The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly …

A Shahid, S MacLennan, BR Jones… - Journal of …, 2024 - Am Soc Microbiol
Within-host HIV populations continually diversify during untreated infection, and this diversity
persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better …

HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy

A Shahid, BR Jones, JSW Yang, W Dong… - PLoS …, 2022 - journals.plos.org
The lung is an understudied site of HIV persistence. We isolated 898 subgenomic proviral
sequences (nef) by single-genome approaches from blood and lung from nine individuals …

HIV proviral burden, genetic diversity, and dynamics in viremic controllers who subsequently initiated suppressive antiretroviral therapy

FH Omondi, H Sudderuddin, A Shahid, NN Kinloch… - MBio, 2021 - Am Soc Microbiol
Curing HIV will require eliminating the reservoir of integrated, replication-competent
proviruses that persist despite antiretroviral therapy (ART). Understanding the burden …

HIV reservoirs are dominated by genetically younger and clonally enriched proviruses

NN Kinloch, A Shahid, W Dong, D Kirkby, BR Jones… - Mbio, 2023 - Am Soc Microbiol
In order to cure human immunodeficiency virus (HIV), we need to better understand the
within-host evolutionary origins of the small reservoir of genome-intact proviruses that …

HIV-1 diversity in viral reservoirs obtained from circulating T-cell subsets during early ART and beyond

Y Zhang, F Otte, M Stoeckle, A Thielen… - PLoS …, 2024 - journals.plos.org
Even during extended periods of effective immunological control, a substantial dynamic of
the viral genome can be observed in different cellular compartments in HIV-1 positive …

The persistent pool of HIV-1-infected cells is formed episodically during untreated infection

OD Council, L Tyers, M Moeser, A Sondgeroth… - Journal of …, 2024 - journals.asm.org
Previous studies have shown that the majority of long-lived cells harboring persistent HIV-1
proviral genomes originates from viruses circulating in the year prior to antiretroviral therapy …

Comparison of HIV DNA decay and immune recovery between early and chronic HIV‐infected individuals 96 weeks after ART

Y Qin, T Song, B Su, Y Jiao, L Liu, Z Liu, Y Zhou… - HIV …, 2022 - Wiley Online Library
Objectives Although antiretroviral therapy (ART) has prolonged the lives of HIV‐infected
individuals, HIV reservoir remains the main stumbling block to HIV cure. Presently, early …

Phylogenetic methods for estimating human immunodeficiency virus 1 proviral integration dates

BR Jones - 2023 - open.library.ubc.ca
Human immunodeficiency virus 1 (HIV) maintains an ongoing pandemic. Despite combined
antiretroviral therapies (cART) that can suppress viral load, halt progression to acquired …