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Zeeb M, Frischknecht P, Huber M, Schenkel CD, Neumann K, Leeman C, Notter J, Rauch A, Stöckle M, Cavassini M, Bernasconi E, Braun DL, Günthard HF, Metzner KJ, Kouyos RD. Genetic Diversity From Proviral DNA as a Proxy for Time Since HIV-1 Infection. J Infect Dis 2024; 230:e631-e636. [PMID: 38507572 PMCID: PMC11420808 DOI: 10.1093/infdis/jiae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/11/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024] Open
Abstract
HIV-1 RNA genetic diversity predicts time since infection, which is important for clinical care and research. It is unclear, however, whether proviral DNA genetic diversity sampled under suppressive antiretroviral therapy can be used for this purpose. We tested whether proviral genetic diversity from next-generation sequencing predicts time since infection and recency in 221 people with HIV-1 with known infection time. Proviral diversity was significantly associated with time since infection (P < 5×10-7, R2 up to 25%) and predictive of treatment initiation during recent infection (area under the curve-receiver operating characteristic up to 0.85). This shows the utility of proviral genetic diversity as a proxy for time since infection.
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Affiliation(s)
- Marius Zeeb
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University Zurich, Zurich, Switzerland
| | - Paul Frischknecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University Zurich, Zurich, Switzerland
| | - Corinne D Schenkel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Christine Leeman
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Medical Faculty, University of Basel, Basel, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Dominique L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University Zurich, Zurich, Switzerland
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Zeeb M, Pasin C, Cavassini M, Bieler-Aeschlimann M, Frischknecht P, Kusejko K, Fellay J, Blanquart F, Metzner KJ, Neumann K, Jörimann L, Tschumi J, Bernasconi E, Huber M, Kovari H, Leuzinger K, Notter J, Perreau M, Rauch A, Ramette A, Stöckle M, Yerly S, Günthard HF, Kouyos RD. Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study. Brain Commun 2024; 6:fcae188. [PMID: 38961872 PMCID: PMC11220509 DOI: 10.1093/braincomms/fcae188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/03/2024] [Accepted: 05/30/2024] [Indexed: 07/05/2024] Open
Abstract
People with HIV may report neurocognitive complaints, with or without associated neurocognitive impairment, varying between individuals and populations. While the HIV genome could play a major role, large systematic viral genome-wide screens to date are lacking. The Swiss HIV Cohort Study biannually enquires neurocognitive complaints. We quantified broad-sense heritability estimates using partial 'pol' sequences from the Swiss HIV Cohort Study resistance database and performed a viral near full-length genome-wide association study for the longitudinal area under the curve of neurocognitive complaints. We performed all analysis (i) restricted to HIV Subtype B and (ii) including all HIV subtypes. From 8547 people with HIV with neurocognitive complaints, we obtained 6966 partial 'pol' sequences and 2334 near full-length HIV sequences. Broad-sense heritability estimates for presence of memory loss complaints ranged between 1% and 17% (Subtype B restricted 1-22%) and increased with the stringency of the phylogenetic distance thresholds. The genome-wide association study revealed one amino acid (Env L641E), after adjusting for multiple testing, positively associated with memory loss complaints (P = 4.3 * 10-6). Other identified mutations, while insignificant after adjusting for multiple testing, were reported in other smaller studies (Tat T64N, Env *291S). We present the first HIV genome-wide association study analysis of neurocognitive complaints and report a first estimate for the heritability of neurocognitive complaints through HIV. Moreover, we could identify one mutation significantly associated with the presence of memory loss complaints. Our findings indicate that neurocognitive complaints are polygenetic and highlight advantages of a whole genome approach for pathogenicity determination.
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Affiliation(s)
- Marius Zeeb
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Chloé Pasin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
| | - Mélanie Bieler-Aeschlimann
- Division of Infectious Diseases, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
| | - Paul Frischknecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Jacques Fellay
- Division of Infectious Diseases, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - François Blanquart
- Centre interdisciplinaire de recherche en biologie, Collége de France, 75231 Paris, France
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Lisa Jörimann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Jasmin Tschumi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, 6500 Lugano, Switzerland
- Division of Infectious Diseases, University of Geneva and University of Southern Switzerland, 6900 Lugano, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Helen Kovari
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland
| | - Karoline Leuzinger
- Division Infection Diagnostics, Department Biomedicine, University of Basel, 4001 Basel Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031 Basel, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, 9007 St. Gallen, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases and Multidisciplinary Center for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031 Basel, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, 1205 Geneva, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
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Freind MC, Tallón de Lara C, Kouyos RD, Wimmersberger D, Kuster H, Aceto L, Kovari H, Flepp M, Schibli A, Hampel B, Grube C, Braun DL, Günthard HF. Cohort Profile: The Zurich Primary HIV Infection Study. Microorganisms 2024; 12:302. [PMID: 38399706 PMCID: PMC10893142 DOI: 10.3390/microorganisms12020302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The Zurich Primary HIV Infection (ZPHI) study is a longitudinal cohort study established in 2002, aiming to study the clinical, epidemiological, and biological characteristics of primary HIV infection. The ZPHI enrolls individuals with documented primary HIV-1 infection. At the baseline and thereafter, the socio-demographic, clinical, and laboratory data are systematically collected, and regular blood sampling is performed for biobanking. By the end of December 2022, 486 people were enrolled, of which 353 were still undergoing active follow-up. Of the 486 participants, 86% had an acute infection, and 14% a recent HIV-1 infection. Men who have sex with men accounted for 74% of the study population. The median time from the estimated date of infection to diagnosis was 32 days. The median time from diagnosis to the initiation of antiretroviral therapy was 11 days, and this has consistently decreased over the last two decades. During the seroconversion phase, 447 (92%) patients reported having symptoms, of which only 73% of the patients were classified as having typical acute retroviral syndrome. The ZPHI study is a well-characterized cohort belonging to the most extensively studied primary HIV infection cohort. Its findings contribute to advancing our understanding of the early stages of HIV infection and pathogenesis, and it is paving the way to further improve HIV translational research and HIV medicine.
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Affiliation(s)
- Matt C. Freind
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Carmen Tallón de Lara
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
- Institute of Medical Virology, University of Zurich, 8006 Zurich, Switzerland
| | - David Wimmersberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Hebert Kuster
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Leonardo Aceto
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland; (L.A.); (H.K.); (M.F.)
| | - Helen Kovari
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland; (L.A.); (H.K.); (M.F.)
| | - Markus Flepp
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland; (L.A.); (H.K.); (M.F.)
| | - Adrian Schibli
- Department of Infectious Diseases, Hospital Epidemiology and Occupational Health, City Hospital Zurich, 8091 Zurich, Switzerland;
| | | | | | - Dominique L. Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
- Institute of Medical Virology, University of Zurich, 8006 Zurich, Switzerland
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
- Institute of Medical Virology, University of Zurich, 8006 Zurich, Switzerland
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