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Hepatitis B virus genotype A: design of reference sequences for sub-genotypes

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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.

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Acknowledgments

This study has received funding from the Specialized Research Fund for the Doctoral Program of Higher Education of China (20093420120005) and the National Science Foundation of China (81273142). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Authors’ contributions

Zhenhua Zhang and Qun Cai conducted the sequence analyses, and wrote the manuscript. Zhenhua Zhang and Xu Li contributed to the study design and the final editing of the paper. Huilan Zhu and Yafei Zhang conducted the sequence analyses, edited the paper for grammatical and stylistic errors.

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Authors and Affiliations

  1. Department of Infectious Diseases, The First Affiliated Hospital, Anhui Medical University, Jixi Road 218, Hefei, 230022, China

    Qun Cai, Huilan Zhu, Yafei Zhang, Xu Li & Zhenhua Zhang

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  1. Qun Cai
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  2. Huilan Zhu
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  3. Yafei Zhang
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  4. Xu Li
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  5. Zhenhua Zhang
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Correspondence to Xu Li or Zhenhua Zhang.

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Edited by Hartmut Hengel.

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Cai, Q., Zhu, H., Zhang, Y. et al. Hepatitis B virus genotype A: design of reference sequences for sub-genotypes. Virus Genes 52, 325–333 (2016). https://doi.org/10.1007/s11262-016-1307-0

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