Figure 1. Phylogenetic tree of 246 gag-sequences, including 118 Bangladeshi HIV-1 C strains in green.

The HIV1-C strains found in Bangladesh do not fall into a country specific clade, instead our results point to repeated introductions with substantial in-country transmission only among PWIDs. Four clades with ≥3 BD strains had a posterior probability of around 0.7 or higher, and are shown in the figure. Clade 1 is a monophyletic clade of 47 BD strains, of which 43 originate from PWIDs in Dhaka. The tMRCA of this clade is around 1975. It is a subset of the large regional Clade 2, which is dominated by strains from Bangladesh, Myanmar, India and China. Over 80% of all BD strains can be found within this clade, which appears to have been introduced to this region around 1962. The intermixing of sequences collected from different countries indicates frequent cross-border transmission in this region. In addition to the 47 strains in Clade 1, the BD strains in Clade 2 includes sequences from returning migrants from Nepal, India and the Middle East as well as some weakly supported clades of strains from sex workers and VCT/STI patients. Clade 3 consists of seven PWID strains from Dhaka, and the short branches in this clade reveal rapid transmission (and detection) within this group. Clade 4 contains five strains from VCT visitors in Dhaka and Chittagong, at least 3 of whom had a history of migrant work in the Middle East. The long branches show that they are not very close genetically and it is possible that they represent separate introductions of related strains. Most of the BD strains found outside these clades appear to represent separate introductions.