of Acquired Immune Deficiency Syndromes, 85(2):227-232.

Bär, Julian; Boumasmoud, Mathilde; Kouyos, Roger D; Zinkernagel, Annelies S; Vulin, Clément (2020). Efficient microbial colony growth dynamics quantification with ColTapp, an automated image analysis application. Scientific Reports, 10:16084.

Osuch, Sylwia; Laskus, Tomasz; Berak, Hanna; Perlejewski, Karol; Metzner, Karin J; Paciorek, Marcin; Radkowski, Marek; Caraballo Cortés, Kamila (2020). Decrease of T-cells exhaustion markers programmed cell death-1 and T-cell immunoglobulin and mucin domain-containing protein 3 and plasma IL-10 levels after successful treatment of chronic hepatitis C. Scientific Reports, 10(1):16060.

Busnadiego, Idoia; Fernbach, Sonja; Pohl, Marie O; Karakus, Umut; Huber, Michael; Trkola, Alexandra; Stertz, Silke; Hale, Benjamin G (2020). Antiviral Activity of Type I, II, and III Interferons Counterbalances ACE2 Inducibility and Restricts SARS-CoV-2. mBio, 11(5):e01928-20.

Spieler, Eva E; Moritz, Eva; Stertz, Silke; Hale, Benjamin G (2020). Application of a biologically contained reporter system to study gain-of-function H5N1 influenza a viruses with pandemic potential. mSphere, 5(4):e00423-20.

Thorball, Christian W; Borghesi, Alessandro; Bachmann, Nadine; Von Siebenthal, Chantal; Vongrad, Valentina; Turk, Teja; Neumann, Kathrin; Beerenwinkel, Niko; Bogojeska, Jasmina; Roth, Volker; Kok, Yik Lim; Parbhoo, Sonali; Wieser, Mario; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Battegay, Manuel; Rauch, Andri; Schmid, Patrick; Bernasconi, Enos; Cavassini, Matthias; Kouyos, Roger D; Günthard, Huldrych F; Metzner, Karin J; Fellay, Jacques; Swiss HIV Cohort Study (2020). Host genomics of the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment. Journal of Acquired Immune Deficiency Syndromes, 85(4):517-524.

Combes, Jean-Damien; Clifford, Gary M; Günthard, Huldrych F; Hauser, Christoph; Darling, Katharine E A; Valladares, Pablo; Battegay, Manuel; Waldeck, Frederike; Bernasconi, Enos; Bertisch, Barbara; Hirsch, Hans H; Brenner, Nicole; Waterboer, Tim; Scherrer, Alexandra U; Swiss HIV Cohort Study (2020). Antibodies against HPV16E6 oncoprotein in the Swiss HIV cohort study: Kinetics and anal cancer risk prediction. International Journal of Cancer, 147(3):757-765.

McHugh, Donal; Myburgh, Renier; Caduff, Nicole; Spohn, Michael; Kok, Yik Lim; Keller, Christian W; Murer, Anita; Chatterjee, Bithi; Rühl, Julia; Engelmann, Christine; Chijioke, Obinna; Quast, Isaak; Shilaih, Mohaned; Strouvelle, Victoria P; Neumann, Kathrin; Menter, Thomas; Dirnhofer, Stephan; Lam, Janice K P; Hui, Kwai F; Bredl, Simon; Schlaepfer, Erika; Sorce, Silvia; Zbinden, Andrea; Capaul, Riccarda; Lünemann, Jan D; Aguzzi, Adriano; Chiang, Alan K S; Kempf, Werner; Trkola, Alexandra; Metzner, Karin J; et al (2020). EBV renders B cells susceptible to HIV-1 in humanized mice. Life Science Alliance, 3(8):e202000640.

Kusejko, Katharina; Salazar-Vizcaya, Luisa; Braun, Dominique L; Tarr, Philip E; Bernasconi, Enos; Doco-Lecompte, Thanh; Cavassini, Matthias; Schmid, Patrick; Du Pasquier, Renaud; Hauser, Christoph; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2020). Self-reported neurocognitive impairment in people living with HIV: Characterizing clusters of patients with similar changes in self-reported neurocognitive impairment 2013-2017 in the Swiss HIV Cohort Study. Clinical Infectious Diseases, 71(3):637-644.

Osuch, Sylwia; Metzner, Karin J; Caraballo Cortés, Kamila (2020). Reversal of T cell exhaustion in chronic HCV infection. Viruses, 12(8):799.

Surial, Bernard; Ledergerber, Bruno; Calmy, Alexandra; Cavassini, Matthias; Günthard, Huldrych F; Kovari, Helen; Stöckle, Marcel; Bernasconi, Enos; Schmid, Patrick; Fux, Christoph A; Furrer, Hansjakob; Rauch, Andri; Wandeler, Gilles; Swiss HIV Cohort Study (2020). Changes in renal function after switching from TDF to TAF in HIV-infected individuals: a prospective cohort study. Journal of Infectious Diseases, 222(4):637-645.

Courlet, Perrine; Livio, Françoise; Alves Saldanha, Susana; Scherrer, Alexandra; Battegay, Manuel; Cavassini, Matthias; Stoeckle, Marcel; Decosterd, Laurent Arthur; Marzolini, Catia; Swiss HIV Cohort Study (2020). Real-life management of drug-drug interactions between antiretrovirals and statins. Journal of Antimicrobial Chemotherapy, 75(7):1972-1980.

Hassan-Harrirou, Hussein; Zhang, Ce; Lemmin, Thomas (2020). RosENet: Improving binding affinity prediction by leveraging molecular mechanics energies with an ensemble of 3D convolutional neural networks. Journal of Chemical Information and Modeling, 60(6):2791-2802.

Courlet, Perrine; Alves Saldanha, Susana; Cavassini, Matthias; Marzolini, Catia; Choong, Eva; Csajka, Chantal; Günthard, Huldrych F; André, Pascal; Buclin, Thierry; Desfontaine, Vincent; Decosterd, Laurent Arthur (2020). Development and validation of a multiplex UHPLC-MS/MS assay with stable isotopic internal standards for the monitoring of the plasma concentrations of the antiretroviral drugs bictegravir, cabotegravir, doravirine, and rilpivirine in people living with HIV. Journal of Mass Spectrometry, 55(6):e4506.

Roth, Jan A; Ballouz, Tala; Kouyos, Roger D; Battegay, Manuel (2020). Early off-label treatment during pandemics? A dilemma. Swiss Medical Weekly, 150:w20281.

Mbunkah, Herbert A; Bertagnolio, Silvia; Hamers, Raph L; Hunt, Gillian; Inzaule, Seth; Rinke de Wit, Tobias F; Paredes, Roger; Parkin, Neil T; Jordan, Michael R; Metzner, Karin J (2020). Low-abundance drug-resistant HIV-1 variants in antiretroviral drug-naïve individuals: A systematic review of detection methods, prevalence, and clinical impact. Journal of Infectious Diseases, 221(10):1584-1597.

Spieler, Eva. Characterization of Bioluminescent Reporter Influenza Viruses and Implementationto Identify Novel Restriction Factors. 2020, University of Zurich, Institute of Medical Virology, Faculty of Medicine.

Hampel, B; Kusejko, K; Kouyos, R D; Böni, J; Flepp, M; Stöckle, M; Conen, A; Béguelin, C; Künzler-Heule, P; Nicca, D; Schmidt, A J; Nguyen, H; Delaloye, J; Rougemont, M; Bernasconi, E; Rauch, A; Günthard, H F; Braun, D L; Fehr, J; Swiss HIV Cohort Study (2020). Chemsex drugs on the rise: a longitudinal analysis of the Swiss HIV Cohort Study from 2007 to 2017. HIV Medicine, 21(4):228-239.

Kusejko, Katharina; Marzel, Alex; Nguyen, Huyen; Chaudron, Sandra E; Bachmann, Nadine; Weber, Rainer; Bruggmann, Philip; Roth, Jan A; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Bregenzer, Andrea; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Perreau, Matthieu; Walti, Laura N; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2020). Differences in social and mental well-being of long-term survivors among people who inject drugs and other participants in the Swiss HIV Cohort Study: 1980-2018. Antiviral Therapy, 25(1):43-54.

Kufner, Verena. Metagenomic Sequencing of Viral Pathogens in Clinical Samples for Improved Infectious Disease Diagnostics and Management. 2020, University of Zurich, Institute of Medical Virology, Faculty of Medicine.

Redli, Patrick M; Wanzenried, Adrian; Huder, Jon B; Berger, Christoph; Berlinger, Livia; Capaul, Riccarda; Böni, Jürg; Zbinden, Andrea (2020). Evaluation of the RIDA®GENE RT-PCR assays for detection of sapovirus, astrovirus, adenovirus, and rotavirus in stool samples of adults in Switzerland. Diagnostic Microbiology and Infectious Disease, 96(2):114924.

Barceló, Catalina; Guidi, Monia; Thorball, Christian W; Hammer, Christian; Chaouch, Aziz; Scherrer, Alexandra U; Hasse, Barbara; Cavassini, Matthias; Furrer, Hansjakob; Calmy, Alexandra; Haubitz, Sebastian; Bernasconi, Enos; Buclin, Thierry; Fellay, Jacques; Tarr, Philip E; Csajka, Chantal; Swiss HIV Cohort Study (2020). Impact of genetic and nongenetic factors on body mass index and waist-hip ratio change in HIV-infected individuals initiating antiretroviral therapy. Open Forum Infectious Diseases, 7(1):ofz464.

Günther, Sira Carolin; Maier, Julian David; Vetter, Janine; Podvalnyy, Nikita; Khanzhin, Nikolay; Hennet, Thierry; Stertz, Silke (2020). Antiviral potential of 3'-sialyllactose- and 6'-sialyllactose-conjugated dendritic polymers against human and avian influenza viruses. Scientific Reports, 10(1):768.

Salazar-Vizcaya, Luisa; Kusejko, Katharina; Schmidt, Axel J; Carrillo-Montoya, Germán; Nicca, Dunja; Wandeler, Gilles; Braun, Dominique L; Fehr, Jan; Darling, Katharine E A; Bernasconi, Enos; Schmid, Patrick; Günthard, Huldrych F; Kouyos, Roger D; Rauch, Andri (2020). Clusters of sexual behaviour in HIV-positive men who have sex with men reveal highly dissimilar time trends. Clinical Infectious Diseases, 70(3):416-424.

