“Founder effect” among HIV-positive IDU in Karachi, Pakistan

Pakistan has >74,000 HIV-positive people out of a population of 162 million; with a recent shift in acquisition of HIV via IDU.

Mohammad Rai and co-workers reported findings from a study to determine whether an HIV outbreak among a community of 15 IDU in Karachi was from a single source.

Viral DNA was extracted from blood samples collected between January and December 2004. Sequence alignment of the nef gene from HIV-1-positive patients from Pakistan indicated that the HIV-1 strains differed from the strains circulating in neighbouring India, and were genetically closer to HIV-1 subtype A strains from Senegal, Uganda, and Kenya. Additionally, phylogenetic analysis of the complete nef gene sequence revealed highly congruent topologies, using the neighbour-joining method. The HIV-1 strains from Pakistan formed a monophyletic group.

The investigators wrote: “Our data suggest that the HIV-1 sequences circulating among IDU in Karachi, Pakistan, belong to only 1 HIV subtype, subtype A. Moreover, the intra-sequence identity of 98% indicates a founder effect.”

They noted that these data contrast with a previous observation demonstrating presence of multiple HIV-1 subtypes among overseas contract workers.

They concluded: “The HIV-1 epidemic in Pakistan is shifting from imported cases, such as among the overseas contract workers, to the spread of HIV among local high-risk behavior populations. More prevention and control studies are urgently warranted to curtail the spread of HIV in Pakistan.”


Rai M, Nerurkar V, Yanagihara R et al. Founder effect among HIV-1-infected Injection drug users in Karachi, Pakistan. 14th CROI, 2007, Los Angeles. Poster Abstract 241.

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