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Hepatitis

Viral quasispecies quantitative analysis: a novel approach for appraising the immune tolerant phase of chronic hepatitis B virus infection

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Pages 842-851 | Received 11 Nov 2020, Accepted 14 Apr 2021, Published online: 01 May 2021

References

  • European Association for the Study of the Liver, Electronic address: [email protected], European Association for the Study of the Liver. EASL 2017 clinical practice guidelines on the management of hepatitis B virus infection. J Hepatol, 2017;67(2):370–398.
  • Terrault NA, Lok ASF, McMahon BJ, et al. Update on prevention, diagnosis, and treatment of chronic hepatitis B: AASLD 2018 hepatitis B guidance. Hepatology. 2018;67(4):1560–1599.
  • Sarin SK, Kumar M, Lau GK, et al. Asian-Pacific clinical practice guidelines on the management of hepatitis B: a 2015 update. Hepatol Int. 2016;10(1):1–98.
  • Terrault NA, Bzowej NH, Chang K-M, et al. AASLD guidelines for treatment of chronic hepatitis B. Hepatology. 2016;63(1):261–283.
  • Domingo E, Martín V, Perales C, et al. Viruses as quasispecies: biological implications. Curr Top Microbiol Immunol. 2006;299:51–82.
  • Domingo E, Gomez J. Quasispecies and its impact on viral hepatitis. Virus Res. 2007;127(2):131–150.
  • Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev. 2012;76(2):159–216.
  • Lauring AS, Andino R. Quasispecies theory and the behavior of RNA viruses. PLoS Pathog. 2010;6(7):e1001005.
  • Lim SG, Cheng Y, Guindon S, et al. Viral quasi-species evolution during hepatitis Be antigen seroconversion. Gastroenterology. 2007;133(3):951–958.
  • Chen L, Gan QR, Zhang DQ, et al. Increased intrahepatic quasispecies heterogeneity correlates with off-treatment sustained response to nucleos(t)ide analogues in e antigen-positive chronic hepatitis B patients. Clin Microbiol Infect. 2016;22(2):201–207.
  • Wagner J, Yuen L, Littlejohn M, et al. Analysis of Hepatitis B virus haplotype diversity detects striking sequence conservation across genotypes and chronic disease phase. Hepatology. 2020. doi:https://doi.org/10.1002/hep.31516. PMID: 32780526.
  • Ayres A, Yuen L, Jackson KM, et al. Short duration of lamivudine for the prevention of hepatitis B virus transmission in pregnancy: lack of potency and selection of resistance mutations. J Viral Hepat. 2014;21(11):809–817.
  • Bayliss J, Nguyen T, Lesmana C, et al. Advances in the molecular diagnosis of hepatitis B infection: providing insight into the next generation of disease. Semin Liver Dis. 2013;33(2):113–121.
  • Barzon L, Lavezzo E, Costanzi G, et al. Next-generation sequencing technologies in diagnostic virology. J Clin Virol. 2013;58(2):346–350.
  • Bayliss J, Yuen L, Rosenberg G, et al. Deep sequencing shows that HBV basal core promoter and precore variants reduce the likelihood of HBsAg loss following tenofovir disoproxil fumarate therapy in HBeAg-positive chronic hepatitis B. Gut. 2017;66(11):2013–2023.
  • Tseng TC, Liu C-J, Yang H-C, et al. Higher proportion of viral basal core promoter mutant increases the risk of liver cirrhosis in hepatitis B carriers. Gut. 2015;64(2):292–302.
  • Wang M, Li J, Zhang X, et al. An integrated software for virus community sequencing data analysis. BMC Genomics. 2020;21(1):363.
  • Desmet VJ, Gerber M, Hoofnagle JH, et al. Classification of chronic hepatitis: diagnosis, grading and staging. Hepatology. 1994;19(6):1513–1520.
  • Sterling RK, Lissen E, Clumeck N, et al. Development of a simple noninvasive index to predict significant fibrosis in patients with HIV/HCV coinfection. Hepatology. 2006;43(6):1317–1325.
  • Wai CT, Greenson JK, Fontana RJ, et al. A simple noninvasive index can predict both significant fibrosis and cirrhosis in patients with chronic hepatitis C. Hepatology. 2003;38(2):518–526.
  • Chisari FV, Isogawa M, Wieland SF. Pathogenesis of hepatitis B virus infection. Pathologie Biologie. 2010;58(4):258–266.
  • Vanlandschoot P, Cao T, Leroux-Roels G. The nucleocapsid of the hepatitis B virus: a remarkable immunogenic structure. Antiviral Res. 2003;60(2):67–74.
