Open Access Research article

Evidence for a "Founder Effect" among HIV-infected injection drug users (IDUs) in Pakistan

Mohammad A Rai1, Vivek R Nerurkar2, Suhail Khoja1, Saeed Khan1, Richard Yanagihara23, Arish Rehman1, Shahana U Kazmi4 and Syed H Ali1*

Author Affiliations

1 Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan

2 Retrovirology Research Laboratory, Department of Tropical Medicine, Medical Microbiology and Pharmacology, Hawaii, USA

3 Department of Pediatrics, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813, USA

4 Department of Microbiology, University of Karachi, Pakistan

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BMC Infectious Diseases 2010, 10:7  doi:10.1186/1471-2334-10-7

Published: 12 January 2010



We have previously reported a HIV-1 subtype A infection in a community of injection drug users (IDUs) in Karachi, Pakistan. We now show that this infection among the IDUs may have originated from a single source.


Phylogenetic analysis was performed of partial gag sequences, generated using PCR, from 26 HIV-positive IDU samples.


Our results showed formation of a tight monophyletic group with an intra-sequence identity of < 98% indicating a "founder effect". Our data indicate that the HIV-1 epidemic in this community of IDUs may have been transmitted by an HIV positive overseas contract worker who admitted to having contact with commercial sex workers during stay abroad.


Specific measures need to implemented to control transmission of HIV infection in Pakistan through infected migrant workers.