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Open Access Highly Accessed Methodology

A type-specific nested PCR assay established and applied for investigation of HBV genotype and subgenotype in Chinese patients with chronic HBV infection

Jing-Jing Nie, Kui-Xia Sun, Jie Li*, Jie Wang, Hui Jin, Ling Wang, Feng-Min Lu, Tong Li, Ling Yan, Jing-Xian Yang, Mi-Shu Sun and Hui Zhuang*

Author Affiliations

Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China

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Virology Journal 2012, 9:121  doi:10.1186/1743-422X-9-121

Published: 19 June 2012

Abstract

Background

Many studies have suggested that hepatitis B virus (HBV) genotypes show not only geographical distribution and race specificity, but also are associated with disease progression and response to interferon treatment. The objective of this study was to develop a nested polymerase chain reaction (nPCR) assay for genotypes A-D and subgenotypes B1, B2, C1 and C2 of hepatitis B virus (HBV) and to investigate the distribution characteristics of HBV genotypes/subgenotype in China.

Methods

After redesigning the primers and optimizing the reaction conditions using common Taq polymerase, the sensitivity, specificity and reproducibility of the method were evaluated using plasmids and serum samples. In total, 642 serum samples from patients with chronic HBV infection were applied to investigate the distribution of HBV genotype and subgenotype in China.

Results

The genotype and subgenotype could be identified when the HBV DNA load of a sample was ≥102.3 IU/mL. For the 639 successfully genotyped samples, the sequencing results of 130 randomly selected samples (20.3%, 130/639) were consistent with those of the nPCR method. The present study showed that HBV genotype B (11.2%, 72/642), C (68.2%, 438/642) and D (7.2%, 46/642) were circulating in China, while genotype C was the dominant strain except for western region where genotype D was the prevalent strain. The main subgenotypes of genotypes B and C were B2 (87.5%, 63/72) and C2 (92.9%, 407/438), respectively.

Conclusions

The low-cost nPCR method would be a useful tool for clinical and epidemiological investigation in the regions where genotypes A-D are predominant.

Keywords:
Genotype; Hepatitis B virus; Nested PCR; Subgenotype; Type-specific nested PCR