Background:  In a 1-year period, HIV surveillance in Pakistan found a dramatic rise in HIV prevalence among injection drug users (IDU) in the city of Sargodha, evidence of an explosive outbreak. Sargodha has a needle exchange program in place; however, the common use of professional injectors and an innovative method of payment for drugs and services likely fueled the outbreak. We evaluated the molecular characteristics of HIV from IDU in Sargodha to determine whether the epidemic was caused by multiple introductions of HIV or from a single source.

Methods:  Comparative phylogenetic analyses, using the Neighbor-Joining method (Kimura 2-Parameter model) and bootstrap re-sampling as implemented in MEGA4, were performed on HIV protease and reverse transcriptase, and env gp41 sequences generated from dried blood spots collected from 400 IDU as part of the Canada–Pakistan HIV/AIDS Surveillance Project. Pairwise distances of clustered sequences were compared to those from Canadian transmission clusters and from Karachi IDU.

Results:  Sequences of at least 1 genetic region were obtained from 151 (75.5%) of the 200 available HIV⁺ IDU dried blood spots. Phylogenetic analysis revealed these to be subtype A1 (n = 143) and CRF02_AG (n = 8). Further analysis revealed clustering of the sequences into 2 distinct infection groups: 142 within subtype A1 and 7 within CRF02_AG. The mean distance between clustered Sargodha pol sequences was 0.41% and 1.45%, for each cluster respectively, compared to 0.36% between clustered Ontario Polaris Seroconverter Study sequences. Similarly, analysis of env gp41 revealed distances of 0.80% and 0.72% for Sargodha A1 and AG clusters, respectively, compared to 0.34% for sequences from another well characterized cluster. Preliminary analysis found that 7 of 17 sequences from Karachi also grouped with the same distinct cluster.

Conclusions:  Based on the findings of this analysis, the 95% of specimens formed a single distinct cluster of highly related sequences, suggesting a single, recent, common source of infection, and a true outbreak among the Sargodha IDU population, with links to Karachi IDU. Until the recent introduction of HIV, this had remained a high-risk, low-prevalence community. While interventions such as needle exchange programs may be reaching a significant proportion of Sargodha IDU, outreach programs must be implemented or expanded in order that those susceptible, as well as peers and injectors, can better appreciate how to minimize risk.