  • Sede M, Lopez-Ledesma M, Frider B, et al. Hepatitis B virus depicts a high degree of conservation during the immune-tolerant phase in familiarly transmitted chronic hepatitis B infection: deep-sequencing and phylogenetic analysis. J Viral Hepat. 2014;21(9):650–661.
  • Kennedy PTF, Sandalova E, Jo J, et al. Preserved T-cell function in children and young adults with immune-tolerant chronic hepatitis B. Gastroenterology. 2012;143(3):637–645.
  • Mason WS, Gill US, Litwin S, et al. HBV DNA integration and clonal hepatocyte expansion in chronic Hepatitis B patients considered immune tolerant. Gastroenterology. 2016;151(5):986–998.e4.
  • Yuen L, Revill PA, Rosenberg G, et al. HBV variants are common in the ‘immune-tolerant’ phase of chronic hepatitis B. J Viral Hepat. 2020;27(10):1061–1070.
  • Yang L, Ma S, Hu X, et al. Presence of valine at position 27 of the hepatitis B virus core gene is associated with severe liver inflammation in Chinese patients. J Med Virol. 2011;83(2):218–224.
  • Ducancelle A, Pivert A, Bertrais S, et al. Different precore/core mutations of hepatitis B interact with, limit, or favor liver fibrosis severity. J Gastroenterol Hepatol. 2016;31(10):1750–1756.
  • Li F, Zhang D, Li Y, et al. Whole genome characterization of hepatitis B virus quasispecies with massively parallel pyrosequencing. Clin Microbiol Infect. 2015;21(3):280–287.
  • Zhu S, Zhang H, Dong Y, et al. Antiviral therapy in hepatitis B virus-infected children with immune-tolerant characteristics: a pilot open-label randomized study. Journal of Hepatology. 2018;68(6):1123–1128.
  • Kumar M, Sarin SK, Hissar S, et al. Virologic and histologic features of chronic hepatitis B virus-infected asymptomatic patients with persistently normal ALT. Gastroenterology. 2008;134(5):1376–1384.
  • Lai M, Hyatt BJ, Nasser I, et al. The clinical significance of persistently normal ALT in chronic hepatitis B infection. J Hepatol. 2007;47(6):760–767.
  • Martinot-Peignoux M, Carvalho-Filho R, Lapalus M, et al. Hepatitis B surface antigen serum level is associated with fibrosis severity in treatment-naïve, e antigen-positive patients. J Hepatol. 2013;58(6):1089–1095.
  • Afdhal NH, Bacon BR, Patel K, et al. Accuracy of fibroscan, compared with histology, in analysis of liver fibrosis in patients with hepatitis B or C: a United States multicenter study. Clin Gastroenterol Hepatol. 2015;13(4):772–779.e1-3.
  • Ettel MG, Appelman HD. Approach to the liver biopsy in the patient with chronic low-level aminotransferase elevations. Arch Pathol Lab Med. 2018;142(10):1186–1190.
  • Gao S, Li X-Y, Fan Y-C, et al. A noninvasive model to predict liver histology in HBeAg-positive chronic hepatitis B with alanine aminotransferase ≤2 upper limit of normal. J Gastroenterol Hepatol. 2017;32(1):215–220.
  • Chen J, Xu CR, Xi M, et al. Predictors of liver histological changes and a sustained virological response to peginterferon among chronic hepatitis B e antigen-positive patients with normal or minimally elevated alanine aminotransferase levels. J Viral Hepat. 2017;24(7):573–579.
  • Rodriguez-Frias F, Buti M, Tabernero D, et al. Quasispecies structure, cornerstone of hepatitis B virus infection: mass sequencing approach. World J Gastroenterol. 2013;19(41):6995–7023.
  • McNaughton AL, D’Arienzo V, Ansari MA, et al. Insights from deep sequencing of the HBV genome-unique, tiny, and misunderstood. Gastroenterology. 2019;156(2):384–399.
  • Liu F, Chen L, Yu D-M, et al. Evolutionary patterns of hepatitis B virus quasispecies under different selective pressures: correlation with antiviral efficacy. Gut. 2011;60(9):1269–1277.
  • Chen L, Zhang Q, Yu D-m, et al. Early changes of hepatitis B virus quasispecies during lamivudine treatment and the correlation with antiviral efficacy. J Hepatol. 2009;50(5):895–905.
  • Gregori J, Perales C, Rodriguez-Frias F, et al. Viral quasispecies complexity measures. Virology. 2016;493:227–237.
  • Sarangi AN, Goel A, Aggarwal R. Methods for studying gut microbiota: a primer for physicians. J Clin Exp Hepatol. 2019;9(1):62–73.
  • Porter TM, Hajibabaei M. Scaling up: a guide to high-throughput genomic approaches for biodiversity analysis. Mol Ecol. 2018;27(2):313–338.
  • Libbrecht MW, Noble WS. Machine learning applications in genetics and genomics. Nat Rev Genet. 2015;16(6):321–332.