Conveners
Evolutionary Dynamics of HIV: part 1
- Matthew Hall (University of Oxford)
- Abayomi Olabode (Western University)
Evolutionary Dynamics of HIV: Part 2
- Abayomi Olabode (Western University)
- Matthew Hall (University of Oxford)
It is 20 years since the perplexing observation that HIV evolves around five times faster when measured within, compared to between, hosts. Emergence of CTL- and antibody-escape mutations within individuals, followed by their reversion after transmission, has been proposed to explain the mismatch in evolutionary rates at nonsynonymous sites, but a compelling explanation for the mismatch at...
Between 2010 and 2019, new HIV diagnoses in the United States declined 14.8% from 42,665 to 36,349 diagnoses. The federal Ending the HIV Epidemic (EHE) Initiative was developed in 2019 to accelerate the decline of annual HIV diagnoses in the United States by 90% by 2030. In 2020, the number of HIV diagnoses fell by 16.4%, coinciding with the first waves of the COVID-19 pandemic. However, HIV...
HIV-1 has a high rate of recombination that has significantly shaped its evolutionary history. Identifying these past recombination events will require accurate and scalable computational methods. We previously adapted the dynamic stochastic block model (DynSBM) from social network analysis to recombination detection, demonstrating greater accuracy on simulated data. We describe further...
The development of durable antibody-based HIV treatments requires understanding not only which mutations confer resistance, but also how frequently those mutations emerge. Prior work has characterized the effects of individual mutations on viral fitness and antigenic escape; however, these evolutionary outcomes are also constrained by the mutational supply of new variants. How these mutational...
HIV integration into the human genome establishes long‑lived proviruses that persist despite antiretroviral therapy (ART) and remain a central barrier to cure. Comparative HIV integration site (IS) analyses across individuals have revealed persistent features of proviral landscapes and differences associated with age at exposure, timing of ART initiation and duration on ART. However, IS...
The short period of time prior to the establishment of a large and systemically replicating HIV-1 population provides a narrow window of time when the virus is at its most vulnerable to eradication. However, our understanding of these earliest stages of infection remains incomplete. To resolve these early dynamics, we used a non-human primate model to track the replication of clonal but...
Numerous experimental evolution studies have suggested that adaptation rate of microbial populations evolving in stable environments decline over time. To investigate the characteristics of adaptation deceleration in a fast-evolving virus, we propagated HIV-1 in two human T-cell lines (MT-2 and MT-4) for approximately 4.8 years and tracked its genome evolution through next-generation...
Background - British Columbia (BC), Canada, is rare in maintaining daily HIV phylogenetic monitoring for over a decade. Long-term monitoring enables evaluation of the impact large-scale prevention strategies have on HIV transmission suppression.
Methods - We analyzed HIV-1 pol sequences derived from 11,000+ individuals collected between 1996 and 2024, representing >80% of the estimated...
