title: Hepatitis B virus genotype A: design of reference sequences for sub-genotypes.
abstract: Genotype A of hepatitis B virus (HBV/A) is widespread and is currently divided into six sub-genotypes. Suitable reference sequences for different sub-genotypes can facilitate research on HBV/A. However, the current reference sequences for this virus are insufficient. In the present work, we retrieved 442 full-length HBV/A genomic sequences from the GenBank database and classified them into sub-genotypes by phylogenetic analysis. By the maximum likelihood method using the MEGA6.0 software, we established the reference sequences for different HBV/A sub-genotypes. Our analyses demonstrated that these reference sequences clustered phylogenetically with known strains, indicating that the reference sequences we established indeed belonged to the right sub-genotypes. HBV/A subtype sequences were selected by geographic origins and grouped as sub-genotypes including A1-South Africa, A2-Europe, A3-Cameroon, and A5-Haiti. Reference sequences of sub-genotypes A1, A2, A3, and A5 were constructed and deposited into GenBank (KP234050-KP234053). By applying phylogenetic analyses, we further determined the time to most recent common ancestor of HBV/A lineages. In conclusion, these newly established reference sequences can provide suitable reference standards for studies on the molecular biology and virology of HBV genotype A.
authors.affiliation: Department of Infectious Diseases, The First Affiliated Hospital, Anhui Medical University, Jixi Road 218, Hefei, 230022, China.
authors.forename: Qun
authors.initials: Q
authors.lastname: Cai
authors.affiliation: Department of Infectious Diseases, The First Affiliated Hospital, Anhui Medical University, Jixi Road 218, Hefei, 230022, China.
authors.forename: Huilan
authors.initials: H
authors.lastname: Zhu
authors.affiliation: Department of Infectious Diseases, The First Affiliated Hospital, Anhui Medical University, Jixi Road 218, Hefei, 230022, China.
authors.forename: Yafei
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Infectious Diseases, The First Affiliated Hospital, Anhui Medical University, Jixi Road 218, Hefei, 230022, China. aaylixu@qq.com.
authors.forename: Xu
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Infectious Diseases, The First Affiliated Hospital, Anhui Medical University, Jixi Road 218, Hefei, 230022, China. zzh1974cn@163.com.
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D004279:DNA, Viral / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D006509:Hepatitis B / Q000821:virology; D006515:Hepatitis B virus / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D005810:Multigene Family; D010802:Phylogeny; D058974:Phylogeography; D012016:Reference Values; D017422:Sequence Analysis, DNA / Q000379:methods / Q000592:standards; D012984:Software
chemical_list: D004279:DNA, Viral
keywords: Genotype; Hepatitis B virus; Reference sequences; Sequence analysis