Roth, Jan A; Franzeck, Fabian C; Balakrishna, Suraj; Lautenschlager, Stephan; Thurnheer, Maria Christine; Trellu, Laurence Toutous; Cavassini, Matthias; Vernazza, Pietro; Bernasconi, Enos; Braun, Dominique; Kouyos, Roger D; Battegay, Manuel; Swiss HIV Cohort Study (2020). Repeated syphilis episodes in HIV-infected men who have sex with men: a multicenter prospective cohort study on risk factors and the potential role of syphilis immunity. Open Forum Infectious Diseases, 7(1):ofaa019.

Abela, Irene A; Scherrer, Alexandra U; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Perreau, Matthieu; Hirsch, Hans H; Furrer, Hansjakob; Calmy, Alexandra; Schmid, Patrick; Cavassini, Matthias; Bernasconi, Enos; Günthard, Huldrych F; Swiss HIV Cohort Study (2020). Emergence of drug resistance in the Swiss HIV Cohort Study under potent antiretroviral therapy is observed in socially disadvantaged patients. Clinical Infectious Diseases, 70(2):297-303.

Karakus, Umut; Pohl, Marie O; Stertz, Silke (2020). Breaking the convention: Sialoglycan variants, Co-receptors and Alternative Receptors for Influenza A Virus Entry. Journal of Virology, 94(4):e01357-19.

Keller, Emanuela; Brandi, Giovanna; Winklhofer, Sebastian; Imbach, Lukas L; Kirschenbaum, Daniel; Frontzek, Karl Joachim; Steiger, Peter; Dietler, Sabeth Aurelia; Haeberlin, Marcellina Isabelle; Willms, Jan Folkard; Porta, Francesca; Waeckerlin, Adrian; Abela, Irene Alma; Lutterotti, Andreas; Stippich, Christoph; Jelčić, Ilijas (2020). Central Nervous System Disorders in Severe SARS-CoV-2 Infection: detailed clinical work-up of eight cases. Research Square 32488, University of Zurich.

Buetti, Niccolò; Trimboli, Pierpaolo; Mazzuchelli, Timothy; Lo Priore, Elia; Balmelli, Carlo; Trkola, Alexandra; Conti, Marco; Martinetti, Gladys; Elzi, Luigia; Ceschi, Alessandro; Consonni, Vera; Ogna, Adam; Forni-Ogna, Valentina; Bernasconi, Enos (2020). Diabetes mellitus is a risk factor for prolonged SARS-CoV-2 viral shedding in lower respiratory tract samples of critically ill patients. Endocrine, 70(3):454-460.

Inderbitzin, Anne; Kok, Yik Lim; Jörimann, Lisa; Kelley, Audrey; Neumann, Kathrin; Heinzer, Daniel; Cathomen, Toni; Metzner, Karin J (2020). HIV-1 promoter is gradually silenced when integrated into BACH2 in Jurkat T-cells. PeerJ, 8:e10321.

Neesgaard, Bastian; Mocroft, Amanda; Zangerle, Robert; Wit, Ferdinand; Lampe, Fiona; Günthard, Huldrych F; et al (2020). Virologic and immunologic outcomes of treatment with integrase inhibitors in a real-world setting: The RESPOND cohort consortium. PLoS ONE, 15(12):e0243625.

2019

Schwarz, Hila; Böni, Jürg; Kouyos, Roger D; Turk, Teja; Battegay, Edouard; Kohler, Malcolm; Müller, Rouven; Petry, Heidi; Sax, Hugo; Weber, Rainer; McGeer, Allison; Trkola, Alexandra; Kuster, Stefan P (2019). The TransFLUas influenza transmission study in acute healthcare - recruitment rates and protocol adherence in healthcare workers and inpatients. BMC Infectious Diseases, 19(1):446.

Olearo, Flaminia; Nguyen, Huyen; Bonnet, Fabrice; Yerly, Sabine; Wandeler, Gilles; Stoeckle, Marcel; Cavassini, Matthias; Scherrer, Alexandra; Costagliola, Dominique; Schmid, Patrick; Günthard, Huldrych F; Bernasconi, Enos; Boeni, Jürg; D'arminio Monforte, Antonella; Zazzi, Maurizio; Rossetti, Barbara; Neau, Didier; Bellecave, Pantxika; Rijnders, Bart; Reiss, Peter; Wit, Ferdinand; Kouyos, Roger; Calmy, Alexandra (2019). Corrigendum to: Impact of the M184V/I Mutation on the Efficacy of Abacavir/Lamivudine/Dolutegravir Therapy in HIV Treatment-Experienced Patients. Open Forum Infectious Diseases, 6(12):ofz500.

Tepekule, Burcu; Abel Zur Wiesch, Pia; Kouyos, Roger D; Bonhoeffer, Sebastian (2019). Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota. Proceedings of the National Academy of Sciences of the United States of America, 116(46):23106-23116.

Lodi, Sara; Günthard, Huldrych F; Gill, John; Phillips, Andrew N; Dunn, David; Vu, Quang; Siemieniuk, Reed; Garcia, Federico; Logan, Roger; Jose, Sophie; Bucher, Heiner C; Scherrer, Alexandra U; et al (2019). Effectiveness of Transmitted Drug Resistance Testing Before Initiation of Antiretroviral Therapy in HIV-Positive Individuals. Journal of Acquired Immune Deficiency Syndromes, 82(3):314-320.

Bertels, Frederic; Leemann, Christine; Metzner, Karin J; Regoes, Roland (2019). Parallel evolution of HIV-1 in a long-term experiment. Molecular Biology and Evolution, 36(11):2400-2414.

Lemmin, Thomas; Soto, Cinque (2019). Glycosylator: a Python framework for the rapid modeling of glycans. BMC Bioinformatics, 20(1):513.

Braun, Dominique L; Turk, Teja; Tschumi, Fabian; Grube, Christina; Hampel, Benjamin; Depmeier, Carsten; Schreiber, Peter W; Brugger, Silvio D; Greiner, Michael; Steffens, Daniela; de Torrenté-Bayard, Cornelia; Courlet, Perrine; Neumann, Kathrin; Kuster, Herbert; Flepp, Markus; Bertisch, Barbara; Decosterd, Laurent; Böni, Jürg; Metzner, Karin J; Kouyos, Roger D; Günthard, Huldrych F (2019). Non-inferiority of simplified dolutegravir monotherapy compared to continued combination antiretroviral therapy that was initiated during primary HIV infection: a randomized, controlled, multi-site, open-label, non-inferiority trial. Clinical Infectious Diseases, 69(9):1489-1497.

Günthard, Huldrych F; Kouyos, Roger (2019). Can Directionality of HIV Transmission be Predicted by Next-Generation Sequencing Data? Journal of Infectious Diseases, 220(9):1393-1395.

Schmidt, Nora. Novel Functions of Host TRIM28 in Restricting Influenza Virus Infections. 2019, University of Zurich, Faculty of Medicine.

Künzler-Heule, Patrizia; Engberg, Sandra; Battegay, Manuel; Schmidt, Axel J; Fierz, Katharina; Nguyen, Huyen; Kocher, Agnes; Nöstlinger, Christiana; Hampel, Benjamin; Stöckle, Marcel; Béguelin, Charles; Delaloye, Julie; Schmid, Patrick; Flepp, Markus; Rougement, Mathieu; Braun, Dominique Laurent; Fehr, Jan; Nicca, Dunja; Swiss HIV Cohort Study (2019). Screening HIV-positive men who have sex with men for hepatitis C re-infection risk: is a single question on condom-use enough? A sensitivity analysis. BMC Infectious Diseases, 19(1):821.

Janiak, Maciej; Perlejewski, Karol; Grabarczyk, Piotr; Kubicka-Russel, Dorota; Zagordi, Osvaldo; Berak, Hanna; Osuch, Sylwia; Pawełczyk, Agnieszka; Bukowska-Ośko, Iwona; Płoski, Rafał; Laskus, Tomasz; Caraballo Cortés, Kamila (2019). Hepatitis C virus (HCV) genotype 1b displays higher genetic variability of hypervariable region 1 (HVR1) than genotype 3. Scientific Reports, 9(1):12846.

Liechti, Thomas; Kadelka, Claus; Braun, Dominique L; Kuster, Herbert; Böni, Jürg; Robbiani, Melissa; Günthard, Huldrych F; Trkola, Alexandra (2019). Widespread B cell perturbations in HIV-1 infection afflict naive and marginal zone B cells. Journal of Experimental Medicine, 216(9):2071-2090.

Wójtowicz, Agnieszka; Bibert, Stéphanie; Taffé, Patrick; Bernasconi, Enos; Furrer, Hansjakob; Günthard, Huldrych F; Hoffmann, Matthias; Osthoff, Michael; Cavassini, Matthias; Bochud, Pierre-Yves; Swiss HIV Cohort Study (2019). IL-4 polymorphism influences susceptibility to Pneumocystis jirovecii pneumonia in HIV-positive patients. AIDS, 33(11):1719-1727.

Barcelo, Catalina; Aouri, Manel; Courlet, Perrine; Guidi, Monia; Braun, Dominique L; Günthard, Huldrych F; Piso, Rein J; Cavassini, Matthias; Buclin, Thierry; Decosterd, Laurent A; Csajka, Chantal; Swiss HIV Cohort Study (2019). Population pharmacokinetics of dolutegravir: influence of drug-drug interactions in a real-life setting. Journal of Antimicrobial Chemotherapy, 74(9):2690-2697.

Wensing, Annemarie M; Calvez, Vincent; Ceccherini-Silberstein, Francesca; Charpentier, Charlotte; Günthard, Huldrych F; Paredes, Roger; Shafer, Robert W; Richman, Douglas D (2019). 2019 update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine, 27(3):111-121.

Schreiber, Peter W; Kufner, Verena; Hübel, Kerstin; Schmutz, Stefan; Zagordi, Osvaldo; Kaur, Amandeep; Bayard, Cornelia; Greiner, Michael; Zbinden, Andrea; Capaul, Riccarda; Böni, Jürg; Hirsch, Hans H; Mueller, Thomas F; Mueller, Nicolas J; Trkola, Alexandra; Huber, Michael (2019). Metagenomic virome sequencing in living donor-recipient kidney transplant pairs revealed JC Polyomavirus transmission. Clinical Infectious Diseases, 69(6):987-994.

Kufner, Verena; Plate, Andreas; Schmutz, Stefan; Braun, Dominique L; Günthard, Huldrych F; Capaul, Riccarda; Zbinden, Andrea; Mueller, Nicolas J; Trkola, Alexandra; Huber, Michael (2019). Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases. Genes, 10(9):pii: E661.

