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2023

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.

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.

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.

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.

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.

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.

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.

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: Blenheim Chalcot Company.

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; Brandenberger, M; Schöni-Affolter, F; Scherrer, A U; Gunthard, H F (2012). Diagnostic performance of line-immunoassay based algorithms for incident HIV-1 infection. BMC Infectious Diseases, 12(88):1471-2334.

Reynell, Lucie; Trkola, Alexandra (2012). HIV vaccines: an attainable goal? Swiss Medical Weekly, 142:online.

Abela, Irene A; Berlinger, Livia; Schanz, Merle; Reynell, Lucy; Günthard, Huldrych F; Rusert, Peter; Trkola, Alexandra (2012). Cell-cell transmission enables HIV-1 to evade inhibition by potent CD4bs directed antibodies. PLoS Pathogens, 8(4):e1002634.

Mann, Axel M. HIV entry and its inhibition. 2012, University of Zurich, Faculty of Science.

Mekker, Andrea; Tchang, Vincent S; Haeberli, Lea; Oxenius, Annette; Trkola, Alexandra; Karrer, Urs (2012). Immune senescence: relative contributions of age and cytomegalovirus infection. PLoS Pathogens, 8(8):e1002850.

von Wyl, V; Yerly, S; Böni, J; Shah, C; Cellerai, C; Klimkait, T; Battegay, M; Bernasconi, E; Cavassini, M; Furrer, H; Hirschel, B; Vernazza, P L; Ledergerber, B; Günthard, H F (2012). Incidence of HIV-1 drug resistance among antiretroviral treatment-naive individuals starting modern therapy combinations. Clinical Infectious Diseases, 54(1):131-140.

Leventhal, Gabriel E; Kouyos, Roger; Stadler, Tanja; von Wyl, Viktor; Yerly, Sabine; Böni, Jürg; Cellerai, Cristina; Klimkait, Thomas; Günthard, Huldrych F; Bonhoeffer, Sebastian (2012). Inferring epidemic contact structure from phylogenetic trees. PLoS Computational Biology, 8(3):e1002413.

Scherrer, Alexandra U; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Furrer, Hansjakob; Calmy, Alexandra; Cavassini, Matthias; Elzi, Luigia; Vernazza, Pietro L; Bernasconi, Enos; Ledergerber, Bruno; Günthard, Huldrych F (2012). Long-Lasting Protection of Activity of Nucleoside Reverse Transcriptase Inhibitors and Protease Inhibitors (PIs) by Boosted PI Containing Regimens. PLoS ONE, 7(11):e50307.

Scherrer, Alexandra U; Ledergerber, Bruno; von Wyl, Viktor; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Cellerai, Cristina; Furrer, Hansjakob; Calmy, Alexandra; Cavassini, Matthias; Elzi, Luigia; Vernazza, Pietro L; Bernasconi, Enos; Günthard, Huldrych F (2012). Minor protease inhibitor mutations at baseline do not increase the risk for a virological failure in HIV-1 subtype B infected patients. PLoS ONE, 7(6):e37983.

Scherrer, A U; von Wyl, V; Götte, M; Klimkait, T; Cellerai, C; Yerly, S; Böni, J; Held, L; Ledergerber, B; Günthard, H F (2012). Polymorphic mutations associated with the emergence of the multi-nucleoside/tide resistance mutations 69 insertion and Q151M. Journal of Acquired Immune Deficiency Syndromes, 59(2):105-112.

Ludersdorfer, Thomas. Rack1 is required for interferon induced expression of secondary response genes and influenza a virus entry. 2012, University of Zurich, Faculty of Science.

Althaus, Claudia F; Vongrad, Valentina; Niederöst, Barbara; Joos, Beda; Di Giallonardo, Francesca; Rieder, Philip; Pavlovic, Jovan; Trkola, Alexandra; Günthard, Huldrych F; Metzner, Karin J; Fischer, Marek (2012). Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells. Retrovirology, 9:27.

Abela, Irene A. The role of neutralizing antibodies in inhibition of cell-cell transmission. 2012, University of Zurich, Faculty of Science.

2011

Riedel, T; Ghasparian, A; Moehle, K; Rusert, P; Trkola, A; Robinson, J A (2011). Synthetic virus-like particles and conformationally constrained peptidomimetics in vaccine design. ChemBioChem, 12(18):2829-2836.

Wisskirchen, C; Ludersdorfer, T H; Müller, D A; Moritz, E; Pavlovic, J (2011). Interferon-induced antiviral protein MxA interacts with the cellular RNA helicases UAP56 and URH49. Journal of Biological Chemistry, 286(40):34743-34751.

Damond, F; Benard, A; Balotta, C; Böni, J; Cotten, M; Duque, V; Ferns, B; Garson, J; Gomes, P; Gonçalves, F; Gottlieb, G; Kupfer, B; Ruelle, J; Rodes, B; Soriano, V; Wainberg, M; Taieb, A; Matheron, S; Chene, G; Brun-Vezinet, F (2011). An international collaboration to standardize HIV-2 viral load assays: results from the 2009 ACHI(E)V(2E) quality control study. Journal of Clinical Microbiology, 49(10):3491-3497.

Wisskirchen, C; Ludersdorfer, T H; Müller, D A; Moritz, E; Pavlovic, J (2011). The cellular RNA helicase UAP56 is required for prevention of double-stranded RNA formation during influenza A virus infection. Journal of Virology, 85(17):8646-8655.

