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Naturally occurring genotype 2b/1a hepatitis C virus in the United States

Dipankar Bhattacharya1, Molly A Accola2, Israr H Ansari1, Rob Striker13 and William M Rehrauer24*

Author Affiliations

1 University of Wisconsin-Madison, School of Medicine and Public Health, Department of Medicine, Madison WI 53706 USA

2 University of Wisconsin Hospitals and Clinics, Clinical Laboratories, Highland Avenue, Madison WI 53792 USA

3 W. S. Middleton Memorial Veteran's Association Hospital, 2500 Overlook Terrace, Madison, WI 53705 USA

4 University of Wisconsin-Madison, School of Medicine and Public Health, Department of Pathology and Laboratory Medicine, Madison WI 53792 USA

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Virology Journal 2011, 8:458  doi:10.1186/1743-422X-8-458

Published: 3 October 2011



Hepatitis C Virus (HCV) infected patients are frequently repeatedly exposed to the virus, but very few recombinants between two genotypes have been reported.


We describe the discovery of an HCV recombinant using a method developed in a United States clinical lab for HCV genotyping that employs sequencing of both 5' and 3' portions of the HCV genome. Over twelve months, 133 consecutive isolates were analyzed, and a virus from one patient was found with discordant 5' and 3' sequences suggesting it was a genotype 2b/1a recombinant. We ruled out a mixed infection and mapped a recombination point near the NS2/3 cleavage site.


This unique HCV recombinant virus described shares some features with other recombinant viruses although it is the only reported recombinant of a genotype 2 with a subtype 1a. This recombinant represents a conundrum for current clinical treatment guidelines, including treatment with protease inhibitors. This recombinant is also challenging to detect by the most commonly employed methods of genotyping that are directed primarily at the 5' structural portion of the HCV genome.