Junier, Thomas; Huber, Michael; Schmutz, Stefan; Kufner, Verena; Zagordi, Osvaldo; Neuenschwander, Stefan; Ramette, Alban; Kubacki, Jakub; Bachofen, Claudia; Qi, Weihong; Laubscher, Florian; Cordey, Samuel; Kaiser, Laurent; Beuret, Christian; Barbié, Valérie; Fellay, Jacques; Lebrand, Aitana (2019). Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide ring trial. Genes, 10(9):E655.

Schmidt, Nora; Domingues, Patricia; Golebiowski, Filip; Patzina, Corinna; Tatham, Michael H; Hay, Ronald T; Hale, Benjamin G (2019). An influenza virus-triggered SUMO switch orchestrates co-opted endogenous retroviruses to stimulate host antiviral immunity. Proceedings of the National Academy of Sciences of the United States of America, 116(35):17399-17408.

Subbaraman, Harini. Determinants of HIV-1 Broadly Neutralizing Antibody Induction and Antigenic Features of the HIV-1 Envelope Glycoprotein. 2019, University of Zurich, Faculty of Medicine.

Ruffieux, Yann; Lemsalu, Liis; Aebi-Popp, Karoline; Calmy, Alexandra; Cavassini, Matthias; Fux, Christoph A; Günthard, Huldrych F; Marzolini, Catia; Scherrer, Alexandra; Vernazza, Pietro; Keiser, Olivia; Egger, Matthias; Swiss HIV Cohort Study; Swiss National Cohort Study Group (2019). Mortality from suicide among people living with HIV and the general Swiss population: 1988-2017. Journal of the International Aids Society, 22(8):e25339.

Nguyen, Huyen; Thorball, Christian W; Fellay, Jacques; Böni, Jürg; Yerly, Sabine; Perreau, Matthieu; Klimkait, Thomas; Kusejko, Katharina; Bachmann, Nadine; Chaudron, Sandra E; Paioni, Paolo; Thurnheer, Maria C; Battegay, Manuel; Cavassini, Matthias; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger; Swiss HIV Cohort Study (2019). HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected. Journal of Acquired Immune Deficiency Syndromes, 81(5):508-515.

Domingues, Patricia; Eletto, Davide; Magnus, Carsten; Turkington, Hannah L; Schmutz, Stefan; Zagordi, Osvaldo; Lenk, Matthias; Beer, Martin; Stertz, Silke; Hale, Benjamin G (2019). Profiling host ANP32A splicing landscapes to predict influenza A virus polymerase adaptation. Nature Communications, 10(1):3396.

Bachmann, Nadine; von Siebenthal, Chantal; Vongrad, Valentina; Turk, Teja; Neumann, Kathrin; Beerenwinkel, Niko; Bogojeska, Jasmina; Fellay, Jaques; Roth, Volker; Kok, Yik Lim; Thorball, Christian W; Borghesi, Alessandro; Parbhoo, Sonali; Wieser, Mario; Böni, Jürg; Perreau, Matthieu; Klimkait, Thomas; Yerly, Sabine; Battegay, Manuel; Rauch, Andri; Hoffmann, Matthias; Bernasconi, Enos; Cavassini, Matthias; Kouyos, Roger D; Günthard, Huldrych F; Metzner, Karin J; Swiss HIV Cohort Study (2019). Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART. Nature Communications, 10(1):3193.

Karakus, Umut. Identification of MHC Class II as Entry Determinant of Bat Influenza Viruses. 2019, University of Zurich, Faculty of Medicine.

Olearo, Flaminia; Nguyen, Huyen; Bonnet, Fabrice; Yerly, Sabine; Wandeler, Gilles; Stoeckle, Marcel; Cavassini, Matthias; Scherrer, Alexandra; Costagiola, Dominique; Schmid, Patrick; Günthard, Huldrych F; Bernasconi, Enos; Boeni, Jürg; D'arminio Monforte, Antonella; Zazzi, Maurizio; Rossetti, Barbara; Neau, Didier; Bellecave, Pantxika; Rijnders, Bart; Reiss, Peter; Wit, Ferdinand; Kouyos, Roger; Calmy, Alexandra (2019). Impact of the M184V/I Mutation on the Efficacy of Abacavir/Lamivudine/Dolutegravir Therapy in HIV Treatment-Experienced Patients. Open Forum Infectious Diseases, 6(10):ofz330.

Tschumi, Fabian; Schmutz, Stefan; Kufner, Verena; Heider, Maike; Pigny, Fiona; Schreiner, Bettina; Capaul, Riccarda; Achermann, Yvonne; Huber, Michael (2019). Meningitis and epididymitis caused by Toscana virus infection imported to Switzerland diagnosed by metagenomic sequencing: a case report. BMC Infectious Diseases, 19(1):591.

Abela, Irene A; Kadelka, Claus; Trkola, Alexandra (2019). Correlates of broadly neutralizing antibody development. Current opinion in HIV and AIDS, 14(4):279-285.

Hachfeld, A; Darling, K; Calmy, A; Ledergerber, B; Weber, R; Battegay, M; Wissel, K; Di Benedetto, C; Fux, C A; Tarr, P E; Kouyos, R; Ruggia, L S; Furrer, H J; Wandeler, G; Swiss HIV Cohort Study (2019). Why do sub-Saharan Africans present late for HIV care in Switzerland? HIV Medicine, 20(6):418-423.

Kusejko, Katharina; Bachmann, Nadine; Chaudron, Sandra E; Nguyen, Huyen; Braun, Dominique L; Hampel, Benjamin; Battegay, Manuel; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Hoffmann, Matthias; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Perreau, Matthieu; Rauch, Andri; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2019). A Systematic Phylogenetic Approach to Study the Interaction of HIV-1 With Coinfections, Noncommunicable Diseases, and Opportunistic Diseases. Journal of Infectious Diseases, 220(2):244-253.

Carlisle, Louisa A; Turk, Teja; Kusejko, Katharina; Metzner, Karin J; Leemann, Christine; Schenkel, Corinne D; Bachmann, Nadine; Posada, Susana; Beerenwinkel, Niko; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Perreau, Matthieu; Braun, Dominique L; Rauch, Andri; Calmy, Alexandra; Cavassini, Matthias; Battegay, Manuel; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2019). Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection. Journal of Infectious Diseases, 220(2):254-265.

Salazar-Vizcaya, Luisa; Kouyos, Roger D; Metzner, Karin J; Caraballo Cortes, Kamila; Böni, Jürg; Shah, Cyril; Fehr, Jan; Braun, Dominique L; Bernasconi, Enos; Mbunkah, Herbert A; Hoffmann, Matthias; Labhardt, Niklaus; Cavassini, Matthias; Rougemont, Mathieu; Günthard, Huldrych F; Keiser, Olivia; Rauch, Andri; Swiss HIV Cohort Study (2019). Changing Trends in International Versus Domestic HCV Transmission in HIV-Positive Men Who Have Sex With Men: A Perspective for the Direct-Acting Antiviral Scale-Up Era. Journal of Infectious Diseases, 220(1):91-99.

Hauser, Anthony; Kusejko, Katharina; Johnson, Leigh F; Wandeler, Gilles; Riou, Julien; Goldstein, Fardo; Egger, Matthias; Kouyos, Roger D (2019). Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa. PLoS Computational Biology, 15(6):e1007083.

Di Giallonardo, Francesca; Pinto, Angie N; Keen, Phillip; Shaik, Ansari; Carrera, Alex; Salem, Hanan; Telfer, Barbara; Cooper, Craig; Price, Karen; Selvey, Christine; Holden, Joanne; Bachmann, Nadine; Lee, Frederick J; Dwyer, Dominic E; Duchêne, Sebastián; Holmes, Edward C; Grulich, Andrew E; Kelleher, Anthony D (2019). Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia. Viruses, 11(5):482.

Günthard, Huldrych F; Calvez, Vincent; Paredes, Roger; Pillay, Deenan; Shafer, Robert W; Wensing, Annemarie M; Jacobsen, Donna M; Richman, Douglas D (2019). Reply to Ambrosioni et al. Clinical Infectious Diseases, 68(11):1977-1978.

Chatterjee, Bithi; Deng, Yun; Holler, Angelika; Núñez, Nicolás Gonzalo; Azzi, Tarik; Vanoaica, Liliana Danusia; Müller, Anne; Zdimerova, Hana; Antsiferova, Olga; Zbinden, Andrea; Capaul, Riccarda; Dreyer, Johannes H; Nadal, David; Becher, Burkhard; Robinson, Mark D; Stauss, Hans; Münz, Christian (2019). CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo. PLoS Pathogens, 15(5):e1007748.

Euler, Zelda; Van Den Kerkhof, Tom L; Kouyos, Roger D; Tully, Damien C; Allen, Todd M; Trkola, Alexandra; Sanders, Rogier W; Schuitemaker, Hanneke; Van Gils, Marit J (2019). Lower Broadly Neutralizing Antibody Responses in Female Versus Male HIV-1 Infected Injecting Drug Users. Viruses, 11(4):E384.

Young, Jim; Scherrer, Alexandra U; Calmy, Alexandra; Tarr, Philip E; Bernasconi, Enos; Cavassini, Matthias; Hachfeld, Anna; Vernazza, Pietro; Günthard, Huldrych F; Bucher, Heiner C; Swiss HIV Cohort Study (2019). The comparative effectiveness of NRTI-sparing dual regimens in emulated trials using observational data from the Swiss HIV Cohort Study. Antiviral Therapy, 24(5):343-353.

Gujer, Cornelia; Murer, Anita; Müller, Anne; Vanoaica, Danusia; Sutter, Kathrin; Jacque, Emilie; Fournier, Nathalie; Kalchschmidt, Jens; Zbinden, Andrea; Capaul, Riccarda; Dzionek, Andrzej; Mondon, Philippe; Dittmer, Ulf; Münz, Christian (2019). Plasmacytoid dendritic cells respond to Epstein-Barr virus infection with a distinct type I interferon subtype profile. Blood Advances, 3(7):1129-1144.

Compagno, Francesca; Naegele, Klaudia; Kahlert, Christian R; Hösli, Irene; Aebi-Popp, Karoline; Martinez de Tejada, Begona; Paioni, Paolo; Yerly, Sabine; Böni, Jürg; Battegay, Manuel; Rudin, Christoph; Hirsch, Hans H; Swiss HIV Cohort Study (2019). The rate of mother-to-child transmission of antiretroviral drug-resistant HIV strains is low in the Swiss Mother and Child HIV Cohort Study. Swiss Medical Weekly, 149:w20059.

