Morgan Geniviva
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
The circulating recombinant form CRF01_AE accounts for most HIV-1 infections in South-East Asia. Here we characterized CRF01_AE’s population dynamics, including its introduction, in Thailand.
HIV-1 sequences sampled from people living with HIV-1 CRF01_AE in Thailand were downloaded from the LANL HIV database and combined with new sequences we derived from different Thai cohorts. Recombination was evaluated using RAPR and GARD and a phylodynamic analysis was conducted using BEAST v1.10.4.
We analyzed 419 gag, 276 pol and 382 env sequences sampled between 1990 and 2020. Maximum likelihood trees showed a clock-like signal with an intermixing of cohorts for each gene. We removed 100 recombinant sequences from the gag alignment and identified breakpoints in env (n=1) and pol (n=2) which were used to define partitions in the phylogenetic analyses.
We tested an uncorrelated lognormal relaxed clock (UCLD) with the GMRF Bayesian Skyride population model and the GTR+F+G4 substitution model. BEAST was run for 750 million generations with sampling every 50,000 iterations. We estimated a TMRCA of 1974 [95 % highest posterior density (HPD): 1971–1978] based on the gag sequences, 1975 [95% HPD: 1972-1979] based on the pol sequences and 1974 [95% HPD: 1972-1977] based on the env sequences. The analysis of the effective population size showed similar patterns across genes with an exponential increase followed by a plateau that started around the early 2000s. While estimates were similar across genes, some parameters showed low effective sample size (ESS) estimates and further BEAST analyses with different parameters are ongoing.
Together, our results indicate that CRF01_AE was introduced in Thailand in the mid 1970s and spread exponentially until HIV-1 prevention measures and particularly the larger availability of antiretrovirals post-2006 took effect. These results are consistent with the first documented report of a person living with HIV-1 in Thailand was in 1984.
Morgan Geniviva
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Bethany Dearlove
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Yifan Li
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Claire Henley
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Eric Lewitus
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Elizabeth Comeau
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Inzali Htut
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Harper Montgomery
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Jennifer Hoang
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Meera Bose
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Eric Sanders-Buell
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Sodsai Tovanabutra
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Suwanna Puttamaswin
(SEARCH Research Foundation, Bangkok, Thailand)
Pathariya Promsena
(SEARCH Research Foundation, Bangkok, Thailand)
Eugène Kroon
(SEARCH Research Foundation, Bangkok, Thailand)
Nittaya Phanuphak
(Institute of HIV Research and Innovation, Bangkok, Thailand)
Carlo Sacdalan
(SEARCH Research Foundation, Bangkok, Thailand; Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand)
Merlin Robb
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Julie Ake
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA)
Sandhya Vasan
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
Morgane Rolland
(U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)
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