Journal of Medical Virology 85:1170–1179 (2013) Hepatitis C Genotype Distribution and Homology Among Geographically Disparate Injecting Drug Users in Afghanistan Eric Sanders-Buell, 1 Wiriya Rutvisuttinunt, 2 Catherine S. Todd, 3 * Abdul Nasir, 4 Andrea Bradfield, 1 Esther Lei, 1 Kultida Poltavee, 2 Hathairat Savadsuk, 2 Jerome H. Kim, 1 Paul T. Scott, 5 Mark de Souza, 2 and Sodsai Tovanabutra 1 1 Department of Molecular Virology and Pathogenesis, United States Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, Maryland 2 Department of Retrovirology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand 3 Department of Obstetrics and Gynecology, Columbia University, New York, New York 4 International Rescue Committee, Kabul, Afghanistan 5 Department of Threat Assessment and Prevention, United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland Hepatitis C virus (HCV) prevalence is high among injecting drug users in Afghanistan, but transmission dynamics are poorly understood. Samples from HCV-infected injecting drug users were sequenced to determine circulating genotypes and potential transmission linkages. Serum samples were obtained from injecting drug user participants in Hirat, Jalalabad, and Mazar-i-Sharif between 2006 and 2008 with reactive anti-HCV rapid tests. Specimens with detected HCV viremia were amplified and un- derwent sequence analysis. Of 113 samples evaluated, 25 samples (35.2%) were only type- able in NS5B, nine samples (12.7%) were only typeable in CE1, and 37 samples (52.1%) were genotyped in both regions. Of those with typeable HCV, all were Afghan males with a mean age of 31.1 (standard deviation [SD]  8.0) years and mean duration of injecting of 3.9 (SD  4.3) years. Most reported residence outside Afghanistan in the last decade (90.1%) and prior incarceration (76.8%). HCV genotypes detected were: 1a, (35.2%, n ¼ 25), 3a (62.0%, n ¼ 44), and 1b (2.8%, n ¼ 2). Cluster forma- tion was detected in NS5B and CE1 and were generally from within the same city. All partic- ipants within clusters reported being a refugee in Iran compared to 93.5% of those outside clusters. Only 22.2% (4/11) of those within clusters had been refugees in Pakistan and these four individuals had also been refugees in Iran. Predominance of genotype 3a and the association between HCV viremia and having been a refugee in Iran potentially reflects migration between Afghanistan and Iran among IDUs from Mazar-i-Sharif and Hirat and carry implications for harm reduction programs for this migratory population. J. Med. Virol. 85:1170–1179, 2013. # 2013 Wiley Periodicals, Inc. KEY WORDS: hepatitis C genotype; molecu- lar epidemiology; HCV Type 3a; linkage cluster INTRODUCTION Hepatitis C virus (Flaviviridae hepacivirus C) infection is endemic in many Central and South Grant sponsor: Walter Reed Army Institute of Research; Grant sponsor: Fogarty International Center of the National Institutes of Health.; Grant number: K01TW007408 Disclaimer: Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the author, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense. Site of work performance: Viral extraction and detection, APHI laboratory, Kabul, Afghanistan; Viral amplification and sequen- cing, AFRIMS, Bangkok, Thailand, and MHRP, Silver Spring, Maryland.  Correspondence to: Catherine Todd, MD, MPH, PH 16-69, 622 West 168th Street, New York, NY 10032. E-mail: cst2121@columbia.edu Accepted 30 January 2013 DOI 10.1002/jmv.23575 Published online in Wiley Online Library (wileyonlinelibrary.com).  C 2013 WILEY PERIODICALS, INC.