Molecular epidemiology of a primarily MSM acute HIV‐1 cohort in Bangkok, Thailand and connections within networks of transmission in Asia

INTRODUCTION: Thailand plays a substantial role in global HIV‐1 transmission of CRF01_AE. Worldwide, men who have sex with men (MSM) are at elevated risk for HIV‐1 infection. Hence, understanding HIV‐1 diversity in a primarily Thai MSM cohort with acute infection, and its connections to the broader HIV‐1 transmission network in Asia is crucial for research and development of HIV‐1 vaccines, treatment and cure. METHODS: Subtypes and diversity of infecting viruses from individuals sampled from 2009 to 2015 within the RV254/SEARCH 010 cohort were assessed by multiregion hybridization assay (MHAbce), multiregion subtype‐specific PCR assay (MSSPbce) and full‐length single‐genome sequencing (SGS). Phylogenetic analysis was performed by maximum likelihood. Pairwise genetic distances of envelope gp160 sequences obtained from the cohort and from Asia (Los Alamos National Laboratory HIV Database) were calculated to identify potential transmission networks. RESULTS: MHAbce/MSSPbce results identified 81.6% CRF01_AE infecting strains in RV254. CRF01_AE/B recombinants and subtype B were found at 7.3% and 2.8% respectively. Western subtype B strains outnumbered Thai B′ strains. Phylogenetic analysis revealed one C, one CRF01_AE/CRF02_AG recombinant and one CRF01_AE/B/C recombinant. Asian network analysis identified one hundred and twenty‐three clusters, including five clusters of RV254 participants. None of the RV254 sequences clustered with non‐RV254 sequences. The largest international cluster involved 15 CRF01_AE strains from China and Vietnam. The remaining clusters were mostly intracountry connections, of which 31.7% included Thai nodes and 43.1% included Chinese nodes. CONCLUSION: While the majority of strains in Thailand are CRF01_AE and subtype B, emergence of unique recombinant forms (URFs) are found in a moderate fraction of new HIV‐1 infections. Approaches to vaccine design and immunotherapeutics will need to monitor and consider the expanding proportion of recombinants and the increasing genetic diversity in the region. Identified HIV‐1 transmission networks indicate ongoing spread of HIV‐1 among MSM. As HIV‐1 epidemics continue to expand in other Asian countries, transmission network analyses can inform strategies for prevention, intervention, treatment and cure.