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Journal of Clinical Microbiology, November 2003, p. 5240-5244, Vol. 41, No. 11
0095-1137/03/$08.00+0     DOI: 10.1128/JCM.41.11.5240-5244.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Comparison of Hepatitis C Virus Genotyping by 5' Noncoding Region- and Core-Based Reverse Transcriptase PCR Assay with Sequencing and Use of the Assay for Determining Subtype Distribution in India

Kavita S. Lole,1 Jyotsna A. Jha,1 Sandhya P. Shrotri,1 Badri N. Tandon,2 V. G. Mohan Prasad,3 and Vidya A. Arankalle1*

Hepatitis Division, National Institute of Virology, Pune,1 Metro Center for Liver and Digestive Diseases, Noida, Delhi,2 KG Hospital and Post Graduate Research Institute, Coimbatore, India3

Received 29 May 2003/ Returned for modification 14 July 2003/ Accepted 18 August 2003

Phylogenetic analysis of the sequences of the 5' noncoding regions (5'NCR) of 149 samples from hepatitis C virus (HCV) RNA-positive chronic carriers representing northern, southern, eastern, and western India showed that type 3 and type 1 are the predominant genotypes circulating in India, with an overall prevalence of 53.69 and 38.25%, respectively. Type 4 viruses (6.04%) were seen only in southern India. Sequence analysis of the core region of 51 of the above isolates enabled us to classify them further into subtypes as 1b (number of isolates [n] = 10), 1a (n = 6), 3a (n = 9), 3g (n = 14), 3f (n = 1), and 4d (n = 3). Three new subtypes were identified for the first time and designated as 3i (n = 5), 3j (n = 2), and 6l (n = 1). Sequencing the 5'NCR could differentiate HCV types, whereas classification at the level of subtype was possible with sequence analysis of the core region.

* Corresponding author. Mailing address: Hepatitis Division, National Institute of Virology, 20-A Dr. Ambedkar Rd., Pune 411001, India. Phone: 91-20-612-7301. Fax: 91-20-612-2669. E-mail: aarankalle{at}hotmail.com.

Journal of Clinical Microbiology, November 2003, p. 5240-5244, Vol. 41, No. 11
0095-1137/03/$08.00+0     DOI: 10.1128/JCM.41.11.5240-5244.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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