1887

Journal of General Virology header logo

Volume 102, Issue 7

High prevalence of tryptophan-truncated S quasispecies in treatment-naïve chronic hepatitis B patients No Access

Abstract

Hepatitis B virus surface antigen (HBsAg) encoded by the S gene is highly expressed during the replication cycle of hepatitis B virus (HBV). However, the frequent usage of tryptophan in HBsAg, which leads to a high cost of biosynthesis, is inconsistent with the high expression level of this protein. Tryptophan-truncated mutation of HBsAg, that is, a tryptophan to stop codon mutation resulting in truncated HBsAg, might help to maintain its high expression with lower biosynthetic cost. We aimed to investigate the prevalence of tryptophan-truncated S quasispecies in treatment-naïve patients with chronic hepatitis B (CHB) by applying CirSeq as well as a site-by-site algorithm developed by us to identify variants at extremely low frequencies in the carboxyl terminus of HBsAg. A total of 730 mutations were identified in 27 patients with CHB, varying from seven to 56 mutations per sample. The number of synonymous mutations was much higher than that of nonsynonymous mutations in the reverse transcriptase (RT) coding region and vice versa in the S coding region, implying that the evolutionary constraints on the RT and S genes might be different. We showed that 25 (92.6 %) of 27 patients had at least one S-truncated mutation, most of which were derived from tryptophan, indicating a high prevalence of tryptophan-truncated S mutations in treatment-naïve patients with CHB. In terms of the RT gene, 21 (77.8 %) patients had pre-existing drug-resistant mutations, while no truncated mutations were detected. Our findings that tryptophan-truncated S quasispecies and drug-resistant RT mutants were highly prevalent in treatment-naïve patients with CHB provide new insights into the composition of the HBV population, which might help optimize the treatment and management of patients with CHB.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): circle sequencing , drug-resistant mutation , Hepatitis B virus surface antigen , truncated mutation and tryptophan
Funding
This study was supported by the:
  • National Major Science and Technology Projects of China (Award 2017ZX10202203-007-005)
    • Principle Award Recipient: LungenLu
  • Shanghai General Hospital (Award 02.06.01.20.01)
    • Principle Award Recipient: huidong
  • Science and Technology Commission of Shanghai Municipality (Award 18ZR1427300)
    • Principle Award Recipient: huidong
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001623
2021-07-22
2024-04-18
Loading full text...

Full text loading...

