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A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study


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.

Abstract

BACKGROUND: Studying human immunodeficiency virus type 1 (HIV-1) superinfection is important to understand virus transmission, disease progression, and vaccine design. But detection remains challenging, with low sampling frequencies and insufficient longitudinal samples.

METHODS: Using the Swiss HIV Cohort Study (SHCS), we developed a molecular epidemiology screening for superinfections. A phylogeny built from 22 243 HIV-1 partial polymerase sequences was used to identify potential superinfections among 4575 SHCS participants with longitudinal sequences. A subset of potential superinfections was tested by near-full-length viral genome sequencing (NFVGS) of biobanked plasma samples.

RESULTS: Based on phylogenetic and distance criteria, 325 potential HIV-1 superinfections were identified and categorized by their likelihood of being detected as superinfections due to sample misidentification. NFVGS was performed for 128 potential superinfections; of these, 52 were confirmed by NFVGS, 15 were not confirmed, and for 61 sampling did not allow confirming or rejecting superinfection because the sequenced samples did not include the relevant time points causing the superinfection signal in the original screen. Thus, NFVGS could support 52 of 67 adequately sampled potential superinfections.

CONCLUSIONS: This cohort-based molecular approach identified, to our knowledge, the largest population of confirmed superinfections, showing that, while rare with a prevalence of 1%-7%, superinfections are not negligible events.

Abstract

BACKGROUND: Studying human immunodeficiency virus type 1 (HIV-1) superinfection is important to understand virus transmission, disease progression, and vaccine design. But detection remains challenging, with low sampling frequencies and insufficient longitudinal samples.

METHODS: Using the Swiss HIV Cohort Study (SHCS), we developed a molecular epidemiology screening for superinfections. A phylogeny built from 22 243 HIV-1 partial polymerase sequences was used to identify potential superinfections among 4575 SHCS participants with longitudinal sequences. A subset of potential superinfections was tested by near-full-length viral genome sequencing (NFVGS) of biobanked plasma samples.

RESULTS: Based on phylogenetic and distance criteria, 325 potential HIV-1 superinfections were identified and categorized by their likelihood of being detected as superinfections due to sample misidentification. NFVGS was performed for 128 potential superinfections; of these, 52 were confirmed by NFVGS, 15 were not confirmed, and for 61 sampling did not allow confirming or rejecting superinfection because the sequenced samples did not include the relevant time points causing the superinfection signal in the original screen. Thus, NFVGS could support 52 of 67 adequately sampled potential superinfections.

CONCLUSIONS: This cohort-based molecular approach identified, to our knowledge, the largest population of confirmed superinfections, showing that, while rare with a prevalence of 1%-7%, superinfections are not negligible events.

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Additional indexing

Contributors:Swiss HIV Cohort Study
Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Institute of Medical Virology
04 Faculty of Medicine > University Hospital Zurich > Clinic for Infectious Diseases
Dewey Decimal Classification:610 Medicine & health
Scopus Subject Areas:Health Sciences > Immunology and Allergy
Health Sciences > Infectious Diseases
Language:English
Date:28 September 2022
Deposited On:17 Nov 2022 12:09
Last Modified:27 Jun 2024 01:41
Publisher:Oxford University Press
ISSN:0022-1899
Additional Information:This is a pre-copy-editing, author-produced PDF of an article accepted for publication in the Journal of Infectious Diseases following peer review. The definitive publisher-authenticated version Sandra E Chaudron, Christine Leemann, Katharina Kusejko, Huyen Nguyen, Nadine Tschumi, Alex Marzel, Michael Huber, Jürg Böni, Matthieu Perreau, Thomas Klimkait, Sabine Yerly, Alban Ramette, Hans H Hirsch, Andri Rauch, Alexandra Calmy, Pietro Vernazza, Enos Bernasconi, Matthias Cavassini, Karin J Metzner, Roger D Kouyos, Huldrych F Günthard, for the Swiss HIV Cohort Study , A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study, The Journal of Infectious Diseases, Volume 226, Issue 7, 1 October 2022, Pages 1256–1266 is available online at: https://doi.org/10.1093/infdis/jiac166.
OA Status:Green
Publisher DOI:https://doi.org/10.1093/infdis/jiac166
PubMed ID:35485458