Hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), and hepatitis E virus (HEV) are the most common causes of viral hepatitis in India. HCV causes both acute and chronic liver disease known as hepatitis C. HCV genotypes (GTs) identification is important as it helps in determining the rate of continuing virological response, which influences the course of treatment length. HCV genotyping is useful in molecular epidemiology because it identifies different strains that are prevalent among various regions. Our study aimed to determine the molecular detection and characterization of HCV and its genotypes circulating in the central India during January 2023 to March 2024. HCV antibody ELISA was performed on n=3250 serum samples and a total of n=91 samples tested seropositive for HCV antibody with the seropositivity rate of 2.8%. Among the seropositive samples, n=62 (68.13%) was found to be real time RT-PCR positive and were subjected to the NS5B region specific amplification by conventional PCR. Sequencing of these amplified products revealed Genotype 1 (GT 1) in 20 samples followed by GT 3 in 17 samples. The subtypes detected were 1a (n=18, 48.65%), 1b (n=2, 5.40%), 3a (n=13, 35.14%) and 3b (n=4, 10.81%). In our study, HCV GT 1 (54.05%) was detected in higher followed by GT 3 (45.95%) in this region. Our study findings showed a shift in HCV genotypic distribution patterns when compared to other regions of India. Given the documented differences in the pathogenicity of different HCV genotypes, HCV genotype detection appears to be necessary for better patient management.

During a routine surveillance for exotic and emerging swine viral diseases in India, five samples (four faecal, one serum) showed cytopathic effects in Vero cells. Transmission electron microscopy of infective cell supernatant revealed the presence of two types of virions. De novo metavirome sequencing enabled complete genome assembly of Mammalian orthorubulavirus 5 (MRuV5) and Mammalian orthoreovirus (MRV). The MRuV5 isolates possessed a whole genome of 15246 bp with seven genes (NP, V/P, M, F, SH, HN, L), while the MRV isolates had segmented genome with three large (L1, L2, L3), three medium (M1, M2, M3) and four small (S1, S2, S3, S4) segments. The MRuV5 isolates were genetically grouped with those from various mammalian species reported from South Korea and China. Deduced amino acid sequences of the HN, NP and F gene coding regions of MRuV5 isolates showed the substitutions of three (92L, 111R, 447H), two (86S, 121S) and two (139T, 246T) amino acids, respectively, compared to previously reported strains of the virus. However, they did not reveal any change in predicted amino acid residues at the receptor binding site in HN protein, cleavage site or HN stalk region. S1 gene of the MRV isolates showed the highest nucleotide identity (97.73%) with the MRV3 strain ZJ2013 isolated from pig in China, and these isolates were grouped into MRV type-3. Deduced amino acid sequences of MRV3 S1 gene revealed amino acid residues 198-204NLAIRLP, 249I, 340D, 419E known for sialic acid binding site and neurotropism. We report the co-infection of MRuV5 and MRV3 detected incidentally for the first time in domestic pigs in India. Although MRuV5 and MRV3 develop asymptomatic infections or mild disease in animals and humans, continuous monitoring of evolution and spread of such viruses is important in the current global scenario of increasing threats due to emerging novel pathogens.

African swine fever (ASF), considered as the most dreadful swine disease due to its very high mortality, emerged in India in 2020. The complete genome analysis of ASF viruses isolated during the first outbreaks in India showed a few unique non-synonymous mutations in MGF 369-11L, MGF 505-4R, K205R and B263R genes. Frame shiftsin the protein coding sequences were observed in DP60R, ASFV-G_ACD 00190, MGF 110-10-L- MGF110-14L fusion, MGF 360-14L and I267L genes of Indian ASFVs as compared to ASFV/Georgia/2007. Complete genome based phylogenetic analysis of p72-genotype-II viruses showed the clustering of Indian isolates with ASFV/Wuhan/2019 in a separate clade. Phylogenetic analysis of concatenated sequences of 14 open reading frames (ORF) having single nucleotide polymorphisms (SNP) showed distinct grouping of Indian ASFVs with other Asian ASFVs.Thisis the first complete genome characterization of ASF viruses isolated from domestic pigs in India. The resultsindicate that number of Tandem Repeat Sequence in the intergenic region between I73R and I329L genes, and the 14 ORFs with SNP reported in this study could be the genetic determinants to differentiate the closely related p72-genotype II viruses circulating in Asia.