Genetic History of Hepatitis C Virus in Pakistan

Genetic History of Hepatitis C Virus in Pakistan

• Irshad ur Rehman^a, 1, 
• Gilberto Vaughan^b, 1, , , 
• Michael A. Purdy^b, 
• Guo-liang Xia^b, 
• Joseph C. Forbi^b,
• Livia Maria Gonçalves Rossi^b, c, 
• Sadia Butt^a, 
• Muhammad Idrees^a, 
• Yury E. Khudyakov^b

Highlights

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Analysis of genetic heterogeneity of HCV NS3 and NS5b subgenomic regions from genotype 3a variants obtained from Pakistan.

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Analyses showed that Pakistani isolates were as genetically diverse as global variants, with extensive intermixing.

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Bayesian estimates showed that tMRCA for genotype 3a in Pakistan was last extant in ∼1896-1914 C.E.

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Death/birth models suggest that HCV 3a reached saturating diversity with decreasing turnover rate and positive extinction.

Abstract

Hepatitis C virus (HCV) genotype 3a accounts for ∼80% of HCV infections in Pakistan, where ∼ 10 million people are HCV-infected. Here, we report analysis of the genetic heterogeneity of HCV NS3 and NS5b subgenomic regions from genotype 3a variants obtained from Pakistan. Phylogenetic analyses showed that Pakistani genotype 3a variants were as genetically diverse as global variants, with extensive intermixing. Bayesian estimates showed that the most recent ancestor for genotype 3a in Pakistan was last extant in ∼1896-1914 C.E. (range: 1851-1932). This genotype experienced a population expansion starting from ∼1905 until ∼1970 after which the effective population leveled. Death/birth models suggest that HCV 3a has reached saturating diversity with decreasing turnover rate and positive extinction. Taken together, these observations are consistent with a long and complex history of HCV 3a infection in Pakistan.

Keywords

• Hepatitis C Virus; 
• Genetic diversity; 
• Pakistan

Corresponding author. Address: Division of Viral Hepatitis, Centers for Diseases Control and Prevention, 1600 Clifton Road, N.E., Mailstop A33, Atlanta, GA, USA.

1

These authors contributed equally to this work.