title: Whole genome characterization of hepatitis B virus quasispecies with massively parallel pyrosequencing.
abstract: Viral quasispecies analysis is important for basic and clinical research. This study was designed to detect hepatitis B virus (HBV) genome-wide mutation profiling with detailed variant composition in individual patients, especially quasispecies evolution correlating with liver disease progression. We characterized viral populations by massively parallel pyrosequencing at whole HBV genome level in 17 patients with advanced liver disease (ALD) and 30 chronic carriers (CC). An average sequencing coverage of 2047× and 687× in ALD and CC groups, respectively, were achieved. Deep sequencing data resolved the landscapes of HBV substitutions and a more complicated quasispecies composition than previously observed. The values of substitution frequencies in quasispecies were clustered as either more than 80% or less than 20%, forming a unique U-shaped distribution pattern in both clinical groups. Furthermore, quantitative comparison of mutation frequencies of each site between two groups resulted in a spectrum of substitutions associated with liver disease progression, and among which, C2288A/T, C2304A, and A/G2525C/T were novel candidates. Moreover, distinct deletion patterns in preS, X, and C regions were shown between the two groups. In conclusion, pyrosequencing of the whole HBV genome revealed a panorama of viral quasispecies composition, characteristics of substitution distribution, and mutations correlating to severe liver disease.
authors: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors: F
authors: F
authors: Li
authors: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: zhangdk@big.ac.cn.
authors: D
authors: D
authors: Zhang
authors: Central Laboratory of Southwest Hospital, Third Military Medical University, Chongqing, China.
authors: Y
authors: Y
authors: Li
authors: Department of Clinical Laboratory, Jining Hospital for Infectious Diseases, Jining, China.
authors: D
authors: D
authors: Jiang
authors: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China.
authors: S
authors: S
authors: Luo
authors: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors: N
authors: N
authors: Du
authors: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors: W
authors: W
authors: Chen
authors: Basic Medical Institute of Nanchang University, Nanchang, China.
authors: L
authors: L
authors: Deng
authors: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: czeng@big.ac.cn.
authors: C
authors: C
authors: Zeng
mesh_terms: D019943:Amino Acid Substitution; D002353:Carrier State; D016000:Cluster Analysis; D018450:Disease Progression; D005814:Genes, Viral; D014644:Genetic Variation; D016679:Genome, Viral; D023281:Genomics; D006515:Hepatitis B virus / Q000235:genetics*; D019694:Hepatitis B, Chronic / Q000473:pathology / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D017384:Sequence Deletion
keywords: Hepatitis B virus; liver disease; mutations; quasispecies; sequencing