Karakus, Umut; Thamamongood, Thiprampai; Ciminski, Kevin; et al; Oderbolz, Josua; Stertz, Silke (2019). MHC class II proteins mediate cross-species entry of bat influenza viruses. Nature, 567(7746):109-112.

Braun, Dominique L; Hampel, Benjamin; Kouyos, Roger; Nguyen, Huyen; Shah, Cyril; Flepp, Markus; Stöckle, Marcel; Conen, Anna; Béguelin, Charles; Künzler-Heule, Patrizia; Nicca, Dunja; Schmid, Patrick; Delaloye, Julie; Rougemont, Mathieu; Bernasconi, Enos; Rauch, Andri; Günthard, Huldrych F; Böni, Jürg; Fehr, Jan S; Swiss HIV Cohort Study (2019). High Cure Rates With Grazoprevir-Elbasvir With or Without Ribavirin Guided by Genotypic Resistance Testing Among Human Immunodeficiency Virus/Hepatitis C Virus-coinfected Men Who Have Sex With Men. Clinical Infectious Diseases, 68(4):569-576.

Braun, Dominique L; Hampel, Benjamin; Martin, Eileen; Kouyos, Roger; Kusejko, Katharina; Grube, Christina; Flepp, Markus; Stöckle, Marcel; Conen, Anna; Béguelin, Charles; Schmid, Patrick; Delaloye, Julie; Rougemont, Mathieu; Bernasconi, Enos; Rauch, Andri; Günthard, Huldrych F; Böni, Jürg; Fehr, Jan S; Swiss HIV Cohort Study (2019). High Number of Potential Transmitters Revealed in a Population-based Systematic Hepatitis C Virus RNA Screening Among Human Immunodeficiency Virus-infected Men Who Have Sex With Men. Clinical Infectious Diseases, 68(4):561-568.

Bachmann, Nadine; von Braun, Amrei; Labhardt, Niklaus D; Kadelka, Claus; Günthard, Huldrych F; Sekaggya-Wiltshire, Christine; Castelnuovo, Barbara; Kambugu, Andrew; Lejone, Thabo I; Böni, Jürg; Yerly, Sabine; Perreau, Matthieu; Klimkait, Thomas; Kouyos, Roger D; Fehr, Jan; Swiss HIV Cohort Study (2019). Importance of routine viral load monitoring: higher levels of resistance at ART failure in Uganda and Lesotho compared with Switzerland. Journal of Antimicrobial Chemotherapy, 74(2):468-472.

Murer, Anita; Rühl, Julia; Zbinden, Andrea; Capaul, Riccarda; Hammerschmidt, Wolfgang; Chijioke, Obinna; Münz, Christian (2019). MicroRNAs of Epstein-Barr Virus Attenuate T-Cell-Mediated Immune Control In Vivo. mBio, 10:e01941-18.

Günthard, Huldrych F; Calvez, Vincent; Paredes, Roger; Pillay, Deenan; Shafer, Robert W; Wensing, Annemarie M; Jacobsen, Donna M; Richman, Douglas D (2019). Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel. Clinical Infectious Diseases, 68(2):177-187.

Ivan, Branislav; Sun, Zhaozhi; Subbaraman, Harini; Friedrich, Nikolas; Trkola, Alexandra (2019). CD4 occupancy triggers sequential pre-fusion conformational states of the HIV-1 envelope trimer with relevance for broadly neutralizing antibody activity. PLoS Biology, 17(1):e3000114.

Turkington, H L. Investigating the Role of the NS1 Protein from Different Influenza A, Virus Strains in Host Cell Interferon Antagonism and Phosphoinositide-3 Kinase Signaling. 2019, University of Zurich, Faculty of Medicine.

2018

Kusejko, K; Marzel, A; Hampel, B; Bachmann, N; Nguyen, H; Fehr, J; Braun, D L; Battegay, M; Bernasconi, E; Calmy, A; Cavassini, M; Hoffmann, M; Böni, J; Yerly, S; Klimkait, T; Perreau, M; Rauch, A; Günthard, H F; Kouyos, R D; Swiss HIV Cohort Study (2018). Quantifying the drivers of HIV transmission and prevention in men who have sex with men: a population model-based analysis in Switzerland. HIV Medicine, 19(10):688-697.

Haller, Otto; Arnheiter, Heinz; Pavlovic, Jovan; Staeheli, Peter (2018). The Discovery of the Antiviral Resistance Gene Mx: A Story of Great Ideas, Great Failures, and Some Success. Annual Review of Virology, 5(1):33-51.

Dobay, Maria Pamela; Stertz, Silke; Delorenzi, Mauro (2018). Context-based retrieval of functional modules in protein-protein interaction networks. Briefings in Bioinformatics, 19(5):995-1007.

Yángüez, Emilio; Hunziker, Annika; Dobay, Maria Pamela; Yildiz, Soner; Schading, Simon; Elshina, Elizaveta; Karakus, Umut; Gehrig, Peter; Grossmann, Jonas; Dijkman, Ronald; Schmolke, Mirco; Stertz, Silke (2018). Phosphoproteomic-based kinase profiling early in influenza virus infection identifies GRK2 as antiviral drug target. Nature Communications, 9:3679.

Kouyos, Roger D; Rusert, Peter; Kadelka, Claus; Huber, Michael; Marzel, Alex; Ebner, Hanna; Schanz, Merle; Liechti, Thomas; Friedrich, Nikolas; Braun, Dominique L; Scherrer, Alexandra U; Weber, Jacqueline; Uhr, Therese; Leemann, Christine; Kuster, Herbert; Cavassini, Matthias; Bernasconi, Enos; Hoffmann, Matthias; Calmy, Alexandra; Battegay, Manuel; Rauch, Andri; Yerly, Sabine; Aubert, Vincent; Klimkait, Thomas; Böni, Jürg; Metzner, Karin J; Günthard, Huldrych F; Trkola, Alexandra; Swiss HIV Cohort Study; et al (2018). Tracing HIV-1 strains that imprint broadly neutralizing antibody responses. Nature, 561(7723):406-410.

Subbaraman, Harini; Schanz, Merle; Trkola, Alexandra (2018). Broadly neutralizing antibodies: What is needed to move from a rare event in HIV-1 infection to vaccine efficacy? Retrovirology, 15(1):52.

Kusejko, Katharina; Kadelka, Claus; Marzel, Alex; Battegay, Manuel; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Hoffmann, Matthias; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Perreau, Matthieu; Rauch, Andri; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2018). Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study. Virus Evolution, 4(2):vey024.

Kadelka, Claus; Liechti, Thomas; Ebner, Hanna; Schanz, Merle; Rusert, Peter; Friedrich, Nikolas; Stiegeler, Emanuel; Braun, Dominique L; Huber, Michael; Scherrer, Alexandra U; Weber, Jacqueline; Uhr, Therese; Kuster, Herbert; Misselwitz, Benjamin; Cavassini, Matthias; Bernasconi, Enos; Hoffmann, Matthias; Calmy, Alexandra; Battegay, Manuel; Rauch, Andri; Yerly, Sabine; Aubert, Vincent; Klimkait, Thomas; Böni, Jürg; Kouyos, Roger D; Günthard, Huldrych F; Trkola, Alexandra; Swiss HIV Cohort Study (2018). Distinct, IgG1-driven antibody response landscapes demarcate individuals with broadly HIV-1 neutralizing activity. Journal of Experimental Medicine, 215(6):1589-1608.

Liechti, Thomas; Günthard, Huldrych F; Trkola, Alexandra (2018). OMIP-047: High-Dimensional phenotypic characterization of B cells. Cytometry. Part A, 93(6):592-596.

Marzel, Alex; Kusejko, Katharina; Weber, Rainer; Bruggmann, Philip; Rauch, Andri; Roth, Jan A; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Hoffmann, Matthias; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Perreau, Matthieu; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2018). The Cumulative Impact of Harm Reduction on the Swiss HIV Epidemic: Cohort Study, Mathematical Model, and Phylogenetic Analysis. Open Forum Infectious Diseases, 5(5):ofy078.

Murer, Anita; McHugh, Donal; Caduff, Nicole; Kalchschmidt, Jens; Barros, Mario; Zbinden, Andrea; Capaul, Riccarda; Niedobitek, Gerald; Allday, Martin; Chijioke, Obinna; Münz, Christian (2018). EBV persistence without its EBNA3A and 3C oncogenes in vivo. PLoS Pathogens, 14(4):e1007039.

Stertz, Silke; Paul Duprex, W; Harris, Mark (2018). A novel mutation in the neuraminidase gene of the 2009 pandemic H1N1 influenza A virus confers multidrug resistance. Journal of General Virology, 99(3):275-276.

Zbinden, Andrea. Combining conventional and novel molecular diagnostic methods for the identification of bacteria and viruses. 2018, University of Zurich, Faculty of Medicine.

Kühnert, Denise; Kouyos, Roger; Shirreff, George; Pečerska, Jūlija; Scherrer, Alexandra U; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Günthard, Huldrych F; Stadler, Tanja; Bonhoeffer, Sebastian; Swiss HIV Cohort Study (2018). Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics. PLoS Pathogens, 14(2):e1006895.

Bertels, Frederic; Marzel, Alex; Leventhal, Gabriel; Mitov, Venelin; Fellay, Jacques; Günthard, Huldrych F; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Battegay, Manuel; Rauch, Andri; Cavassini, Matthias; Calmy, Alexandra; Bernasconi, Enos; Schmid, Patrick; Scherrer, Alexandra U; Müller, Viktor; Bonhoeffer, Sebastian; Kouyos, Roger; Regoes, Roland R; Swiss HIV Cohort Study (2018). Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T Cell Decline and Per-Parasite Pathogenicity. Molecular Biology and Evolution, 35(1):27-37.

Lewandowska, Dagmara W; Capaul, Riccarda; Prader, Seraina; Zagordi, Osvaldo; Geissberger, Fabienne-Desirée; Kügler, Martin; Knorr, Marcus; Berger, Christoph; Güngör, Tayfun; Reichenbach, Janine; Shah, Cyril; Böni, Jürg; Zbinden, Andrea; Trkola, Alexandra; Pachlopnik Schmid, Jana; Huber, Michael (2018). Persistent mammalian orthoreovirus, coxsackievirus and adenovirus co-infection in a child with a primary immunodeficiency detected by metagenomic sequencing: a case report. BMC Infectious Diseases, 18:33.