References

  1. Summers J, Mason WS. Replication of the genome of a hepatitis B--like virus by reverse transcription of an RNA intermediate. Cell 1982; 29:403–415 [View Article] [PubMed]
     [Google Scholar]
  2. Seeger C, Mason WS. Hepatitis B virus biology. Microbiol Mol Biol Rev 2000; 64:51–68 [View Article] [PubMed]
     [Google Scholar]
  3. Nowak MA, Bonhoeffer S, Hill AM, Boehme R, Thomas HC et al. Viral dynamics in hepatitis B virus infection. Proc Natl Acad Sci U S A 1996; 93:4398–4402 [View Article] [PubMed]
     [Google Scholar]
  4. Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev 2012; 76:159–216 [View Article] [PubMed]
     [Google Scholar]
  5. Zhou B, Dong H, He Y et al. Composition and interactions of hepatitis B virus quasispecies defined the virological response during telbivudine therapy. Sci Rep 2015; 5:17123 [View Article] [PubMed]
     [Google Scholar]
  6. Ning X, Nguyen D, Mentzer L et al. Secretion of genome-free hepatitis B virus—single strand blocking model for virion morphogenesis of para-retrovirus. PLoS Pathog 2011; 7:e1002255 [View Article] [PubMed]
     [Google Scholar]
  7. Bruss V. Hepatitis B virus morphogenesis. World J Gastroenterol 2007; 13:65–73 [View Article] [PubMed]
     [Google Scholar]
  8. Seligmann H. Cost-Minimization of Amino Acid Usage. J Mol Evol 2003; 56:151–161 [View Article] [PubMed]
     [Google Scholar]
  9. Heizer EM, Raymer ML, Krane DE. Amino Acid Biosynthetic Cost and Protein Conservation. J Mol Evol 2011; 72:466–473 [View Article] [PubMed]
     [Google Scholar]
  10. Wagner A. Energy constraints on the evolution of gene expression. Mol Biol Evol 2005; 22:1365–1374 [View Article] [PubMed]
     [Google Scholar]
  11. Zhang H, Wang YR, Li J et al. Biosynthetic energy cost for amino acids decreases in cancer evolution. Nat Commun 2018; 9:4124 [View Article] [PubMed]
     [Google Scholar]
  12. Dong H, Zhou B, Kang H et al. Small surface antigen variants of HBV associated with responses to telbivudine treatment in chronic hepatitis B patients. Antivir Ther 2017; 22:43–51 [View Article] [PubMed]
     [Google Scholar]
  13. Ding H, Liu B, Zhao C et al. Amino acid similarities and divergences in the small surface proteins of genotype C hepatitis B viruses between nucleos(t)ide analogue-naïve and lamivudine-treated patients with chronic hepatitis B. Antiviral Res 2014; 102:29–34 [View Article] [PubMed]
     [Google Scholar]
  14. Cento V, Van Hemert F, Neumann-Fraune M et al. Anti-HBV treatment induces novel reverse transcriptase mutations with reflective effect on HBV S antigen. J Infect 2013; 67:303–312 [View Article] [PubMed]
     [Google Scholar]
  15. Komla-Soukha I, Sureau C. A tryptophan-rich motif in the carboxyl terminus of the small envelope protein of hepatitis B virus is central to the assembly of hepatitis delta virus particles. J Virol 2006; 80:4648–4655 [View Article] [PubMed]
     [Google Scholar]
  16. Margeridon-Thermet S, Shulman NS, Ahmed A et al. Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis 2009; 199:1275–1285 [View Article] [PubMed]
     [Google Scholar]
  17. Loman NJ, Misra RV, Dallman TJ et al. Performance comparison of benchtop highthroughput sequencing platforms. Nat Biotechnol 2012; 30:434–439 [View Article] [PubMed]
     [Google Scholar]
  18. Lou DI, Hussmann JA, McBee RM et al. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc Natl Acad Sci U S A 2013; 110:19872–19877 [View Article] [PubMed]
     [Google Scholar]
  19. Acevedo A, Brodsky L, Andino R. Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature 2014; 505:686–690 [View Article] [PubMed]
     [Google Scholar]
  20. Korboukh VK, Lee CA, Acevedo A et al. RNA virus population diversity, an optimum for maximal fitness and virulence. J Biol Chem 2014; 289:29531–29544 [View Article] [PubMed]
     [Google Scholar]
  21. Zhou B, Xiao L, Wang Z, Chang ET, Chen J et al. Geographical and ethnic distribution of the HBV C/D recombinant on the Qinghai-Tibet Plateau. PLoS One 2011; 6:e18708 [View Article] [PubMed]
     [Google Scholar]
  22. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article] [PubMed]
     [Google Scholar]
  23. Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci USA 2011; 108:20166–20171 [View Article] [PubMed]
     [Google Scholar]
  24. Yamani LN, Yano Y, Utsumi T et al. Ultradeep Sequencing for detection of quasispecies variants in the major hydrophilic region of hepatitis B virus in Indonesian patients. J Clin Microbiol 2015; 53:3165–3175 [View Article] [PubMed]
     [Google Scholar]
  25. Yeh CT, Chen T, Hsu CW et al. Emergence of the rtA181T/sW172* mutant increased the risk of hepatoma occurrence in patients with lamivudine-resistant chronic hepatitis B. BMC Cancer 2011; 11:398 [View Article] [PubMed]
     [Google Scholar]
  26. Lee SA, Kim K, Kim H, Kim BJ. Nucleotide change of codon 182 in the surface gene of hepatitis B virus genotype C leading to truncated surface protein is associated with progression of liver diseases. J Hepatol 2012; 56:63–69 [View Article] [PubMed]
     [Google Scholar]
  27. Pavesi A. Different patterns of codon usage in the overlapping polymerase and surface genes of hepatitis B virus suggest a de novo origin by modular evolution. J Gen Virol 2015; 96:3577–3586 [View Article] [PubMed]
     [Google Scholar]
  28. Li F, Ding SW. Virus counterdefense: diverse strategies for evading the RNA-silencing immunity. Annu Rev Microbiol 2006; 60:503–531 [View Article] [PubMed]
     [Google Scholar]
  29. Rancurel C, Khosravi M, Dunker AK, Romero PR, Karlin D. Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. J Virol 2009; 83:10719–10736 [View Article] [PubMed]
     [Google Scholar]
  30. Cortese MF, González C, Gregori J et al. Sophisticated viral quasispecies with a genotype-related pattern of mutations in the hepatitis B X gene of HBeAg-ve chronically infected patients. Sci Rep 2021; 11:4215 [View Article] [PubMed]
     [Google Scholar]
  31. Li X, Wang L, Zhong Y et al. 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; 48:4363–4369 [View Article] [PubMed]
     [Google Scholar]
  32. Wenger AM, Peluso P, Rowell WJ et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol 2019; 37:1155–1162 [View Article] [PubMed]
     [Google Scholar]
  33. Wooddell C, Yuen MF, Chan H-Y et al. RNAi-based treatment of chronically infected patients and chimpanzees reveals that integrated hepatitis B virus DNA is a source of HBsAg. Sci Transl Med 2017; 9:eaan0241 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001623
Loading
High prevalence of tryptophan-truncated S quasispecies in treatment-naïve chronic hepatitis B patients
J. Gen. Virol. 102, 001623 (2021); https://doi.org/10.1099/jgv.0.001623
/content/journal/jgv/10.1099/jgv.0.001623
/content/journal/jgv/10.1099/jgv.0.001623
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error