Kouyos, R D; von Wyl, V; Yerly, S; Böni, J; Rieder, P; Joos, B; Taffé, P; Shah, C; Bürgisser, P; Klimkait, T; Weber, R; Hirschel, B; Cavassini, M; Rauch, A; Battegay, M; Vernazza, P L; Bernasconi, E; Ledergerber, B; Bonhoeffer, S; Günthard, H F (2011). Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection. Clinical Infectious Diseases, 52(4):532-539.

Oufir, M; Bisset, L R; Hoffmann, S R K; Xue, G; Klauser, S; Bergamaschi, B; Gervaix, A; Böni, J; Schüpbach, J; Gutte, B (2011). Artificial 64-residue HIV-1 enhancer-binding peptide is a potent inhibitor of viral replication in HIV-1-infected cells. Advances in Virology, 2011:165871.

Kouyos, R D; von Wyl, V; Hinkley, T; Petropoulos, C J; Haddad, M; Whitcomb, J M; Böni, J; Yerly, S; Cellerai, C; Klimkait, T; Günthard, H F; Bonhoeffer, S (2011). Assessing predicted HIV-1 replicative capacity in a clinical setting. PLoS Pathogens, 7(11):e1002321.

Wunderli, W; Meerbach, A; Güngör, Tayfun; Berger, C; Greiner, O; Caduff, R; Trkola, A; Bossart, W; Gerlach, D; Schibler, M; Cordey, S; McKee, T A; Van Belle, S; Kaiser, L; Tapparel, C (2011). Astrovirus infection in hospitalized infants with severe combined immunodeficiency after allogeneic hematopoietic stem cell transplantation. PLoS ONE, 6(11):e27483.

Rieder, P; Joos, B; Scherrer, A U; Kuster, H; Braun, D; Grube, C; Niederöst, B; Leemann, C; Gianella, S; Metzner, K J; Böni, J; Weber, R; Günthard, H F (2011). Characterization of human immunodeficiency virus type 1 (HIV-1) diversity and tropism in 145 patients with primary HIV-1 infection. Clinical Infectious Diseases, 53(12):1271-1279.

Mekker, A. Cytomegalovirus infection and immune senescence: an example of collateral damage. 2011, University of Zurich, Faculty of Science.

Young, J; Scherrer, A; Günthard, H; Opravil, M; Yerly, S; Böni, J; Rickenbach, M; Fux, C; Cavassini, M; Bernasconi, E; Vernazza, P; Hirschel, B; Battegay, M; Bucher, H (2011). Efficacy, tolerability and risk factors for virological failure of darunavir-based therapy for treatment-experienced HIV-infected patients: the Swiss HIV Cohort Study. HIV Medicine, 12(5):299-307.

Schüpbach, J; Bisset, L R; Regenass, S; Bürgisser, P; Gorgievski, M; Steffen, I; Andreutti, C; Martinetti, G; Shah, C; Yerly, S; Klimkait, T; Gebhardt, M; Schöni-Affolter, F; Rickenbach, M (2011). High specificity of line-immunoassay based algorithms for recent HIV-1 infection independent of viral subtype and stage of disease. BMC Infectious Diseases, 11(1):254.

Scherrer, A U; Ledergerber, B; von Wyl, V; Böni, J; Yerly, S; Klimkait, T; Bürgisser, P; Rauch, A; Hirschel, B; Cavassini, M; Elzi, L; Vernazza, P L; Bernasconi, E; Held, L; Günthard, H F (2011). Improved virological outcome in white patients infected with HIV-1 non-B subtypes compared to subtype B. Clinical Infectious Diseases, 53(11):1143-1152.

Rusert, P; Krarup, A; Magnus, C; Brandenberg, O F; Weber, J; Ehlert, A K; Regoes, R R; Günthard, H F; Trkola, A (2011). Interaction of the gp120 V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies. Journal of Experimental Medicine, 208(7):1419-1433.

Althaus, Claudia. Interplay between HIV-1 transcription and the pathways of intracellular innate defense. 2011, University of Zurich, Faculty of Science.

Ruprecht, C R; Krarup, A; Reynell, L; Mann, A M; Brandenberg, O F; Berlinger, L; Abela, I A; Regoes, R R; Günthard, H F; Rusert, P; Trkola, A (2011). MPER-specific antibodies induce gp120 shedding and irreversibly neutralize HIV-1. Journal of Experimental Medicine, 208(3):439-454.

Bansal, V; Metzner, K J; Niederost, B; Leemann, C; Böni, J; Gunthard, H F; Fehr, J S (2011). Minority K65R variants and early failure of antiretroviral therapy in HIV-1-infected Eritrean Immigrant. Emerging Infectious Diseases, 17(10):1966-1968.

Scherrer, A U; von Wyl, V; Joos, B; Klimkait, T; Bürgisser, P; Yerly, S; Böni, J; Ledergerber, B; Günthard, H F (2011). Predictors for the emergence of the 2 multi-nucleoside/nucleotide resistance mutations 69 insertion and Q151M and their impact on clinical outcome in the Swiss HIV cohort study. Journal of Infectious Diseases, 203(6):791-797.

Rieder, Philip. Primary HIV-1 infection in Zurich: molecular studies of transmission biology and epidemiology. 2011, University of Zurich, Faculty of Science.

Fehr, J; Glass, T R; Louvel, S; Hamy, F; Hirsch, H H; von Wyl, V; Böni, J; Yerly, S; Bürgisser, P; Cavassini, M; Fux, C A; Hirschel, B; Vernazza, P; Martinetti, G; Bernasconi, E; Günthard, H F; Battegay, M; Bucher, H C; Klimkait, T (2011). Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals--the Swiss HIV Cohort Study. Journal of Translational Medicine, 9:14.