Reh, Lucia; Magnus, Carsten; Kadelka, Claus; Kühnert, Denise; Uhr, Therese; Weber, Jacqueline; Morris, Lynn; Moore, Penny L; Trkola, Alexandra (2018). Phenotypic deficits in the HIV-1 envelope are associated with the maturation of a V2-directed broadly neutralizing antibody lineage. PLoS Pathogens, 14:e1006825.

Steiner, Fiona. Antiviral function of Mx proteins: role of cellular factors and subcellular localization. 2018, University of Zurich, Faculty of Science.

McHugh, Donal. Cooperation of the Epstein-Barr virus with Karposi sarcoma associated herpes virus or the human immunodeficiency virus enhances viral pathology in vivo. 2018, University of Zurich, Faculty of Science.

Liechti, Thomas; Kadelka, Claus; Ebner, Hanna; Friedrich, Nikolas; Kouyos, Roger D; Gunthard, Huldrych F; Trkola, Alexandra (2018). Development of a high-throughput bead based assay system to measure HIV-1 specific immune signatures in clinical samples. Journal of Immunological Methods, 454:48-58.

Crameri, Michel; Bauer, Michael; Caduff, Nicole; Walker, Raphael; Steiner, Fiona; Franzoso, Francesca D; Gujer, Cornelia; Boucke, Karin; Kucera, Talissa; Zbinden, Andrea; Münz, Christian; Fraefel, Cornel; Greber, Urs F; Pavlovic, Jovan (2018). MxB is an interferon-induced restriction factor of human herpesviruses. Nature Communications, 9(1):1980.

Ivan, Branislav. Structure-function analysis of the HIV-1 envelope trimer to resolve interplay of envelope subunits required for entry and shielding. 2018, University of Zurich, Faculty of Science.

Crameri, Michel Stefan. The interferon system - insights into a novel antiviral effector function and viral evasion strategy. 2018, University of Zurich, Faculty of Science.

Ebner, Hanna. The role of humoral immunity in HIV infection : understanding broadly neutralizing antibody evolution. 2018, University of Zurich, Faculty of Science.

Turkington, H L; Juozapaitis, M; Tsolakos, N; Corrales-Aguilar, E; Schwemmle, M; Hale, B G (2018). Unexpected Functional Divergence of Bat Influenza Virus NS1 Proteins. Journal of Virology, 92(5):e02097-17.

2017

Ebner, Hanna. The role of humorl immunity in HIV infectio - understanding broadly neutralizing antibody evolution. 2017, University of Zurich, Faculty of Medicine.

Ivan, Branislav. Structure-functionanalysis of the HIV-1 envelope trimer to resolve the interplay of envelope subunits required for entry and shielding. 2017, University of Zurich, Faculty of Medicine.

Hampel, Benjamin; Kusejko, K; Braun, D L; Harrison-Quintana, J; Kouyos, Roger; Fehr, J (2017). Assessing the need for a pre-exposure prophylaxis programme using the social media app Grindr®. HIV Medicine, 18(10):772-776.

Lewandowska, Dagmara Wanda; Zagordi, Osvaldo; Geissberger, Fabienne-Desirée; Kufner, Verena; Schmutz, Stefan; Böni, Jürg; Metzner, Karin J; Trkola, Alexandra; Huber, Michael (2017). Correction to: Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. Microbiome, 5(1):137.

Lopes, A M; Domingues, P; Zell, R; Hale, B G (2017). Structure-Guided Functional Annotation of the Influenza A Virus NS1 Protein Reveals Dynamic Evolution of the p85β-Binding Site during Circulation in Humans. Journal of Virology, 91(21):e01081-17.

Lopes, A M. Structure-guided Functional Annotation of the Influenza A Virus NS1 p85β-Binding Site. 2017, University of Zurich, Faculty of Medicine.

Domingues, P; Hale, B G (2017). Functional Insights into ANP32A-Dependent Influenza A Virus Polymerase Host Restriction. Cell Reports, 20(11):2538-2546.

Swiss HIV Cohort Study; Turk, Teja; Bachmann, Nadine; Kadelka, Claus; Böni, Jürg; Yerly, Sabine; Aubert, Vincent; Klimkait, Thomas; Battegay, Manuel; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Furrer, Hansjakob; Hoffmann, Matthias; Günthard, Huldrych F; Kouyos, Roger D; et al (2017). Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis. eLife, 6:e28721.

Patzina, C; Botting, C H; García-Sastre, A; Randall, R E; Hale, B G (2017). Human interactome of the influenza B virus NS1 protein. Journal of General Virology, 98(9):2267-2273.

Pohl, M O; Von Recum-Knepper, Jessica; Rodriguez-Frandsen, Ariel; Lanz, Caroline; Yangüez, Emilio; Soonthornvacharin, Stephen; Wolff, Thorsten; Chanda, Sumit K; Stertz, Silke (2017). Identification of Polo-like kinases as potential novel drug targets for influenza A virus. Scientific Reports, 7(1):8629.

Lewandowska, Dagmara W; Zagordi, Osvaldo; Geissberger, Fabienne-Desirée; Kufner, Verena; Schmutz, Stefan; Böni, Jürg; Metzner, Karin J; Trkola, Alexandra; Huber, Michael (2017). Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. Microbiome, 5(1):94.

Wittkop, L; Arsandaux, J; Trevino, A; et al; Böni, Jürg; Calmy, A; COHERE in EuroCoord; ACHIeV2e Study Group (2017). CD4 cell count response to first-line combination ART in HIV-2+ patients compared with HIV-1+ patients: a multinational, multicohort European study. Journal of Antimicrobial Chemotherapy, 72:2869-2878.

McHugh, Donal; Caduff, Nicole; Barros, Mario Henrique M; Rämer, Patrick C; Raykova, Ana; Murer, Anita; Landtwing, Vanessa; Quast, Isaak; Styles, Christine T; Spohn, Michael; Fowotade, Adeola; Delecluse, Henri-Jacques; Papoudou-Bai, Alexandra; Lee, Yong-Moon; Kim, Jin-Man; Middeldorp, Jaap; Schulz, Thomas F; Cesarman, Ethel; Zbinden, Andrea; Capaul, Riccarda; White, Robert E; Allday, Martin J; Niedobitek, Gerald; Blackbourn, David J; Grundhoff, A; Münz, Christian (2017). Persistent KSHV Infection Increases EBV-Associated Tumor Formation In Vivo via Enhanced EBV Lytic Gene Expression. Cell Host & Microbe, 22(1):61-73.

Shaw, Megan L; Stertz, S (2017). Role of Host Genes in Influenza Virus Replication. In: Shaw, Megan L; Stertz, S. Current Topics in Microbiology and Immunology. Berlin, Heidelberg: Springer, 1-39.

Bachmann, Nadine; Turk, Teja; Kadelka, Claus; Marzel, Alex; Shilaih, Mohaned; Böni, Jürg; Aubert, Vincent; Klimkait, Thomas; Leventhal, Gabriel E; Günthard, Huldrych F; Kouyos, Roger; Swiss HIV Cohort Study (2017). Parent-offspring regression to estimate the heritability of an HIV-1 trait in a realistic setup. Retrovirology, 14(1):33.

Akers, Isabel E; Weber, Rainer; Sax, Hugo; Böni, Jürg; Trkola, Alexandra; Kuster, Stefan P (2017). Influence of time to diagnosis of severe influenza on antibiotic use, length of stay, isolation precautions, and mortality: a retrospective study. Influenza and Other Respiratory Viruses, 11(4):337-344.

Brandenberg, Oliver F; Magnus, Carsten; Rusert, Peter; Günthard, Huldrych F; Regoes, Roland Robert; Trkola, Alexandra (2017). Predicting HIV-1 transmission and antibody neutralization efficacy in vivo from stoichiometric parameters. PLoS Pathogens, 13(5):e1006313.

Lanz, Caroline. Characterization of Human and Swine IFITM-Mediated Restriction of Influenza A Virus. 2017, University of Zurich, Faculty of Medicine.

Marzel, A; Shilaih, Mohaned; Turk, T; Campbell, Nottania K; Yang, Wan-Lin; Böni, J; Yerly, S; Klimkait, T; Aubert, V; Furrer, H; Calmy, A; Battegay, M; Cavassini, M; Bernasconi, E; Schmid, P; Metzner, K J; Gunthard, H F; Kouyos, R D; Swiss HIV Cohort Study (2017). Mining for pairs: shared clinic visit dates identify steady HIV-positive partnerships. HIV Medicine, 18(9):667-676.

Kletenkov, K; Hoffmann, D; Böni, J; Yerly, S; Aubert, V; Schöni-Affolter, F; Struck, D; Verheyen, J; Klimkait, T (2017). Role of Gag mutations in PI resistance in the Swiss HIV cohort study: bystanders or contributors? Journal of Antimicrobial Chemotherapy, 72(3):866-875.

Beauparlant, David; Rusert, Peter; Magnus, Carsten; Kadelka, Claus; Weber, Jacqueline; Uhr, Therese; Zagordi, Osvaldo; Oberle, Corinna; Duenas-Decamp, Maria J; Clapham, Paul R; Metzner, Karin J; Günthard, Huldrych F; Trkola, Alexandra (2017). Delineating CD4 dependency of HIV-1: Adaptation to infect low level CD4 expressing target cells widens cellular tropism but severely impacts on envelope functionality. PLoS Pathogens, 13(3):e1006255.

Oberle, Corinna S; Magnus, Carsten; Joos, Beda; Rusert, Peter; Beauparlant, David; Kouyos, Roger; Trkola, Alexandra; Metzner, Karin J; Günthard, Huldrych F (2017). Reply to correspondence 'Conserved signatures indicate HIV-1 transmission is under strong selection and thus is not a "stochastic" process' by Gonzalez et al., Retrovirology 2017. Retrovirology, 14(1):14.

Kovari, Helen; Rauch, Andri; Kouyos, Roger; Rougemont, Mathieu; Cavassini, Matthias; Schmid, Patrick; Stöckle, Marcel; Bernasconi, Enos; Weber, Rainer; Ledergerber, Bruno; Swiss HIV Cohort Study (2017). Hepatitis C Infection and the Risk of Non-Liver-Related Morbidity and Mortality in HIV-Infected Persons in the Swiss HIV Cohort Study. Clinical Infectious Diseases, 64(4):490-497.

