Establishment of reference sequences of hepatitis B virus genotype B subgenotypes

Authors

  • Xiaojun Jin 1. Heibei North University, 11 Zuanshi South Rd, High-Ttech District, Zhangjiakou 075000; 2. Department of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Rd., Shangcheng District, Hangzhou 310003 https://orcid.org/0000-0002-2295-0061
  • Qun Cai Department of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Rd., Shangcheng District, Hangzhou 310003 https://orcid.org/0000-0002-9101-1850
  • Zhenhua Zhang Department of Infectious Diseases, the First Affiliated Hospital, Anhui Medical University, 218 Jixi Rd., Shushan District, Hefei 230022 http://orcid.org/0000-0002-9522-532X
  • Jifang Sheng Department of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Rd., Shangcheng District, Hangzhou 310003 https://orcid.org/0000-0003-0732-1555

DOI:

https://doi.org/10.2298/ABS200817042J

Keywords:

Hepatitis B virus, genotype, phylogenetic analysis, reference strains, bioinformatics

Abstract

Paper description:

  • Some reference sequences of hepatitis B virus genotype B (HBV/B) are not sufficient to represent the reference of individual sub-genotypes. It is necessary to establish new reference sequences of the HBV/B sub-genotype.
  • Genomic sequences of HBV/B were obtained from GenBank and compartmentalized into genomic subtypes. Homology between established HBV/B references was evaluated at the nucleotide level.
  • Reference strains for B1-Japan, B2-China, B3-Indonesia, B4-Vietnam, B6-North America, B7-Indonesia and B9-Southeast Asia were established. Fractional significant mutation sites of strains were observed in the BCP/Pre-C regions.
  • Reference sequences provide reference standards for molecular characterization, virology and pathogenesis of HBV/B.

Abstract: Hepatitis B virus (HBV) has been classified into ten genotypes (A-J). Genotype B (HBV/B) is divided into nine subgenotypes (B1-B9), each with specific geographical predominance. Some reference sequence of HBV/B subgenotypes are currently in use, but these sequences have defects, being insufficient to represent the reference of individual subgenotype. The aim of this study was to establish a more representative reference of HBV/B subgenotypes in different regions. Full genomic sequences of HBV/B were obtained from GenBank and compartmentalized into genomic subtypes. The homology between our established HBV/B subgenotype references was evaluated at the nucleotide level. We established reference strains for B1-Japan, B2-China, B3-Indonesia, B4-Vietnam, B6-North America, B7-Indonesia and B9-Southeast Asia. Fractional significant mutation sites of the strains that were established were observed in the BCP/Pre-C regions. We calculated the genetic divergence time from the most recent common ancestor of HBV/B pedigree. The reference sequences established in the study provide reference standards for studies on molecular characterization, virology and pathogenesis of HBV/B.

Downloads

Download data is not yet available.

References

Scotto G, Fazio V. Hepatitis B and asymptomatic malaria coinfection in Sub-Saharan African immigrants: epidemiological and clinical features of HBV infection. Rev Soc Bras Med Trop. 2018;51(5):578-83.

Terrault N, Lok A, McMahon B, Chang K, Hwang J, Jonas M, Brown R Jr. R, Bzowej N, Wong J. Update on prevention, diagnosis, and treatment of chronic hepatitis B: AASLD 2018 hepatitis B guidance. Hepatology. 2018;67(4):1560-99.

Harding J, Abu-Zeinah G, Chou J, Owen D, Ly M, Lowery M, Capanu M, Do R, Kemeny N, O'Reilly E, Saltz L, Abou-Alfa G. Frequency, Morbidity, and Mortality of Bone Metastases in Advanced Hepatocellular Carcinoma. J Natl Compr Canc Netw. 2018;16(1):50-8.

Malagnino V, Salpini R, Maffongelli G, Battisti A, Fabeni L, Piermatteo L, Colagrossi L, Fini V, Ricciardi A, Sarrecchia C, Perno CF, Andreoni M, Svicher V, Sarmati L. High rates of chronic HBV genotype E infection in a group of migrants in Italy from West Africa: Virological characteristics associated with poor immune clearance. PLoS One. 2018;13(3):e0195045.

Cai Q, Zhu H, Zhang Y, Li X, Zhang Z. Hepatitis B virus genotype A: design of reference sequences for sub-genotypes. Virus Genes. 2016;52(3):325-33.

