Phylodynamic profile of HIV-1 subtype B, CRF01-AE and the recently emerging CRF51-01B among men who have sex with men (MSM) in Singapore

HIV-1 subtype B and CRF01-AE are the predominant infecting subtypes among men who have sex with men (MSM) in Singapore. The genetic history, population dynamics and pattern of transmission networks of these genotypes remain largely unknown. We delineated the phylodynamic profiles of HIV-1 subtype B, CRF01-AE and the recently characterized CRF51-01B strains circulating among the MSM population in Singapore. A total of 105 (49.5%) newly-diagnosed treatmentnaïve MSM were recruited between February 2008 and August 2009. Phylogenetic reconstructions of the protease gene (HXB2: 2239 - 2629), gp120 (HXB2: 6942 - 7577) and gp41 (HXB2: 7803 - 8276) of the env gene uncovered five monophyletic transmission networks (two each within subtype B and CRF01-AE and one within CRF51-01B lineages) of different sizes (involving 3 - 23 MSM subjects, supported by posterior probability measure of 1.0). Bayesian coalescent analysis estimated that the emergence and dissemination of multiple sub-epidemic networks occurred between 1995 and 2005, driven largely by subtype B and later followed by CRF01-AE. Exponential increase in effective population size for both subtype B and CRF01-AE occurred between 2002 to 2007 and 2005 to 2007, respectively. Genealogical estimates suggested that the novel CRF51-01B lineages were probably generated through series of recombination events involving CRF01-AE and multiple subtype B ancestors. Our study provides the first insight on the phylodynamic profiles of HIV-1 subtype B, CRF01-AE and CRF51-01B viral strains circulating among MSM in Singapore. Copyright: