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Hepatitis C virus subtyping in Uttarakhand, India: a comparative study

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Abstract

The objective of this study was to compare Reverse Hybridisation Assay with conventional sequencing for determination of Hepatitis C Virus Genotype and Subtypes. Anti-HCV antibody was determined followed by HCV RNA extraction which was used for (1) viral load determination (2) qualitative real-time PCR RHA for genotyping and (3) conventional sequencing. Compared to conventional sequencing, accuracy of RHA results was 96.55% for determination of genotype (κ = 0.93) and 89.66% for subtype (κ = 0.85). Sensitivity, specificity, negative predictive value (NPV) and positive predictive value (PPV) of the qualitative PCR were 82.29%, 100%, 44.44% and 100% respectively with an accuracy of 86.84%. RHA is a less time consuming and cheaper method for determination of HCV genotype and subtype yet results must be interpreted with caution and quality control monitoring should be strictly followed to ensure validity.

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References

  1. Goletti S, Zuyten S, Goeminne L, Verhofstede C, Rodriguez-Villalobos H, Bodeus M, et al. Comparison of Sanger sequencing for hepatitis C virus genotyping with a commercial line probe assay in a tertiary hospital. BMC Infect Dis. 2019;19(1):738.

    Article  Google Scholar 

  2. Ceccherini Silberstein F, Di Maio VC, Aragri M, Ciotti M, Cento V, Perno CF. Hepatitis C virus gene sequencing as a tool for precise genotyping in the era of new direct antiviral agents. Hepatology. 2016;63(3):1058–9.

    Article  Google Scholar 

  3. Verma V, Chakravarti A. Comparison of 5’ Noncoding-Core with 5’ Noncoding Regions of HCV by RT-PCR: Importance and Clinical Implications. Curr Microbiol. 2008;57:206–11.

    Article  CAS  Google Scholar 

  4. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406–25.

    CAS  PubMed  Google Scholar 

  5. Lole KS, Jha JA, Shrotri SP, Tandon BN, Prasad VGM, Arankalle VA. Comparison of Hepatitis C virus genotyping by 5′ noncoding region- and core-based reverse transcriptase PCR assay with sequencing and use of the assay for determining subtype distribution in India. J Clin Microbiol. 2003;41(11):5240–4.

    Article  CAS  Google Scholar 

  6. Prakash S, Shukla S, Ramakrishna V, Jain A. Distribution of hepatitis C genotypes in Uttar Pradesh, India; rare genotype 4 detected. J Med Virol. 2018;90(12):1875–81.

    Article  CAS  Google Scholar 

  7. International Committee on Taxonomy of Viruses (ICTV). Confirmed HCV genotypes/subtypes (2019) [Internet]. 2019 [cited 2019 Sep 15]. Available from: https://talk.ictvonline.org/ictv_wikis/flaviviridae/w/sg_flavi/634/table-1---confirmed-hcv-genotypes-subtypes-may-2019

  8. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–9.

    Article  CAS  Google Scholar 

  9. Naggie S, Wyles DL. Hepatitis C. In: Bennett JE, Dolin R, Blaser MJ, editors. Mandell, Douglas and Bennett’s Principles and Practices of Infectious Diseases. 9th ed. Philadelphia: Elsevier; 2020. p. 2040–71.

    Google Scholar 

  10. Bartenschlager R, Lohmann V. Replication of hepatitis C virus. J Gen Virol. 2000;81(7):1631–48.

    CAS  PubMed  Google Scholar 

  11. Robertson B, Myers G, Howard C, Brettin T, Bukh J, Gaschen B, et al. Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: Proposals for standardization. Arch Virol. 1998;143(12):2493–503.

    Article  CAS  Google Scholar 

  12. Simmonds P, Smith DB, McOmish F, Yap PL, Kolberg J, Urdea MS, et al. Identification of genotypes of hepatitis C virus by sequence comparisons in the core, E1 and NS-5 regions. J Gen Virol. 1994;75(5):1053–61.

    Article  CAS  Google Scholar 

  13. Chen Z, Weck KE. Hepatitis C virus genotyping: Interrogation of the 5′ untranslated region cannot accurately distinguish genotypes 1a and 1b. J Clin Microbiol. 2002;40(9):3127–34.

    Article  CAS  Google Scholar 

  14. Bukh J, Miller RH, Purcell RH. Genetic heterogeneity of hepatitis C virus: Quasispecies and genotypes. Semin Liver Dis. 1995;15(1):41–63.

    Article  CAS  Google Scholar 

  15. Cai Q, Zhao Z, Liu Y, Shao X, Gao Z. Comparison of three different HCV genotyping methods: Core, NS5B sequence analysis and line probe assay. Int J Mol Med. 2013;31(2):347–52.

    Article  CAS  Google Scholar 

  16. Zeuzem S, Rüster B, Lee JH, Stripf T, Roth WK. Evaluation of a reverse hybridization assay for genotyping of hepatitis C virus. J Hepatol. 1995;23(6):654–61.

    Article  CAS  Google Scholar 

  17. Stelzl E, Van Der MC, Gouw R, Beld M, Grahovac M, Marth E, et al. Determination of the hepatitis C virus subtype: comparison of sequencing and reverse hybridization assays. Clin Chem Lab Med. 2007;45(2):167–70.

    Article  CAS  Google Scholar 

  18. Polilli E, Cento V, Restelli U, Ceccherini-Silberstein F, Aragri M, Di Maio VC, et al. Consequences of inaccurate hepatitis C virus genotyping on the costs of prescription of direct antiviral agents in an Italian district. Clin Outcomes Res. 2016;8:467–73.

    Article  Google Scholar 

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Acknowledgements

We would like to thank all the staff of departments of Microbiology and Gastroenterology at the All India Institute of Medical Sciences, Rishikesh. Above all we would like to thank all the patients who have kindly consented to be a part of study and made this work possible.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

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Authors and Affiliations

  1. Department of Microbiology, All India Institute of Medical Sciences, Veerbhadra Marg, Dehradun, Rishikesh, 249203, Uttarakhand, India

    Kuhu Chatterjee, Deepjyoti Kalita, Balram Ji Omar, Mithilesh Kumar Jha & Pratima Gupta

  2. Department of Gastroenterology, All India Institute of Medical Sciences, Rishikesh, India

    Rohit Gupta

  3. Department of Microbiology, All India Institute of Medical Sciences, Patna, India

    Mithilesh Kumar Jha

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  1. Kuhu Chatterjee
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  2. Deepjyoti Kalita
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  5. Mithilesh Kumar Jha
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Correspondence to Deepjyoti Kalita.

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Ethical approval

This pilot study was done at a tertiary care centre in Uttarakhand protocol for which was approved by Institutional ethics committee (AIIMS/IEC/111/18).

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Informed written consent was obtained from all participants.

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Chatterjee, K., Kalita, D., Omar, B.J. et al. Hepatitis C virus subtyping in Uttarakhand, India: a comparative study. VirusDis. 32, 576–581 (2021). https://doi.org/10.1007/s13337-021-00729-9

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  • DOI: https://doi.org/10.1007/s13337-021-00729-9

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