Okamoto H, Tsuda F, Sakugawa H, Sastrosoewignjo RI, Imai M, Miyakawa Y, Mayumi M. Typing hepatitis B virus by homology in nucleotide sequence: comparison of surface antigen subtypes. J Gen Virol. 1988;69(Pt 10):2575-83.

Yu H, Yuan Q, Ge S, Wang H, Zhang Y, Chen Q, Zhang J, Chen P, Xia N. Molecular and phylogenetic analyses suggest an additional hepatitis B virus genotype "I". PLoS One. 2010;5(2):e9297.

Zhu H, Wang C, Xia J, Li X, Zhang Z. Establishment of reference sequences of hepatitis B virus genotype C subgenotypes. Genet Mol Res. 2015;14(4):16521-34.

Inoue J, Ueno Y, Nagasaki F, Wakui Y, Kondo Y, Fukushima K, Niitsuma H, Shimosegawa T. Enhanced intracellular retention of a hepatitis B virus strain associated with fulminant hepatitis. Virology. 2009;395(2):202-9.

Norder H, Courouce A, Coursaget P, Echevarria J, Lee S, Mushahwar I, Robertson B, Locarnini S, Magnius L. Genetic diversity of hepatitis B virus strains derived worldwide: genotypes, subgenotypes, and HBsAg subtypes. Intervirology. 2004;47(6):289-309.

Baclig M, Alvarez M, Gopez-Cervantes J, Natividad F. Unique surface gene variants of hepatitis B virus isolated from patients in the Philippines. J Med Virol. 2014;86(2):209-16.

Mulyanto, Depamede S, Surayah K, Tsuda F, Ichiyama K, Takahashi M, Okamoto H. A nationwide molecular epidemiological study on hepatitis B virus in Indonesia: identification of two novel subgenotypes, B8 and C7. Arch Virol. 2009;154(7):1047-59.

Li X, Wang L, Zhong Y, Wong VW, Xu Z, Liu Y, Li Q, Xin S, Zhao J, Xu D. Hepatitis B virus (HBV) subgenotypes C2 and B2 differ in lamivudine- and adefovir-resistance-associated mutational patterns in HBV-infected Chinese patients. J Clin Microbiol. 2010;48(12):4363-9.

Zhang Z, Zhang L, Lu M, Yang D, Li X. Establishment of reference sequences of hepatitis B virus genotype B and C in China. Chin J Hepatol. 2009;17(12):891-5.

Shi W, Carr M, Dunford L, Zhu C, Hall W, Higgins D. Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis. Virology. 2012;427(1):51-9.

Hall B. Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol. 2013;30(5):1229-35.

Li H, Wang J, Wang R, Zhao Q, Li L, Zhang J, Shen T. Hepatitis B virus genotypes and genome characteristics in China. World J Gastroenterol. 2015;21(21):6684-97.

Paraskevis D, Magiorkinis G, Magiorkinis E, Ho S, Belshaw R, Allain J, Hatzakis A. Dating the origin and dispersal of hepatitis B virus infection in humans and primates. Hepatology. 2013;57(3):908-16.

Zhang Z, Xia J, Sun B, Dai Y, Li X, Schlaak J, Lu M. In vitro and in vivo replication of a chemically synthesized consensus genome of hepatitis B virus genotype B. J Virol Methods. 2015;213:57-64.

Hannachi N, Fredj N, Bahri O, Thibault V, Ferjani A, Gharbi J, Triki H, Boukadida J. Molecular analysis of HBV genotypes and subgenotypes in the Central-East region of Tunisia. Virol J. 2010;7:302.

Hsieh M, Yeh M, Su T, Liu T, Huang C, Huang C, Wang S, Huang J, Dai C, Kao J, Chuang W, Chen P, Liu C, Yu M. Boceprevir-based triple therapy to rescue HCV genotype 1/HBV dually infected patients refractory to peginterferon plus ribavirin combination therapy in Taiwan. J Formos Med Assoc. 2018;117(6):497-504.

Kao J. Role of viral factors in the natural course and therapy of chronic hepatitis B. Hepatol Int. 2007;1(4):415-30.

Imai M, Watanabe T, Kiso M, Nakajima N, Yamayoshi S, Iwatsuki-Horimoto K, Hatta M, Yamada S, Ito M, Sakai-Tagawa Y, Shirakura M, Takashita E, Fujisaki S, McBride R, Thompson AJ, Takahashi K, Maemura T, Mitake H, Chiba S, Zhong G, Fan S, Oishi K, Yasuhara A, Takada K, Nakao T, Fukuyama S, Yamashita M, Lopes T, Neumann G, Odagiri T, Watanabe S, Shu Y, Paulson J, Hasegawa H, Kawaoka Y. A Highly Pathogenic Avian H7N9 Influenza Virus Isolated from A Human Is Lethal in Some Ferrets Infected via Respiratory Droplets. Cell Host Microbe. 2017;22(5):615-26

Nojiri S, Kusakabe A, Fujiwara K, Shinkai N, Matsuura K, Iio E, Miyaki T, Nomura T, Sobue S, Sano H, Hasegawa I, Ohno T, Takahashi Y, Orito E, Joh T. Clinical factors related to long-term administration of sorafenib in patients with hepatocellular carcinoma. Cancer Manag Res. 2012;4:423-9.

Orito E, Hasebe C, Kurosaki M, Osaki Y, Joko K, Watanabe H, Kimura H, Nishijima N, Kusakabe A, Izumi N. Risk of hepatocellular carcinoma in cirrhotic hepatitis B virus patients during nucleoside/nucleotide analog therapy. Hepatol Res. 2015;45(8):872-9.

Elizalde M, Sevic I, Ledesma M, Campos R, Barbini L, Flichman D. Human hepatocytes apoptosis induced by replication of hepatitis B virus subgenotypes F1b and F4: Role of basal core promoter and preCore mutations. Virology. 2018;513:160-7.

Yang Z, Zhuang L, Lu Y, Xu Q, Tang B, Chen X. Naturally occurring basal core promoter A1762T/G1764A dual mutations increase the risk of HBV-related hepatocellular carcinoma: a meta-analysis. Oncotarget. 2016;7(11):12525-36.

Kao J, Yu M, Peng C, Heo J, Chu C, Chang T, Lee Y, Hu T, Yoon K, Paik S, Lim Y, Ahn S, Isakov V, McPhee F, Hu W, Scott Swenson E, Yin P, Treitel M. Daclatasvir/asunaprevir/beclabuvir, all-oral, fixed-dose combination for patients with chronic hepatitis C virus genotype 1. J Gastroenterol Hepatol. 2017;32(12):1998-2005.

Lee M, Huang C, Lai H, Lin C, Dai C, Liu C, Wang J, Huang J, Su W, Yang H, Kee K, Yeh M, Chuang P, Hsu S, Huang C, Kao J, Chen C, Chen S, Jeng W, Yang H, Yuan Y, Lu S, Sheen I, Liu C, Peng C, Kao J, Yu M, Chuang W, Chen C. Clinical Efficacy and Post-Treatment Seromarkers Associated with the Risk of Hepatocellular Carcinoma among Chronic Hepatitis C Patients. Sci Rep. 2017;7(1):3718.

Liu C, Chuang W, Sheen I, Wang H, Chen C, Tseng K, Chang T, Massetto B, Yang J, Yun C, Knox S, Osinusi A, Camus G, Jiang D, Brainard D, McHutchison J, Hu T, Hsu Y, Lo G, Chu C, Chen J, Peng C, Chien R, Chen P. Efficacy of Ledipasvir and Sofosbuvir Treatment of HCV Infection in Patients Coinfected with HBV. Gastroenterology. 2018;154(4):989-97.

Milosevic I, Delic D, Lazarevic I, Pavlovic I, Korac M, Bojovic K, Jevtovic D. The significance of hepatitis B virus (HBV) genotypes for the disease and treatment outcome among patients with chronic hepatitis B in Serbia. J Clin Virol. 2013;58(1):54-8.

Downloads

Published

2020-12-25

How to Cite

1.
Jin X, Cai Q, Zhang Z, Sheng J. Establishment of reference sequences of hepatitis B virus genotype B subgenotypes. Arch Biol Sci [Internet]. 2020Dec.25 [cited 2024Nov.23];72(4):483-90. Available from: https://serbiosoc.org.rs/arch/index.php/abs/article/view/5724

Issue

Vol. 72 No. 4 (2020)

Section

Articles

License

Copyright (c) 2020 Archives of Biological Sciences

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Authors grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution 4.0 International License that allows others to share the work with an acknowledgment of the work’s authorship and initial publication in this journal.