Molecular characterization of Hepatitis C Virus (HCV) from hospitalised cases of hepatitis in six northeastern states of India

Background: Viral hepatitis is of global importance and inflicts a huge healthcare cost in northeast India where its prevalence and the prevalence of drug-resistant variants are not well known. Hepatotropic viruses (hepatitis B virus, hepatitis A virus, hepatitis C virus and hepatitis E virus) are known to cause ‘viral hepatitis.’ This study documents the prevalence and genotype of Hepatitis C Virus (HCV) in northeast India.Aim: Identification of Hepatitis C Virus (HCV) genotypes with their resistance-associated variants (RAVs) could facilitate the development of selective antiviral drug regimens against HCV infection. The present study aims to identify the HCV genotype from six northeastern states of India.Methods: The study was carried out between 2018-2022 from hospitalised cases of viral hepatitis in six northeastern states of India namely Assam, Meghalaya, Mizoram, Nagaland, Tripura and Manipur. A total of 1300 subjects were enrolled, from whom 88 HCV-positive samples were processed for molecular characterisation.Results: Of the 88 samples evaluated for genotyping and sub-typing, 58 (66%) were HCV genotype 3b, 15 (17%) were 3a, 8 (9 %) were 6n, 2 (2%) were 6xa, 3 (3 %) were 1a, and 2 (2 %) were 1b respectively. Genotype 6n was common among injecting drug users (IDUs) (5/8; 62.5%). Resistance-associated variants (RAVs) 30K and 31M of HCV NS5A region were observed in 5/30 (16.6%) HCV genotype 3b. This could indicate likely resistance to directly acting antivirals (DAAs) targeting the NS5A of HCV. RAVs C316N mutation of NS5B region was also observed in 1/1 (100%) of HCV genotypes 1b.Conclusion: A higher prevalence of HCV genotype 3b was observed in the study population. Furthermore, overlapping of RAVs 30K and 31M of HCV NS5A region with HCV genotype 3b may pose treatment failure. Genotypes HCV 6n and HCV 6xa were also identified, which may be the first to be reported from northeastern parts of India.