Huber, M; Metzner, K J; Geissberger, F D; Shah, C; Leemann, C; Klimkait, T; Böni, J; Trkola, A; Zagordi, O (2017). MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing. Journal of Virological Methods, 240:7-13.

Liechti, Thomas. B cell perturbations in HIV-1 infection. 2017, University of Zurich, Faculty of Medicine.

Lewandowska, Dagmara W; Schreiber, Peter W; Schuurmans, Macé M; Ruehe, Bettina; Zagordi, Osvaldo; Bayard, Cornelia; Greiner, Michael; Geissberger, Fabienne D; Capaul, Riccarda; Zbinden, Andrea; Böni, Jürg; Benden, Christian; Mueller, Nicolas J; Trkola, Alexandra; Huber, Michael (2017). Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection. PLoS ONE, 12(5):e0177340.

Marzel, Alex; Heinrich, Henriette; Schilliger, Lukas; Fehr, Jan S; Günthard, Huldrych F; Kouyos, Roger; Rampini, Silvana K (2017). Prescription of post-exposure prophylaxis for HIV-1 in the emergency room: correct transmission risk assessment remains challenging. Journal of Acquired Immune Deficiency Syndromes, 74(4):359-366.

2016

Bader, J; Däumer, M; Schöni-Affolter, F; Böni, J; Gorgievski-Hrisoho, Meri; Martinetti, G; Thielen, A; Klimkait, T (2016). Therapeutic Immune Recovery and Reduction of CXCR4-Tropic HIV-1. Clinical Infectious Diseases, 64(3):295-300.

Nigg, P E; Pavlovic, J (2016). Characterization of multi-subunit protein complexes of human mxa using non-denaturing polyacrylamide gel-electrophoresis. Journal of Visualized Experiments (Jove), 116:online.

Landtwing, Vanessa; Raykova, Ana; Pezzino, Gaetana; Béziat, Vivien; Marcenaro, Emanuela; Graf, Claudine; Moretta, Alessandro; Capaul, Riccarda; Zbinden, Andrea; Ferlazzo, Guido; Malmberg, Karl-Johan; Chijioke, Obinna; Münz, Christian (2016). Cognate HLA absence in trans diminishes human NK cell education. Journal of Clinical Investigation, 126(10):3772-3782.

Rusert, Peter; Kouyos, Roger D; Kadelka, Claus; Ebner, Hanna; Schanz, Merle; Huber, Michael; Braun, Dominique L; Hozé, Nathanael; Scherrer, Alexandra; Magnus, Carsten; Weber, Jacqueline; Uhr, Therese; Cippa, Valentina; Thorball, Christian W; Kuster, Herbert; Cavassini, Matthias; Bernasconi, Enos; Hoffmann, Matthias; Calmy, Alexandra; Battegay, Manuel; Rauch, Andri; Yerly, Sabine; Aubert, Vincent; Klimkait, Thomas; Böni, Jürg; Fellay, Jacques; Regoes, Roland R; Günthard, Huldrych F; Trkola, Alexandra (2016). Determinants of HIV-1 broadly neutralizing antibody induction. Nature Medicine, 22(11):1260-1267.

Ragonnet-Cronin, Manon L; Shilaih, Mohaned; Günthard, Huldrych F; Hodcroft, Emma B; Böni, Jürg; Fearnhill, Esther; Dunn, David; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Yang, Wan-Lin; Brown, Alison E; Lycett, Samantha J; Kouyos, Roger; Brown, Andrew J Leigh (2016). A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland. Scientific Reports, 6:32251.

Kiessling, Michael K; Schuierer, Sven; Stertz, Silke; Beibel, Martin; Bergling, Sebastian; Knehr, Judith; Carbone, Walter; de Vallière, Cheryl; Tchinda, Joelle; Bouwmeester, Tewis; Seuwen, Klaus; Rogler, Gerhard; Roma, Guglielmo (2016). Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening. BMC Genomics, 17(1):723.

Oberle, Corinna S; Joos, Beda; Rusert, Peter; Campbell, Nottania K; Beauparlant, David; Kuster, Herbert; Weber, Jacqueline; Schenkel, Corinne D; Scherrer, Alexandra U; Magnus, Carsten; Kouyos, Roger; Rieder, Philip; Niederöst, Barbara; Braun, Dominique L; Pavlovic, Jovan; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Trkola, Alexandra; Metzner, Karin J; Günthard, Huldrych F (2016). Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs. Retrovirology, 13(1):62.

Montazeri, Hesam; Kuipers, Jack; Kouyos, Roger; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Günthard, Huldrych F; Beerenwinkel, Niko (2016). Large-scale inference of conjunctive Bayesian networks. Bioinformatics, 32(17):i727-i735.

Pohl, M O; Lanz, C; Stertz, S (2016). Late stages of the influenza A virus replication cycle — a tight interplay between virus and host. Journal of General Virology, 97(9):2058 -2072.

Bader, J; Schöni-Affolter, F; Böni, Jürg; Gorgievski-Hrisoho, M; Martinetti, G; Battegay, M; Klimkait, T (2016). Correlating HIV tropism with immunological response under combination antiretroviral therapy. HIV Medicine, 17(8):615-622.

Diene, S M; François, P; Zbinden, A; Entenza, J M; Resch, G (2016). Comparative genomics analysis of streptococcus tigurinus strains identifies genetic elements specifically and uniquely present in highly virulent strains. PLoS ONE, 11(8):online.

Scherrer, Alexandra U; Yang, Wan-Lin; Kouyos, Roger D; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Cavassini, Matthias; Battegay, Manuel; Hauser, Christoph; Calmy, Alexandra; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F (2016). Successful Prevention of Transmission of Integrase Resistance in the Swiss HIV Cohort Study. Journal of Infectious Diseases, 214(3):399-402.

Zbinden, A; Dürig, R; Shah, C; Böni, J; Schüpbach, J (2016). Importance of an Early HIV Antibody Differentiation Immunoassay for Detection of Dual Infection with HIV-1 and HIV-2. PLoS ONE, 11(6):online.

Shilaih, Mohaned; Marzel, Alex; Yang, Wan Lin; Scherrer, Alexandra U; Schüpbach, Jörg; Böni, Jürg; Yerly, Sabine; Hirsch, Hans H; Aubert, Vincent; Cavassini, Matthias; Klimkait, Thomas; Vernazza, Pietro L; Bernasconi, Enos; Furrer, Hansjakob; Günthard, Huldrych F; Kouyos, Roger (2016). Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland. Scientific Reports, 6:27580.

Scherrer, Alexandra U; von Wyl, Viktor; Yang, Wan-Lin; Kouyos, Roger D; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Cavassini, Matthias; Battegay, Manuel; Furrer, Hansjakob; Calmy, Alexandra; Vernazza, Pietro; Bernasconi, Enos; Günthard, Huldrych F (2016). Emergence of acquired HIV-1 drug resistance almost stopped in Switzerland: A 15-year prospective cohort analysis. Clinical Infectious Diseases, 62(10):1310-1317.

Marzel, Alex; Shilaih, Mohaned; Yang, Wan-Lin; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Braun, Dominique L; Calmy, Alexandra; Furrer, Hansjakob; Cavassini, Matthias; Battegay, Manuel; Vernazza, Pietro L; Bernasconi, Enos; Günthard, Huldrych F; Kouyos, Roger D; Swiss HIV Cohort Study (2016). HIV-1 transmission during recent infection and during treatment interruptions as major drivers of new infections in the Swiss HIV Cohort Study. Clinical Infectious Diseases, 62(1):115-122.

Stiegeler, Emanuel. HIV envelope specific DARPins as entry inhibitors. 2016, University of Zurich, Faculty of Medicine.

Magnus, C; Reh, L; Trkola, Alexandra (2016). HIV-1 resistance to neutralizing antibodies: Determination of antibody concentrations leading to escape mutant evolution. Virus Research, 218:57-70.

Pohl, Marie-Theres. Identification of novel host factors of influenza A virus. 2016, University of Zurich, Faculty of Medicine.

Lewandowska, Dagmara Wanda. Metagenomic profiling of viral infections for improved virus diagnostic and infectious disease management in immune compromised patients. 2016, University of Zurich, Faculty of Medicine.

Reh, Lucia. The role of cell-cell transmission in steering HIV-1 neutralization and escape. 2016, University of Zurich, Faculty of Medicine.

2015

Nigg, Patricia E; Pavlovic, Jovan (2015). Oligomerization and GTP-binding requirements of MxA for viral target recognition and antiviral activity against influenza a virus. Journal of Biological Chemistry, 290(50):29893-29906.

Tripathi, S; Pohl, M O; Zhou, Y; Rodriguez-Frandsen, A; Wang, G; Stein, D A; Moulton, H M; Che, J; Mulder, L C F; Yangüez, E; Andenmatten, D; Pache, L; Manicassamy, B; Albrecht, R A; Gonzalez, M G; Nguyen, Quy; Brass, A; Elledge, S; White, M; Shapira, S; Hacohen, N; Karlas, A; Meyer, T F; Shales, M; Gatorano, A; Johnson, J R; Jang, G; Johnson, T; Verschueren, E; Sanders, D; Krogan, N; Shaw, M; König, R; Stertz, S; García-Sastre, A; Chanda, S K; DeJesus, P (2015). Meta- and orthogonal integration of influenza "OMICs" data defines a role for UBR4 in virus budding. Cell Host & Microbe, 18(6):723-735.

Brandenberg, Oliver F; Magnus, Carsten; Regoes, Roland R; Trkola, Alexandra (2015). The HIV-1 entry process: A stoichiometric view. Trends in Microbiology, 23(12):763-774.

Domingues, P; Golebiowski, F; Tatham, M H; Lopes, A M; Taggart, A; Hay, R T; Hale, B G (2015). Global Reprogramming of Host SUMOylation during Influenza Virus Infection. Cell Reports, 13(7):1467-1480.

Schultze, Detlev; Mani, Bernhard; Dollenmaier, Günter; Sahli, Roland; Zbinden, Andrea; Krayenbühl, A (2015). Acute Hepatitis E Virus infection with coincident reactivation of Epstein-Barr virus infection in an immunosuppressed patient with rheumatoid arthritis: a case report. BMC Infectious Diseases, 15(474):online.

Vetter, Beatrice N; Orlowski, Vanessa; Niederhauser, Christoph; Walter, Louise; Schüpbach, J (2015). Impact of naturally occurring amino acid variations on the detection of HIV-1 p24 in diagnostic antigen tests. BMC Infectious Diseases, 15(468):online.

