Transmission Networks of HIV-1 Subtype B CRF01_AE and CRF51_01B Among MSM in Singapore

Background: HIV-1 subtype B and CRF01_AE are the dominating subtypes among men who have sex with men (MSM) in Singapore. However, the evolutionary history, population dynamics and pattern of transmission networks of these genotypes remain unexplored. Here, we elucidated the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and the recently characterized CRF51_01B strains circulating among the MSM population in Singapore. Methodology: A total of 105 (49.5%) consenting treatment-naive MSM were recruited between February 2008 and August 2009. HIV-1 RNA was extracted from plasma specimen, reverse-transcribed, followed by amplification of the protease gene (HXB2: 2239 – 2629), gp120 (HXB2: 6942 – 7577) and gp41 (HXB2: 7803 – 8276) of the env gene. The nucleotide sequences were codon aligned, followed by phylodynamic profiling using neighbour-joining reconstruction, maximum likelihood inference and Bayesian coalescence approach. Results: 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) were observed. Bayesian coalescent analysis estimated that the emergence of multiple sub-epidemic networks occurred between 1995 and 2005, driven largely by subtype B and 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 generated through series of recombination events involving CRF01_AE and multiple subtype B ancestors. The estimation of the divergence times for each node revealed that the median interval between transmission events within these networks were short, namely 0.9 years (0.1 – 4.7) in subtype B, 0.75 years (0.1 – 1.7) in CRF01_AE and 0.65 years (0.1 – 2.2) in CRF51_01B. Conclusions: Our study provides the first insight into the phylodynamic profiles and evolutionary history of HIV-1 subtype B, CRF01_AE and CRF51_01B, suggesting the HIV-1 strains circulating among MSM in Singapore were introduced through multiple sub-epidemic networks. This study also unravels the importance of understanding transmission behaviours as well as evolutionary history of HIV-1 in assessing the risk of outbreak or epidemic expansion.