Wisskirchen, Christian. The cellular RNA helicase UAP56 links influenza A virus replication and the antiviral activity of Mx-proteins. 2011, University of Zurich, Faculty of Science.

von Wyl, V; Kouyos, R D; Yerly, S; Böni, J; Shah, C; Bürgisser, P; Klimkait, T; Weber, R; Hirschel, B; Cavassini, M; Staehelin, C; Battegay, M; Vernazza, P L; Bernasconi, E; Ledergerber, B; Bonhoeffer, S; Günthard, H F (2011). The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland. Journal of Infectious Diseases, 204(7):1095-1103.

Scherrer, A U; von Wyl, V; Böni, J; Yerly, S; Klimkait, T; Bürgisser, P; Garzoni, C; Hirschel, B; Cavassini, M; Battegay, M; Vernazza, P L; Bernasconi, E; Ledergerber, B; Günthard, H F (2011). Viral suppression rates in salvage treatment with raltegravir improved with the administration of genotypic partially active or inactive nucleoside/tide reverse transcriptase inhibitors. JAIDS Journal of Acquired Immune Deficiency Syndromes, 57(1):24-31.

2010

Dorner, M; Zucol, F; Alessi, D; Haerle, S K; Bossart, W; Weber, M; Byland, R; Bernasconi, M; Berger, C; Tugizov, S; Speck, R F; Nadal, D (2010). {beta}1 Integrin Expression Increases Susceptibility of Memory B-Cells to EBV Infection. Journal of Virology, 84(13):6667-6677.

Fritz, R D; Varga, Z; Radziwill, G (2010). CNK1 is a novel Akt interaction partner that promotes cell proliferation through the Akt-FoxO signalling axis. Oncogene, 29(24):3575-3582.

Simova-Curd, Stefka A; Huder, J B; Boeni, J; Robert, N; Hatt, Jean-Michel (2010). Investigations on the diagnosis and retroviral aetiology of renal neoplasia in budgerigars (Melopsittacus undulatus). Avian Pathology, 39(3):161-167.

Kwok, T; Helfer, H; Alam, M I; Heinrich, J; Pavlovic, J; Moelling, K (2010). Inhibition of influenza A virus replication by short double-stranded oligodeoxynucleotides. Archives of Virology, 154(1):109-14.

Lutz, Hans; Hunsmann, Gerhard; Schüpbach, Jörg (2010). Transmission and epidemiology (chapter 8). In: Bannert, Norbert; Kurth, Reinhard. Retroviruses: Molecular Biology, Genomics and Pathogenesis. Norfolk, UK: Caister Academic Press, 217-236.

Joos, B; Rieder, P; Fischer, M; Kuster, H; Rusert, P; Trkola, A; Pillai, S K; Wong, J K; Weber, R; Günthard, H F (2010). Association between specific HIV-1 Env traits and virologic control in vivo. Infection, Genetics and Evolution, 10(3):365-372.

Schüpbach, Jörg (2010). Die vier Fragen der HIV-Diagnostik. Leading Opinions. Infektiologie, 1(1):15-17.

Pugach, P; Krarup, A; Gettie, A; Kuroda, M; Blanchard, J; Piatak Jr, M; Lifson, J D; Trkola, A; Robbiani, M (2010). In vivo binding and retention of CD4-specific DARPin 57.2 in macaques. PLoS ONE, 5(8):e12455.

Berlinger, L. The impact of neutralizing antibodies on HIV-1 attachment and entry. 2010, ETHZ, Faculty of Science.

Abela, I A; Reynell, L; Trkola, A (2010). Therapeutic antibodies in HIV treatment - classical approaches to novel advances. Current Pharmaceutical Design, 16(33):3754-3766.

Mofenson, Lynne M; Sherman, Gayle; Penazzato, Martina; de Baets, Anniek; Schüpbach, Jörg; Ramos, Artur; Fiscus, Susan; Crowley, Siobhan; Vercauteren, Gaby; Sands, Anita; Perez González, Mercedes; Malhotra, Bandana; Yerrakalva, Dharani; Anagbo, Victoria; Girvin, Sally; Kirkwood, John (2010). WHO recommendations on the diagnosis of HIV infection in infants and children. Geneva: World Health Organisation (WHO), Department of HIV/AIDS.

2009

Clerc, O; Cavassini, M; Böni, J; Schüpbach, J; Bürgisser, P (2009). Prolonged seroconversion in an elite controller of HIV-1 infection. Journal of Clinical Virology, 46(4):371-373.

Hessell, A J; Poignard, P; Hunter, M; Hangartner, L; Tehrani, D M; Bleeker, W K; Parren, P W H I; Marx, P A; Burton, D R (2009). Effective, low-titer antibody protection against low-dose repeated mucosal SHIV challenge in macaques. Nature Medicine, 15(8):951-954.

Gaspert, A; Lüthi, B; Mueller, N J; Bossart, W; Heim, A; Wüthrich, R P; Fehr, T (2009). Subacute allograft failure with dysuria and hematuria in a kidney transplant recipient. American Journal of Kidney Diseases, 54(1):154-158.

Magnus, C; Rusert, P; Bonhoeffer, S; Trkola, A; Regoes, R R (2009). Estimating the stoichiometry of HIV entry. Journal of Virology, 83(3):1523-1531.

Geuking, M B; Weber, J; Dewannieux, M; Gorelik, E; Heidmann, T; Hengartner, H; Zinkernagel, R M; Hangartner, L (2009). Recombination of retrotransposon and exogenous RNA virus results in nonretroviral cDNA integration. Science, 323(5912):393-396.

Müller, V; von Wyl, V; Yerly, S; Böni, J; Klimkait, T; Bürgisser, P; Ledergerber, B; Günthard, H F; Bonhoeffer, S (2009). African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study. AIDS, 23(10):1269-1276.

