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Journal of Virology, August 2006, p. 7569-7577, Vol. 80, No. 15
0022-538X/06/$08.00+0     doi:10.1128/JVI.00312-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Identification of a Naturally Occurring Recombinant Genotype 2/6 Hepatitis C Virus

Suwanna Noppornpanth,1 Truong Xuan Lien,2 Yong Poovorawan,3 Saskia L. Smits,1 Albert D. M. E. Osterhaus,1 and Bart L. Haagmans1*

Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands,1 Department of Biological Analysis, Pasteur Institute Ho Chi Minh City, Ho Chi Minh City, Vietnam,2 Center of Excellence in Viral Hepatitis Research, Department of Pediatrics, Chulalongkorn Hospital, Bangkok, Thailand3

Received 13 February 2006/ Accepted 2 May 2006

Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently classified into six genotypes and an increasing number of subtypes. Most likely, this heterogeneity is caused by genetic drift; evidence for recombination is scarce. To study the molecular heterogeneity of HCV in Vietnam, we analyzed 58 HCV RNA-positive sera from Vietnamese blood donors by sequence analysis of the CORE and NS5B regions. Phylogenetic analyses revealed the presence of genotype 1 (38%), genotype 2 (10.3%), and genotype 6 viruses (51.7%). All samples showed concordant results except for two (D3 and D54). Sample D54 was a mixed infection of genotype 2i and 6h viruses. Whole-genome analysis and bootscan analysis of sample D3, on the other hand, revealed a recombinant virus with genotype 2i and genotype 6p sequences at the 5' and 3' ends, respectively. The crossover point was located between nucleotide positions 3405 to 3464 (numbering according to prototype strain HCV-H, M67463) at the NS2/NS3 junction. The identification of this naturally occurring recombinant virus strengthens the concept that recombination may play a role in HCV epidemiology and evolution. Furthermore, the location of the recombination breakpoint may be relevant for constructing infectious chimeric viruses.

* Corresponding author. Mailing address: Department of Virology, Erasmus Medical Center, P.O. Box 1738, 3000 DR, Rotterdam, The Netherlands. Phone: (31) 10-4088066. Fax: (31) 10-4089485. E-mail: b.haagmans{at}erasmusmc.nl.

Journal of Virology, August 2006, p. 7569-7577, Vol. 80, No. 15
0022-538X/06/$08.00+0     doi:10.1128/JVI.00312-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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