A novel hepatitis B virus genotyping system by using restriction fragment length polymorphism patterns of S gene amplicons

doi:10.3748/wjg.v10.i21.3132

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World Journal of Gastroenterology

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1007-9327

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

Viral Hepatitis

World J Gastroenterol. Nov 1, 2004; 10(21): 3132-3136
Published online Nov 1, 2004. doi: 10.3748/wjg.v10.i21.3132

A novel hepatitis B virus genotyping system by using restriction fragment length polymorphism patterns of S gene amplicons

Guo-Bing Zeng, Shu-Juan Wen, Zhan-Hui Wang, Li Yan, Jian Sun, Jin-Lin Hou

Guo-Bing Zeng, Zhan-Hui Wang, Li Yan, Jian Sun, Jin-Lin Hou, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong Province, China

Guo-Bing Zeng, Department of Infectious Diseases, 458 Hospital of PLA, Guangzhou 510602, Guangdong Province, China

Shu-Juan Wen, Genetic Laboratory, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong Province, China

Author contributions: All authors contributed equally to the work.

Supported by the Major State Basic Research Development Program of China. 973 Program, No.G1999054106; and the National Science Fund for Distinguished Young Scholars, No.30225042

Correspondence to: Dr. Jin-Lin Hou, Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong Province, China. jlhou@fimmu.edu.cn

Telephone: +86-20-85141941 Fax: +86-20-87714940

Received: August 3, 2003
Revised: December 15, 2003
Accepted: December 22, 2003
Published online: November 1, 2004

Abstract

AIM: Traditional hepatitis B virus (HBV) genotyping methods using restriction fragment length polymorphism (RFLP) can reliably identify genotypes A to F. As HBV genotypes G and H have been recently identified, this study was to establish an accurate and simple genotyping method for all eight HBV genotypes (A to H).

METHODS: Two hundred and forty HBV small S sequences obtained from GeneBank were analysed for restriction enzyme sites that would be genotype-specific. Restriction patterns following digestion with restriction enzymes BsrI, StyI, DpnI, HpaII, and EaeI, were determined to identify all eight HBV genotypes. Mixed genotype infections were confirmed by cloning and further RFLP analysis.

RESULTS: The new genotyping method could identify HBV genotypes A to H. Genotypes B and C could be determined by a single step digestion with BsrI and StyI in parallel. This was particularly useful in the Far East where genotypes B and C are predominant. Serum samples from 187 Chinese HBV carriers were analysed with this genotyping system, and the genotype distribution was 1.1% (2), 51.9% (97), 40.6% (76) and 4.8% (9) for genotypes A, B, C, and D, respectively. Mixed genotypes were found in only 3 patients (1.6%). Sequence data analysis confirmed the validity of this new method.

CONCLUSION: This HBV genotyping system can identify all eight HBV genotypes. It is accurate and simple, and can be widely used for studies on HBV genotyping.

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