Hessell, A J; Rakasz, E G; Poignard, P; Hangartner, L; Landucci, G; Forthal, D N; Koff, W C; Watkins, D I; Burton, D R (2009). Broadly neutralizing human anti-HIV antibody 2G12 is effective in protection against mucosal SHIV challenge even at low serum neutralizing titers. PLoS Pathogens, 5(5):e1000433.

Schüpbach, Jörg (2009). Chapter 32 Human Retroviruses, HIV and HTLV. In: Specter, Steven; Hodinka, R L; Young, S A; Wiedbrauk, D L. Clinical Virology Manual. Washington D.C.: ASM Press, American Society for Microbiology, 578-629.

Rusert, P; Mann, A; Huber, M; von Wyl, V; Gunthard, H F; Trkola, A (2009). Divergent effects of cell environment on HIV entry inhibitor activity. AIDS, 23(11):1319-1327.

Mann, A M; Rusert, P; Berlinger, L; Kuster, H; Günthard, H F; Trkola, A (2009). HIV sensitivity to neutralization is determined by target and virus producer cell properties. AIDS, 23(13):1659-1667.

Günthard, H F; Huber, M; Kuster, H; Shah, C; Schüpbach, J; Trkola, A; Böni, J (2009). HIV-1 superinfection in an HIV-2-infected woman with subsequent control of HIV-1 plasma viremia. Clinical Infectious Diseases, 48(11):e117-e120.

Ghielmetti, M; Millard, A L; Haeberli, L; Bossart, W; Seebach, J D; Schneider, M K J; Mueller, N J (2009). Human CMV infection of porcine endothelial cells increases adhesion receptor expression and human leukocyte recruitment. Transplantation, 87(12):1792-1800.

von Wyl, V; Yerli, S; Böni, J; Bürgisser, P; Klimkait, T; Battegay, M; Bernasconi, E; Cavassini, M; Furrer, H; Hirschel, B; Vernazza, P; Francioli, P; Bonhoeffer, S; Ledergerber, B; Günthard, H (2009). Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland. Clinical Infectious Diseases, 48(7):979-987.

Scherrer, A U; Hasse, B; von Wyl, V; Yerly, S; Böni, J; Bürgisser, P; Klimkait, T; Bucher, H C; Ledergerber, B; Günthard, H F (2009). Prevalence of etravirine mutations and impact on response to treatment in routine clinical care: the Swiss HIV Cohort Study (SHCS). HIV Medicine, 10(10):647-656.

2008

Daneel, S; Schüpbach, J; Gebhardt, M; Werner, M; Staub, R; Vernazza, P (2008). A prospective evaluation of the feasibility and utility of additional tools to obtain information from recently diagnosed HIV infected patients. Swiss Medical Weekly, 138(31-32):453-458.

Erikstrup, C; Kallestrup, P; Zinyama-Gutsire, R B L; Gomo, E; Lüneborg-Nielsen, M; Gerstoft, J; Schüpbach, J; Ullum, H; Katzenstein, T L (2008). p24 as a predictor of mortality in a cohort of HIV-1-infected adults in rural Africa. JAIDS Journal of Acquired Immune Deficiency Syndromes, 48(3):345-349.

Schüpbach, Jörg (2008). HIV/AIDS: Erfolge, Misserfolge und neue Ziele der Forschung. BioFokus, 18(77):1-11.

Damond, F; Benard, A; Ruelle, J; Alabi, A; Kupfer, B; Gomes, P; Rodes, B; Albert, J; Böni, J; Garson, J; Ferns, B; Matheron, S; Chene, G; Brun-Vezinet, F (2008). Quality control assessment of human immunodeficiency virus type 2 (HIV-2) viral load quantification assays: results from an international collaboration on HIV-2 infection in 2006. Journal of Clinical Microbiology, 46(6):2088-2091.

HIV Cohort Study, Switzerland; von Wyl, V; Yerly, S; Klimkait, T; Böni, J; Bürgisser, P; Battegay, M; Bernasconi, E; Cavassini, M; Furrer, H; Hirschel, B; Vernazza, P L; Rickenbach, M; Ledergerber, B; Guenthard, H F (2008). Factors associated with the emergence of K65R in patients with HIV-1 infection treated with combination antiretroviral therapy containing tenofovir. Clinical Infectious Diseases, 46:1299-1309.

Meerbach, A; Wutzler, P; Haefer, R; Zintl, F; Gruhn, B (2008). Monitoring of Epstein-Barr virus load after hematopoietic stem cell transplantation for early intervention in post-transplant lymphoproliferative disease. Journal of Medical Virology, 80(3):441-454.

Joos, B; Fischer, M; Kuster, H; Pillai, S K; Wong, J K; Böni, J; Hirschel, B; Weber, R; Trkola, A; Günthard, H F (2008). HIV rebounds from latently infected cells, rather than from continuing low-level replication. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 105(43):16725-16730.

2007

Schüpbach, J; Gebhardt, M D; Tomasik, Z; Niederhauser, C; Yerly, S; Bürgisser, P; Matter, L; Gorgievski, M; Dubs, R; Schultze, D; Steffen, I; Andreutti, C; Martinetti, G; Güntert, B; Staub, R; Daneel, S; Vernazza, P (2007). Assessment of recent HIV-1 infection by a line immunoassay for HIV-1/2 confirmation. PLoS Medicine, 4(12):e343.

