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; ... (2022). A systematic molecular epidemiology screen reveals numerous HIV-1 superinfections in the Swiss HIV Cohort Study. The journal of infectious diseases, 226(7), pp. 1256-1266. Oxford University Press 10.1093/infdis/jiac166
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BACKGROUND
Studying 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 4,575 SHCS participants with longitudinal sequences. A subset of potential superinfections was tested by near-full-length viral genome sequencing (NFVGS) of bio-banked plasma samples.
RESULTS
Based on phylogenetic and distance criteria, 325 potential HIV-1 superinfections were identified and categorised by their likelihood of being detected as superinfection due to sample misidentification. NFVGS was performed for 128 potential superinfections: Of these, fifty-two were confirmed by NFVGS, 15 were not confirmed, and for 61 sampling did not allow for 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 52/67 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.
Item Type: |
Journal Article (Original Article) |
|---|---|
Division/Institute: |
04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Infectiology 04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases |
UniBE Contributor: |
Ramette, Alban Nicolas, Rauch, Andri |
Subjects: |
600 Technology > 610 Medicine & health 500 Science > 570 Life sciences; biology |
ISSN: |
1537-6613 |
Publisher: |
Oxford University Press |
Language: |
English |
Submitter: |
Pubmed Import |
Date Deposited: |
02 May 2022 08:01 |
Last Modified: |
02 May 2023 00:25 |
Publisher DOI: |
10.1093/infdis/jiac166 |
PubMed ID: |
35485458 |
Uncontrolled Keywords: |
HIV-1 Superinfection Molecular Epidemiology Screening Phylogenetics |
BORIS DOI: |
10.48350/169641 |
URI: |
https://boris.unibe.ch/id/eprint/169641 |
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