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Genetic diversity from proviral DNA as a proxy for time since HIV-1 infection


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

Abstract

HIV-1 RNA genetic diversity predicts time since infection which is important for clinical care and research. It's 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 NGS sequences 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*10-07, R2 up to 25%) and predictive of treatment initiation during recent infection (AUC-ROC up to 0.85). This shows the utility of proviral genetic diversity as a proxy for time since infection.

Abstract

HIV-1 RNA genetic diversity predicts time since infection which is important for clinical care and research. It's 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 NGS sequences 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*10-07, R2 up to 25%) and predictive of treatment initiation during recent infection (AUC-ROC up to 0.85). This shows the utility of proviral genetic diversity as a proxy for time since infection.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > University Hospital Zurich > Clinic for Infectious Diseases
04 Faculty of Medicine > Institute of Medical Virology
Dewey Decimal Classification:610 Medicine & health
570 Life sciences; biology
Uncontrolled Keywords:Infectious Diseases, Immunology and Allergy
Language:English
Date:20 March 2024
Deposited On:28 Mar 2024 12:07
Last Modified:16 May 2024 12:36
Publisher:Oxford University Press
ISSN:0022-1899
OA Status:Hybrid
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/infdis/jiae149
PubMed ID:38507572
Project Information:
  • : FunderSNSF
  • : Grant ID179571
  • : Project TitleHIV-1 Transmission in Switzerland: viral transmission traits, superinfection and drug resistance
  • : FunderYvonne Jacob Foundation
  • : Grant ID
  • : Project Title
  • : FunderUZH
  • : Grant IDCRPP
  • : Project TitleViral Infectious Diseases
  • : FunderSNSF
  • : Grant ID155851
  • : Project TitleUsing transmission networks for assessing and guiding prevention efforts in hiv
  • Content: Published Version
  • Language: English
  • Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)