Yerly, S; von Wyl, V; Ledergerber, B; Böni, J; Schüpbach, J; Bürgisser, P; Klimkait, T; Rickenbach, M; Kaiser, L; Günthard, H F; Perrin, L (2007). Transmission of HIV-1 drug resistance in Switzerland: a 10-year molecular epidemiology survey. AIDS, 21(16):2223-2229.

von Wyl, V; Yerly, S; Böni, J; Bürgisser, P; Klimkait, T; Battegay, M; Furrer, H; Telenti, A; Hirschel, B; Vernazza, P L; Bernasconi, E; Rickenbach, M; Perrin, L; Ledergerber, B; Günthard, H F; Swiss HIV Cohort Study (2007). Emergence of HIV-1 drug resistance in previously untreated patients initiating combination antiretroviral treatment: a comparison of different regimen types. Archives of Internal Medicine, 167(16):1782-1790.

Hessell, A J; Hangartner, L; Hunter, M; Havenith, C E G; Beurskens, F J; Bakker, J M; Lanigan, C M S; Landucci, G; Forthal, D N; Parren, P W H I; Marx, P A; Burton, D R (2007). Fc receptor but not complement binding is important in antibody protection against HIV. Nature, 449(7158):101-104.

Joos, B; Fischer, M; Schweizer, A; Kuster, H; Böni, J; Wong, J K; Weber, R; Trkola, A; Gunthard, H F (2007). Positive in vivo selection of the HIV-1 envelope protein gp120 occurs at surface-exposed regions. Journal of Infectious Diseases, 196(2):313-320.

Knuchel, M C; Jullu, B; Shah, C; Tomasik, Z; Stoeckle, M P; Speck, R F; Nadal, D; Mshinda, H; Böni, J; Tanner, M; Schüpbach, J (2007). Adaptation of the Ultrasensitive HIV-1 p24 Antigen Assay to Dried Blood Spot Testing. Journal of Acquired Immune Deficiency Syndromes, 44(3):247-253.

Bisset, L R; Böni, J; Lutz, H; Schüpbach, J (2007). Lack of evidence for PERV expression after apoptosis-mediated horizontal gene transfer between porcine and human cells. Xenotransplantation, 14(1):13-24.

Torres, J R; Torres-Viera, M A; Schupbach, J; Rangel, H R; Pujol, F H (2007). Non-immune thrombocytopenia responsive to antiretroviral therapy and HIV-2 infection. Journal of Infection, 54(1):e21-e24.

Sendi, P; Günthard, H F; Simcock, M; Ledergerber, B; Schüpbach, J; Battegay, M (2007). Cost-Effectiveness of Genotypic Antiretroviral Resistance Testing in HIV-Infected Patients with Treatment Failure. PLoS ONE, 2(1):e173.

Lötscher, M; Recher, M; Lang, K S; Navarini, A; Hunziker, L; Santimaria, R; Glatzel, M; Schwarz, P; Böni, J; Zinkernagel, R M (2007). Induced prion protein controls immune-activated retroviruses in the mouse spleen. PLoS ONE, 2(11):e1158.

2006

Tehe, A; Maurice, C; Hanson, D L; Borget, M Y; Abiola, N; Maran, M; Yavo, D; Tomasik, Z; Böni, J; Schüpbach, J; Nkengasong, J N (2006). Quantification of HIV-1 p24 by a highly improved ELISA: An alternative to HIV-1 RNA based treatment monitoring in patients from Abidjan, Côte d'Ivoire. Journal of Clinical Virology, 37(3):199-205.

Schüpbach, J; Tomasik, Z; Knuchel, M C; Opravil, M; Günthard, H F; Nadal, D; Böni, J (2006). Optimized virus disruption improves detection of HIV-1 p24 in particles and uncovers a p24 reactivity in patients with undetectable HIV-1 RNA under long-term HAART. Journal of Medical Virology, 78(8):1003-1010.

Böni, J; Schüpbach, J; Rickenbach, M (2006). Rabbit retrotransposon sequences undetectable in blood donors and lymphoma patients of the Swiss HIV Cohort Study. AIDS Research and Human Retroviruses, 22(6):499-500.

Seemayer, C A; Böni, J; Steiger, J; Schüpbach, J; Mihatsch, M J (2006). No indication for activation of exogenous retroviruses in patients with renal allograft rejection. Clinical Nephrology, 65(5):324-327.

Knuchel, M C; Tomasik, Z; Speck, R F; Lüthy, R; Schüpbach, J (2006). Ultrasensitive quantitative HIV-1 p24 antigen assay adapted to dried plasma spots to improve treatment monitoring in low-resource settings. Journal of Clinical Virology, 36(1):64-67.

Brinkhof, M W G; Böni, J; Steiner, F; Tomasik, Z; Nadal, D; Schüpbach, J (2006). Evaluation of p24-based antiretroviral treatment monitoring in pediatric HIV-1 infection: prediction of the CD4+ T-cell changes between consecutive visits. JAIDS Journal of Acquired Immune Deficiency Syndromes, 41(5):557-562.

Simcock, M; Sendi, P; Ledergerber, B; Keller, T; Schüpbach, J; Battegay, M; Günthard, H F (2006). A longitudinal analysis of healthcare costs after treatment optimization following genotypic antiretroviral resistance testing: does resistance testing pay off? Antiviral Therapy, 11(3):305-314.

2005

Jennings, Cheryl; Fiscus, Susan A; Crowe, Suzanne M; Danilovic, Aleksandra D; Morack, Ralph J; Scianna, Salvatore; Cachafeiro, Ada; Brambilla, Donald J; Schüpbach, Jörg; Stevens, Wendy; Respess, Richard; Varnier, Oliviero E; Corrigan, Gary E; Gronowitz, J Simon; Ussery, Michael A; Bremer, James W (2005). Comparison of two human immunodeficiency virus (HIV) RNA surrogate assays to the standard HIV RNA assay. Journal of Clinical Microbiology, 43(12):5950-5956.