Vetter, B N; Orlowski, V; Schüpbach, J; Boeni, J; Ruehe, B; Huder, J B (2015). Resolution of plasma sample mix-ups through comparison of patient antibody patterns to E. coli. Journal of Immunological Methods, 427:130-133.

Glass, Tracy R; Sterne, Jonathan A C; Schneider, Marie-Paule; De Geest, Sabina; Nicca, Dunja; Furrer, Hansjakob; Günthard, Huldrych F; Bernasconi, Enos; Calmy, Alexandra; Rickenbach, Martin; Battegay, Manuel; Bucher, Heiner C (2015). Self-reported nonadherence to antiretroviral therapy as a predictor of viral failure and mortality. AIDS, 29(16):2195-200.

Montazeri, Hesam; Günthard, Huldrych F; Yang, Wan-Lin; Kouyos, Roger; Beerenwinkel, Niko (2015). Estimating the dynamics and dependencies of accumulating mutations with applications to HIV drug resistance. Biostatistics, 16(4):713-726.

Turkington, H L; Juozapaitis, M; Kerry, P S; Aydillo, T; Ayllon, J; García-Sastre, A; Schwemmle, M; Hale, B G (2015). Novel bat influenza virus NS1 proteins bind double-stranded RNA and antagonize host innate immunity. Journal of Virology, 89(20):10696-10701.

Braun, Dominique L; Kouyos, Roger D; Balmer, Belinda; Grube, Christina; Weber, Rainer; Günthard, Huldrych F (2015). Frequency and spectrum of unexpected clinical manifestations of primary HIV-1 infection. Clinical Infectious Diseases, 61(6):1013-1021.

Yang, Wan-Lin; Kouyos, Roger D; Scherrer, Alexandra U; Böni, Jürg; Shah, Cyril; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Hirzel, Cédric; Battegay, Manuel; Cavassini, Matthias; Bernasconi, Enos; Vernazza, Pietro; Held, Leonhard; Ledergerber, Bruno; Günthard, Huldrych F (2015). Assessing efficacy of different nucleos(t)ide backbones in NNRTI-containing regimens in the swiss HIV cohort study. Journal of Antimicrobial Chemotherapy:3323-3331.

Kouyos, Roger D; Günthard, Huldrych F (2015). Editorial commentary: the irreversibility of HIV drug resistance. Clinical Infectious Diseases, 61(5):837-839.

Swiss HIV Cohort Study; Kovari, Helen; Ledergerber, Bruno; et al (2015). High hepatic and extrahepatic mortality and low treatment uptake in HCV-coinfected persons in the Swiss HIV cohort study between 2001 and 2013. Journal of Hepatology, 63(3):573-580.

Benson, R A; MacLeod, M K L; Hale, B G; Patakas, A; Garside, P; Brewer, J M (2015). Antigen presentation kinetics control T cell/dendritic cell interactions and follicular helper T cell generation in vivo. eLife, 4:e06994.

Schüpbach, J; Niederhauser, C; Yerly, S; Regenass, S; Gorgievski, M; Aubert, V; Ciardo, D; Klimkait, T; Dollenmaier, G; Andreutti, C; Martinetti, G; Brandenberger, M; Gebhardt, M D (2015). Decreasing proportion of recent infections among newly diagnosed HIV-1 cases in Switzerland, 2008 to 2013 based on line-immunoassay-based algorithms. PLoS ONE, 10(7):e0131828.

Zhou, Q; Uhlig, K M; Muth, A; Kimpel, J; Lévy, C; Münch, R C; Seifried, J; Pfeiffer, A; Trkola, A; Coulibaly, C; von Laer, D; Wels, W S; Hartwig, U F; Verhoeyen, E; Buchholz, C J (2015). Exclusive transduction of human CD4+ T Cells upon systemic delivery of CD4-targeted lentiviral vectors. Journal of Immunology, (195):2493-2501.

Reh, Lucia; Magnus, Carsten; Schanz, Merle; Weber, Jacqueline; Uhr, Therese; Rusert, Peter; Trkola, Alexandra (2015). Capacity of broadly neutralizing antibodies to inhibit HIV-1 cell-cell transmission is strain- and epitope-dependent. PLoS Pathogens, 11(7):e1004966.

Yang, Wan-Lin; Kouyos, Roger; Scherrer, Alexandra U; Böni, Jürg; Shah, Cyril; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Furrer, Hansjakob; Battegay, Manuel; Cavassini, Matthias; Bernasconi, Enos; Vernazza, Pietro; Held, Leonhard; Ledergerber, Bruno; Günthard, Huldrych F; Swiss HIV Cohort Study (2015). Assessing the paradox between transmitted and acquired HIV type 1 drug resistance mutations in the Swiss HIV cohort study from 1998 to 2012. Journal of Infectious Diseases, 212(1):28-38.

Ussher, James E; Phalora, Prabhjeet; Cosgrove, Cormac; Hannaway, Rachel F; Rauch, Andri; Günthard, Huldrych F; Goulder, Philip; Phillips, Rodney E; Willberg, Christian B; Klenerman, Paul (2015). Molecular analyses define Vα7.2-Jα33+ MAIT cell depletion in HIV infection: a case-control study. Medicine, 94(29):e1134.

König, R; Stertz, S (2015). Recent strategies and progress in identifying host factors involved in virus replication. Current Opinion in Microbiology, (26):79-88.

Kohler, I; Kouyos, Roger; Bianchi, M; Grube, C; Wyrzucki, A; Gunthard, H F; Hangartner, L (2015). The impact of vaccination on the breadth and magnitude of the antibody response to influenza A viruses in HIV-infected individuals. AIDS, 29(14):1803-1810.

Edinger, T O; Pohl, M O; Yangüez, E; Stertz, S (2015). Cathepsin W is required for escape of influenza a virus from late endosomes. mBio, 6(3):e00297-15.

Nigg, P E. The human MxA protein changes its stoichiometry and conformation upon GTP binding and targets influenza A virus nucleoprotein in its dimeric form. 2015, University of Zurich, Faculty of Science.

Pohl, M O; Stertz, S (2015). Measuring attachment and internalization of influenza a virus in A549 cells by flow cytometry. Journal of Visualized Experiments (Jove), (105):e53372.

Swiss HIV Cohort Study; Kouyos, R D; Hasse, B; et al (2015). Increases in condomless sex in the Swiss HIV cohort study. Open Forum Infectious Diseases, 2(2):ofv077.

Wyrzucki, Arkadiusz; Bianchi, Matteo; Kohler, Ines; Steck, Marco; Hangartner, Lars (2015). Heterosubtypic antibodies to influenza A virus have limited activity against cell-bound virus but are not impaired by strain-specific serum antibodies. Journal of Virology, 89(6):3136-3144.

Yang, Wan-Lin; Kouyos, Roger D; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Scherrer, Alexandra U; Shilaih, Mohaned; Hinkley, Trevor; Petropoulos, Christos; Bonhoeffer, Sebastian; Günthard, Huldrych F (2015). Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds. PLoS Pathogens, 11(3):e1004722.

Edinger, T O. The Human Host Factor Cathepsin W is Required for Escape of Influenza A Virus From Late Endosomes. 2015, University of Zurich, Faculty of Science.

Schanz, M. Tracing Evolution of HIV-1 Neutralizing Antibodies and their Targets, the HIV-1 Envelope Proteins. 2015, University of Zurich, Faculty of Science.

Brandenberg, Oliver F; Magnus, Carsten; Rusert, Peter; Regoes, Roland R; Trkola, Alexandra (2015). Different infectivity of HIV-1 strains is linked to number of envelope trimers required for entry. PLoS Pathogens, 11(1):e1004595.

Zimmermann, Kathrin; Bastidas, Sonia; Knecht, Leandra; Kuster, Herbert; Vavricka, Stephan R; Günthard, Huldrych F; Oxenius, Annette (2015). Gut commensal microbes do not represent a dominant antigenic source for continuous CD4+T-cell activation during HIV-1 infection. European Journal of Immunology, 45(11):3107-3113.

Vongrad, Valentina; Imig, Jochen; Mohammadi, Pejman; Kishore, Shivendra; Jaskiewicz, Lukasz; Hall, Jonathan; Günthard, Huldrych F; Beerenwinkel, Niko; Metzner, Karin J (2015). HIV-1 RNAs are not part of the argonaute 2 associated RNA interference pathway in macrophages. PLoS ONE, 10(7):e0132127.

Birger, Ruthie; Kouyos, Roger; Dushoff, Jonathan; Grenfell, Bryan (2015). Modeling the effect of HIV coinfection on clearance and sustained virologic response during treatment for hepatitis C virus. Epidemics, 12:1-10.

Münch, Robert C; Muth, Anke; Muik, Alexander; Friedel, Thorsten; Schmatz, Julia; Dreier, Birgit; Trkola, Alexandra; Plückthun, Andreas; Büning, Hildegard; Buchholz, Christian J (2015). Off-target-free gene delivery by affinity-purified receptor-targeted viral vectors. Nature Communications, 6:6246.

Lanz, C; Yangüez, E; Andenmatten, D; Stertz, S (2015). Swine IFITM proteins potently inhibit influenza A virus replication. Journal of Virology, 89(1):863-869.

Zbinden, A; Bostanci, N; Belibasakis, G N (2015). The novel species Streptococcus tigurinus and its association with oral infection. Virulence, 6(3):177-182.

Zimmermann, Kathrin; Liechti, Thomas; Haas, Anna; Rehr, Manuela; Trkola, Alexandra; Günthard, Huldrych F; Oxenius, Annette (2015). The orientation of HIV-1 gp120 binding to the CD4 receptor differentially modulates CD4+ T cell activation. Journal of Immunology, 194(2):637-649.

2014

White, K M; De Jesus, P; Chen, Z; et al; Stertz, S (2014). A potent anti-influenza compound blocks fusion through stabilization of the prefusion conformation of the hemagglutinin protein. ACS Infectious Diseases, 1:98-109.

Schanz, Merle; Liechti, Thomas; Zagordi, Osvaldo; Miho, Enkelejda; Reddy, Sai T; Günthard, Huldrych F; Trkola, Alexandra; Huber, Michael (2014). High-throughput sequencing of human immunoglobulin variable regions with subtype identification. PLoS ONE, 9(11):e111726.