Schüpbach, J; Günthard, H F; Joos, B; Fischer, M B; Böni, J; Tomasik, Z; Yerly, S; Perrin, L; Battegay, M; Furrer, H; Vernazza, P; Bernasconi, E; Hirschel, B (2005). HIV-1 p24 may persist during long-term highly active antiretroviral therapy, increases little during short treatment breaks, and its rebound after treatment stop correlates with CD4(+) T cell loss. JAIDS Journal of Acquired Immune Deficiency Syndromes, 40(3):250-256.

Aceto, L; Karrer, U; Grube, Ch; Oberholzer, R; Hasse, B; Presterl, E; Böni, J; Kuster, H; Trkola, A; Weber, R; Günthard, H F (2005). Die akute HIV-1-Infektion in Zürich: 2002–2004. Praxis, 94(32):1199-1205.

Joos, B; Trkola, A; Fischer, M; Kuster, H; Rusert, P; Leemann, C; Böni, J; Oxenius, Annette; Price, D A; Phillips, R E; Wong, J K; Hirschel, B; Weber, R; Günthard, Huldrych F (2005). Low human immunodeficiency virus envelope diversity correlates with low in vitro replication capacity and predicts spontaneous control of plasma viremia after treatment interruptions. Journal of Virology, 79(14):9026-9037.

Deichmann, M; Huder, J B; Kleist, C; Näher, H; Schüpbach, J; Böni, J (2005). Detection of reverse transcriptase activity in human melanoma cell lines and identification of a murine leukemia virus contaminant. Archives of Dermatological Research, 296(8):345-352.

Bisset, L R; Schmid-Grendelmeier, P (2005). Chemokines and their receptors in the pathogenesis of allergic asthma: progress and perspective. Current Opinion in Pulmonary Medicine, 11(1):35-42.

2004

Schüpbach, J (2004). SHCS und die Labordiagnostik der HIV-Infektion - von der Entwicklung des HIV Western Blot über die Virusquantifizierung zur klinisch relevanten individuellen Viruscharakterisierung. Therapeutische Umschau, 61(10):603-607.

Hofmann-Lehmann, R; Meli, Marina L; Dreher, U M; Gönczi, E; Deplazes, P; Braun, Ueli; Engels, M; Schüpbach, J; Jörger, K; Thoma, R; Griot, C; Stärk, K D C; Willi, Barbara; Schmidt, J; Kocan, K M; Lutz, H (2004). Concurrent infections with vector-borne pathogens associated with fatal hemolytic anemia in a cattle herd in Switzerland. Journal of Clinical Microbiology, 42(8):3775-3780.

Soldati, G; Lu, Z H; Vaughan, L; Polkinghorne, A; Zimmermann, D R; Huder, J B; Pospischil, A (2004). Detection of mycobacteria and chlamydiae in granulomatous inflammation of reptiles: a retrospective study. Veterinary Pathology, 41(4):388-397.

Shah, C A; Huder, J B; Böni, J; Schönmann, M; Mühlherr, J; Lutz, H; Schüpbach, J (2004). Direct evidence for natural transmission of small-ruminant lentiviruses of subtype A4 from goats to sheep and vice versa. Journal of Virology, 78(14):7518-7522.

Oxenius, Annette; Price, D A; Hersberger, M; Schlaepfer, E; Weber, R; Weber, M; Kundig, T M; Böni, J; Joller, H; Phillips, R E; Flepp, M; Opravil, M; Speck, R F (2004). HIV-specific cellular immune response is inversely correlated with disease progression as defined by decline of CD4+ T cells in relation to HIV RNA load. Journal of Infectious Diseases, 189(7):1199-1208.

Shah, C A; Böni, J; Huder, J B; Vogt, H R; Mühlherr, J; Zanoni, R; Miserez, R; Lutz, H; Schüpbach, J (2004). Phylogenetic analysis and reclassification of caprine and ovine lentiviruses based on 104 new isolates: evidence for regular sheep-to-goat transmission and worldwide propagation through livestock trade. Virology, 319(1):12-26.

Böni, J; Bisset, L R; Burckhardt, J J; Joller-Jemelka, H I; Bürgisser, P; Perrin, L; Gorgievski, M; Erb, P; Fierz, W; Piffaretti, J C; Schüpbach, J (2004). Prevalence of human T-cell leukemia virus types I and II in Switzerland. Journal of Medical Virology, 72(2):328-337.

Böni, J; Shah, C A; Flepp, M; Lüthy, R; Schüpbach, J (2004). Detection of low copy numbers of HIV-1 proviral DNA in patient PBMCs by a high-input, sequence-capture PCR (Mega-PCR). Journal of Medical Virology, 72(1):1-9.

2003

Schüpbach, J (2003). Viral RNA and p24 antigen as markers of HIV disease and antiretroviral treatment success. International Archives of Allergy and Immunology, 132(3):196-209.

Haupts, S; Ledergerber, B; Böni, J; Schüpbach, J; Kronenberg, A; Opravil, M; Flepp, M; Speck, R F; Grube, C; Rentsch, K; Weber, R; Günthard, H F (2003). Impact of genotypic resistance testing on selection of salvage regimen in clinical practice. Antiviral Therapy, 8(5):443-454.

Ribas, S G; Ondoa, P; Schüpbach, J; van der Groen, G; Fransen, K (2003). Performance of a quantitative human immunodeficiency virus type 1 p24 antigen assay on various HIV-1 subtypes for the follow-up of human immunodeficiency type 1 seropositive individuals. Journal of Virological Methods, 113(1):29-34.

Schüpbach, J; Böni, J; Bisset, L R; Tomasik, Z; Fischer, M; Günthard, H F; Ledergerber, B; Opravil, M (2003). HIV-1 p24 antigen is a significant inverse correlate of CD4 T-cell change in patients with suppressed viremia under long-term antiretroviral therapy. JAIDS Journal of Acquired Immune Deficiency Syndromes, 33(3):292-299.

Shah, C A; Böni, J; Bisset, L R; Seebach, J D; Schüpbach, J (2003). Ultra-sensitive and specific detection of porcine endogenous retrovirus (PERV) using a sequence-capture real-time PCR approach. Journal of Virological Methods, 109(2):209-216.

Hasse, B; Hummel, Y; Böni, J; Schüpbach, J; Flepp, M; Günthard, H F (2003). 25-jähriger therapienaiver Patient mit einem dreiklassenresistenten HI-Virus. Praxis, 92(13):601-605.

2002

Sterling, T R; Hoover, D R; Astemborski, J; Vlahov, D; Bartlett, J G; Schüpbach, J (2002). Heat-denatured human immunodeficiency virus type 1 protein 24 antigen: prognostic value in adults with early-stage disease. Journal of Infectious Diseases, 186(8):1181-1185.

Seemayer, C A; Kolb, S A; Neidhart, M; Ohshima, S; Gay, R E; Michel, B A; Gay, S; Böni, J; Schüpbach, J (2002). Absence of inducible retroviruses from synovial fibroblasts and synovial fluid cells of patients with rheumatoid arthritis. Arthritis and Rheumatism, 46(16):2811-2813.

Huder, J B; Böni, J; Hatt, Jean-Michel; Soldati, G; Lutz, Hans; Schüpbach, Jörg (2002). Identification and characterization of two closely related unclassifiable endogenous retroviruses in pythons (Python molurus and Python curtus). Journal of Virology, 76(15):7607-7615.

Bisset, Leslie R; Lutz, Hans; Böni, Jürg; Hofmann-Lehmann, Regina; Lüthy, Ruedi; Schüpbach, Jörg (2002). Combined effect of zidovudine (ZDV), lamivudine (3TC) and abacavir (ABC) antiretroviral therapy in suppressing in vitro FIV replication. Antiviral Research, 53(1):35-45.

Schüpbach, J (2002). Measurement of HIV-1 p24 antigen by signal-amplification-boosted ELISA of heat-denatured plasma is a simple and inexpensive alternative to tests for viral RNA. AIDS Reviews, 4(2):83-92.

2001

Braun, U; Camenzind, D; Meli, M; Böni, J; Ossent, P (2001). Klinische Befunde und diagnostisches Vorgehen bei einem Milchschaf mit Visna. Schweizer Archiv für Tierheilkunde, 143(11):550-553.

Schüpbach, J; Böni, Jürg; Flepp, M; Tomasik, Z; Joller, H; Opravil, M (2001). Antiretroviral treatment monitoring with an improved HIV-1 p24 antigen test: an inexpensive alternative to tests for viral RNA. Journal of Medical Virology, 65(2):225-232.

Bisset, L R; Bosbach, S; Tomasik, Z; Lutz, H; Schüpbach, J; Böni, J (2001). Quantification of in vitro retroviral replication using a one-tube real-time RT-PCR system incorporating direct RNA preparation. Journal of Virological Methods, 91(2):149-155.

Schüpbach, J (2001). Induction/activation and detection of occult viral agents present in mammalian cells. In: Brown, F; Lewis, A M; Peden, K; Krause, P. Evolving Scientific and Regulatory Perspectives on Cell Substrates for Vaccine Development. Basel: Karger, 425-437.

2000

Schüpbach, J; Tomasik, Z; Nadal, D; Ledergerber, B; Flepp, M; Opravil, M; Böni, J (2000). Use of HIV-1 p24 as a sensitive, precise and inexpensive marker for infection, disease progression and treatment failure. International Journal of Antimicrobial Agents, 16(4):441-445.

Fischer, M; Günthard, H F; Opravil, M; Joos, B; Huber, W; Bisset, L R; Ott, P; Böni, J; Weber, R; Cone, R W (2000). Residual HIV-RNA levels persist for up to 2.5 years in peripheral blood mononuclear cells of patients on potent antiretroviral therapy. AIDS Research and Human Retroviruses, 16(12):1135-1140.

Ledergerber, B; Flepp, M; Böni, J; Tomasik, Z; Cone, R W; Lüthy, R; Schüpbach, J (2000). Human immunodeficiency virus type 1 p24 concentration measured by boosted ELISA of heat-denatured plasma correlates with decline in CD4 cells, progression to AIDS, and survival: comparison with viral RNA measurement. Journal of Infectious Diseases, 181(4):1280-1288.

Bürgisser, P; Vernazza, P; Flepp, M; Böni, J; Tomasik, Z; Hummel, U; Pantaleo, G; Schüpbach, J (2000). Performance of five different assays for the quantification of viral load in persons infected with various subtypes of HIV-1. Swiss HIV Cohort Study. JAIDS Journal of Acquired Immune Deficiency Syndromes, 23(2):138-144.

1999

Böni, J; Pyra, H; Gebhardt, M; Perrin, L; Bürgisser, P; Matter, L; Fierz, W; Erb, P; Piffaretti, J C; Minder, E; Grob, P; Burckhardt, J J; Zwahlen, M; Schüpbach, J (1999). High frequency of non-B subtypes in newly diagnosed HIV-1 infections in Switzerland. JAIDS Journal of Acquired Immune Deficiency Syndromes, 22(2):174-179.