Vetter, B N; Orlowski, V; Fransen, K; Niederhauser, C; Aubert, V; Brandenberger, M; Ciardo, D; Dollenmaier, G; Klimkait, T; Regenass, S; Schmid, P; Schottstedt, V; Suter-Riniker, F; Yerly, S; Shah, C; Böni, J; Schüpbach, J (2014). Generation of a Recombinant Gag Virus-Like-Particle Panel for the Evaluation of p24 Antigen Detection by Diagnostic HIV Test. PLoS ONE, 9(10):e111552-e111552.

Trkola, A (2014). Potency needs constancy. Nature, 514(7523):442-443.

Metzner, K J; Scherrer, A U; von Wyl, V; Böni, J; Yerly, S; Klimkait, T; Aubert, V; Furrer, Hansjakob; Hirsch, Hans H; Vernazza, P L; Cavassini, M; Calmy, A; Bernasconi, E; Weber, R; Gunthard, H F (2014). Limited clinical benefit of minority K103N and Y181C-variant detection in addition to routine genotypic resistance testing in antiretroviral therapy-naive patients. AIDS, 28(15):2231-2239.

Kohler, Ines; Scherrer, A U; Zagordi, O; Bianchi, M; Wyrzucki, A; Steck, M; Ledergerber, B; Gunthard, H F; Hangartner, L (2014). Prevalence and predictors for homo- and heterosubtypic antibodies against influenza a virus. Clinical Infectious Diseases, 59(10):1386-1393.

Kouyos, R D; Rauch, A; Braun, D L; Yang, W L; Böni, Jürg; Yerly, S; Klimkait, T; Aubert, V; Shah, Cyril; Kovari, H; Calmy, A; Cavassini, M; Battegay, M; Vernazza, P L; Bernasconi, E; Ledergerber, B; Gunthard, H F (2014). Higher risk of incident Hepatitis C virus coinfection among men who have sex with men, in whom the HIV genetic bottleneck at transmission was wide. Journal of Infectious Diseases, 210(10):1555-1561.

Braun, D L; Rauch, A; Durisch, N; Eberhard, N; Anagnostopoulos, A; Ledergerber, B; Metzner, K J; Böni, J; Weber, R; Fehr, J (2014). Efficacy of lead-in silibinin and subsequent triple therapy in difficult-to-treat HIV/hepatitis C virus-coinfected patients. HIV Medicine, 15(10):625-630.

Brandenberg, O F. Mechanisms of HIV Entry and Neutralization. 2014, University of Zurich, Faculty of Medicine.

Wyrzucki, A; Dreyfus, C; Kohler, I; Steck, M; Wilson, I A; Hangartner, L (2014). Alternative Recognition of the Conserved Stem Epitope in Influenza A Virus Hemagglutinin by a VH3-30-Encoded Heterosubtypic Antibody. Journal of Virology, 88(12):7083-7092.

Avila, Dorita; Keiser, Olivia; Egger, Matthias; Kouyos, Roger; Böni, Juerg; Yerly, Sabine; Klimkait, Thomas; Vernazza, Pietro L; Aubert, Vincent; Rauch, Andri; Bonhoeffer, Sebastian; Guenthard, Huldrych F; Stadler, Tanja; Spycher, Ben D (2014). Social Meets Molecular: Combining Phylogenetic and Latent Class Analyses to Understand HIV-1 Transmission in Switzerland. American Journal of Epidemiology, 179(12):1514-1525.

Vetter, B N; Shah, C; Huder, J B; Böni, J; Schüpbach, J (2014). Use of reverse-transcriptase-based HIV-1 viral load assessment to confirm low viral loads in newly diagnosed patients in Switzerland. BMC Infectious Diseases, 14:84.

Swenson, L C; Cobb, B; Geretti, A M; et al; Böni, J (2014). Comparative Performances of HIV-1 RNA Load Assays at Low Viral Load Levels: Results of an International Collaboration. Journal of Clinical Microbiology, 52(2):517-523.

Schuurmans, M M; Isenring, B D; Jungo, C; Boeni, J; Mueller, N J; Kohler, M; Benden, C (2014). Clinical features and outcomes of influenza infections in lung transplant recipients: a single-season cohort study. Transplant Infectious Disease, 16(3):430-439.

Kouyos, Roger D; Rauch, Andri; Böni, Jürg; Yerly, Sabine; Shah, Cyril; Aubert, Vincent; Klimkait, Thomas; Kovari, Helen; Calmy, Alexandra; Cavassini, Matthias; Battegay, Manuel; Vernazza, Pietro L; Bernasconi, Enos; Ledergerber, Bruno; Gunthard, Huldrych F (2014). Clustering of HCV coinfections on HIV phylogeny indicates domestic and sexual transmission of HCV. International Journal of Epidemiology, 43(3):887-896.

Boenzli, Eva; Hadorn, Maik; Hartnack, Sonja; Huder, Jon; Hofmann-Lehmann, Regina; Lutz, Hans (2014). Detection of antibodies to the feline leukemia Virus (FeLV) transmembrane protein p15E: an alternative approach for serological FeLV detection based on antibodies to p15E. Journal of Clinical Microbiology, 52(6):2046-2052.

Schüpbach, Jörg; Berger, Christoph; Böni, Jürg; Speck, Roberto F (2014). HIV-Diagnostik in der Schweiz und ärztlicher Abklärungsgang von HIV-Infizierten. Therapeutische Umschau. Revue thérapeutique, 71(8):451-460.

Brandenberg, Oliver F; Rusert, Peter; Magnus, Carsten; Weber, Jacqueline; Böni, Jürg; Günthard, Huldrych F; Regoes, Roland R; Trkola, Alexandra (2014). Partial rescue of V1V2 mutant infectivity by HIV-1 cell-cell transmission supports the domain’s exceptional capacity for sequence variation. Retrovirology, 11:75.

Pohl, M O; Edinger, T O; Stertz, S (2014). Prolidase is required for early trafficking events during influenza a virus entry. Journal of Virology, 88(19):11271-11283.

Drescher, Sara M; von Wyl, Viktor; Yang, Wan-Lin; Böni, Jürg; Yerly, Sabine; Shah, Cyril; Aubert, Vincent; Klimkait, Thomas; Taffé, Patrick; Furrer, Hansjakob; Battegay, Manuel; Ambrosioni, Juan; Cavassini, Matthias; Bernasconi, Enos; Vernazza, Pietro L; Ledergerber, Bruno; Günthard, Huldrych F; Kouyos, Roger D (2014). Treatment-Naive individuals are the major source of transmitted HIV-1 drug resistance in men who have sex with men in the Swiss HIV Cohort Study. Clinical Infectious Diseases, 58(2):285-294.

2013

Magnus, Carsten; Brandenberg, Oliver F; Rusert, Peter; Trkola, Alexandra; Regoes, Roland Robert (2013). Mathematical models: a key to understanding HIV envelope interactions? Journal of Immunological Methods, 398-399:1-18.

Schüpbach, J (2013). Das schweizerische HIV Testkonzept – eine aktualisierte Übersicht. Bulletin Bundesamt für Gesundheit:6-14.

Huber, Michael; Böni, Jürg; Trkola, Alexandra (2013). Molekulare virologische Diagnostik im Wandel: Next Generation Sequencing auf dem Weg in die diagnostische Routine? Pipette, 5:15-17.

Schüpbach, J; Gebhardt, M D; Scherrer, A U; Bisset, L R; Niederhauser, C; Regenass, S; Yerly, S; Aubert, V; Suter, F; Pfister, S; Martinetti, G; Andreutti, C; Klimkait, T; Brandenberger, M; Gunthard, H F (2013). Simple estimation of incident HIV infection rates in notification cohorts based on window periods of algorithms for evaluation of line-immunoassay result patterns. PLoS ONE, 8(8):e71662.

Lohrmann, F; Dijkman, R; Stertz, S; Thiel, V; Haller, O; Staeheli, P; Kochs, G (2013). Emergence of a C-terminal seve 1 n amino acid elongation of NS1 around 1950 2 conferred a minor growth advantage to former seasonal influenza A viruses. Journal of Virology, 87(20):11300-11303.

Medina, R A; Stertz, S; Manicassamy, B; Zimmermann, P; Sun, X; Albrecht, R A; Uusi-Kerttula, H; Zagordi, O; Belshe, R B; Frey, S E; Tumpey, T M; García-Sastre, A (2013). Glycosylations in the globular head of the hemagglutinin protein modulate the virulence and antigenic properties of the H1N1 influenza viruses. Science Translational Medicine, 5(187):187ra70.

Alamares-Sapuay, J G; Martinez-Gil, L; Stertz, S; Miller, M S; Shaw, M L; Palese, P (2013). Serum- and glucocorticoid-regulated kinase 1 is required for nuclear export of the ribonucleoprotein of influenza A virus. Journal of Virology, 87(10):6020-6026.

Hoot, Sam; McGuire, Andrew T; Cohen, Kristen W; Strong, Roland K; Hangartner, Lars; Klein, Florian; Diskin, Ron; Scheid, Johannes F; Sather, D Noah; Burton, Dennis R; Stamatatos, Leonidas (2013). Recombinant HIV Envelope Proteins Fail to Engage Germline Versions of Anti-CD4bs bNAbs. PLoS Pathogens, 9(1):e003106.

Wyrzucki, Arkadiusz. Characterization of influenza a neutralizing, heterosubtypic antibodies isolated with a newly developed antigen. 2013, University of Zurich, Faculty of Science.

Edinger, T O; Pohl, M O; Stertz, S (2013). Entry of influenza A virus: host factors and antiviral targets. Journal of General Virology, 95:263-277.

Kohler, Ines. Prevalence and predictors for homo - and heterosubtypic antibodies against influenza a virus. 2013, University of Zurich, Faculty of Science.

2012

Ota, Takayuki; Doyle-Cooper, Colleen; Cooper, Anthony B; Huber, Michael; Falkowska, Emilia; Doores, Katherine J; Hangartner, Lars; Le, Khoa; Sok, Devin; Jardine, Joseph; Lifson, Jeffrey; Wu, Xueling; Mascola, John R; Poignard, Pascal; Binley, James M; Chakrabarti, Bimal K; Schief, William R; Wyatt, Richard T; Burton, Dennis R; Nemazee, David (2012). Anti-HIV B cell lines as candidate vaccine biosensors. Journal of Immunology, 189:4816-4824.

Schüpbach, J; Bisset, L R; Gebhardt, M D; Regenass, S; Bürgisser, P; Gorgievski, M; Klimkait, T; Andreutti, C; Martinetti, G; Niederhauser, C; Yerly, S; Pfister, S; Schultze, D;