Nadal, D; Böni, J; Kind, C; Varnier, O E; Steiner, F; Tomasik, Z; Schüpbach, J (1999). Prospective evaluation of amplification-boosted ELISA for heat-denatured p24 antigen for diagnosis and monitoring of pediatric human immunodeficiency virus type 1 infection. Journal of Infectious Diseases, 180(4):1089-1095.

Leutenegger, Christian M; Klein, D; Hofmann-Lehmann, Regina; Mislin, Caroline N; Hummel, U; Böni, J; Boretti, Felicitas S; Guenzburg, W H; Lutz, Hans (1999). Rapid feline immunodeficiency virus provirus quantitation by polymerase chain reaction using the TaqMan fluorogenic real-time detection system. Journal of Virological Methods, 78(40575):105-116.

Di Paolo, C; Hefti, H P; Meli, M; Landis, H; Pavlovic, J (1999). Intramolecular backfolding of the carboxyl-terminal end of MxA protein is a prerequisite for its oligomerization. Journal of Biological Chemistry, 274(45):32071-32078.

1998

Holznagel, E; Hofmann-Lehmann, R; Leutenegger, C M; Allenspach, K; Huettner, S; Forster, U; Niederer, E; Joller, H; Willett, B J; Hummel, U; Rossi, G L; Schüpbach, J; Lutz, H (1998). The role of in vitro-induced lymphocyte apoptosis in feline immunodeficiency virus infection: correlation with different markers of disease progression. Journal of Virology, 72(11):9025-9033.

Schüpbach, J; Böni, J (1998). Sensitivity of heat-denatured p24 antigen in the diagnosis of pediatric HIV infection. Journal of Acquired Immune Deficiency Syndromes, 18(4):399-400.

Schüpbach, J (1998). Xenotransplantation and viruses - the model of retroviruses. Swiss Medical Weekly, 128(24):935-943.

Kind, C; Rudin, C; Siegrist, C A; Wyler, C A; Biedermann, K; Lauper, U; Irion, O; Schüpbach, J; Nadal, D (1998). Prevention of vertical HIV transmission: additive protective effect of elective Cesarean section and zidovudine prophylaxis. Swiss Neonatal HIV Study Group. AIDS, 12(2):205-210.

1997

Conrad, B; Weissmahr, R N; Böni, J; Arcari, R; Schüpbach, J; Mach, B (1997). A human endogenous retroviral superantigen as candidate autoimmune gene in type I diabetes. Cell, 90(2):303-313.

Böni, J; Opravil, M; Tomasik, Z; Rothen, M; Bisset, L; Grob, P J; Lüthy, R; Schüpbach, J (1997). Simple monitoring of antiretroviral therapy with a signal-amplification-boosted HIV-1 p24 antigen assay with heat-denatured plasma. AIDS, 11(6):F47-F52.

Weissmahr, R N; Schüpbach, J; Böni, J (1997). Reverse transcriptase activity in chicken embryo fibroblast culture supernatants is associated with particles containing endogenous avian retrovirus EAV-0 RNA. Journal of Virology, 71(4):3005-3012.

1996

Schüpbach, J; Flepp, M; Pontelli, D; Tomasik, Z; Lüthy, R; Böni, J (1996). Heat-mediated immune complex dissociation and enzyme-linked immunosorbent assay signal amplification render p24 antigen detection in plasma as sensitive as HIV-1 RNA detection by polymerase chain reaction. AIDS, 10(10):1085-1090.

Jendis, J; Strack, B; Volkmann, S; Böni, J; Mölling, K (1996). Inhibition of replication of fresh HIV type 1 patient isolates by a polypurine tract-specific self-complementary oligodeoxynucleotide. AIDS Research and Human Retroviruses, 12(12):1161-1168.

Schüpbach, J; Pyra, H; Jendis, J; Tomasik, Z; Böni, J (1996). Isolation of an in vitro transmissible agent with reverse transcriptase activity from a blood donor with a borderline-positive HIV-1 serology for more than five years. Clinical and Diagnostic Virology, 5(2-3):197-203.

Schüpbach, J (1996). Licencing of diagnostic HIV kits-to keep a sensible standpoint in an area of permanent revolution. Clinical and Diagnostic Virology, 5(2-3):137-146.

Böni, J; Pyra, H; Schüpbach, J (1996). Sensitive detection and quantification of particle-associated reverse transcriptase in plasma of HIV-1-infected individuals by the product-enhanced reverse transcriptase (PERT) assay. Journal of Medical Virology, 49(1):23-28.

Böni, J; Stalder, J; Reigel, F; Schüpbach, J (1996). Detection of reverse transcriptase activity in live attenuated virus vaccines. Clinical and Diagnostic Virology, 5(1):43-53.

1994

Pyra, H; Böni, J; Schüpbach, J (1994). Ultrasensitive retrovirus detection by a reverse transcriptase assay based on product enhancement. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 91(4):1544-1548.

1993

Böni, J; Schüpbach, J (1993). Sensitive and quantitative detection of PCR-amplified HIV-1 DNA products by an enzyme linked immunoassay following solution hybridization with two differently labelled oligonucleotide probes. Molecular and Cellular Probes, 7(5):361-371.

Böni, J; Emmerich, B S; Leib, S L; Wiestler, O D; Schüpbach, J; Kleihues, P (1993). PCR identification of HIV-1 DNA sequences in brain tissue of patients with AIDS encephalopathy. Neurology, 43(9):1813-1817.

Schüpbach, J; Böni, J (1993). Quantitative and sensitive detection of immune-complexed and free HIV antigen after boiling of serum. Journal of Virological Methods, 43(2):247-256.