A rare HBV subgenotype D4 with unique genomic signatures identified in north-eastern India--an emerging clinical challenge?

• Published in: PloS one 2014-10, Vol.9 (10), p.e109425
• Main Authors: Banerjee, Priyanka, Mondal, Rajiv Kumar, Nandi, Madhuparna, Ghosh, Sumantra, Khatun, Mousumi, Chakraborty, Nabendu, Bhattacharya, Swatilekha, RoyChoudhury, Arindam, Banerjee, Soma, Santra, Amal, Sil, Samir, Chowdhury, Abhijit, Bhaumik, Pradip, Datta, Simanti
• Format: Article
• Language: English
• Subjects: Adaptive radiation; Adult; Amino acids; Anti-virus software; Antigens; Antiviral agents; Antivirus programs; Biological evolution; Blood & organ donations; Demography; Deoxyribonucleic acid; Diagnostic systems; Divergence; DNA; DNA sequencing; Enzymes; Epidemiology; Female; Gene sequencing; Genome, Viral - genetics; Genomes; Genomics; Genotype; Genotypes; Health education; Hepatitis; Hepatitis B virus - classification; Hepatitis B virus - genetics; Hepatitis B virus - physiology; Hepatitis B, Chronic - epidemiology; Hepatitis B, Chronic - virology; Hepatology; Historic sites; Humans; India - epidemiology; Infections; Lamivudine; Liver diseases; Male; Medical residencies; Medicine and Health Sciences; Migrants; Migration; Minority & ethnic groups; Mitochondrial DNA; Molecular Sequence Data; Mutation; Open Reading Frames - genetics; Phylogeny; Population; Radiation; Recombination; Regulatory Sequences, Nucleic Acid - genetics; Serological tests; Signatures; Vaccination; Viral infections
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0109425

HBV has been classified into ten genotypes (A-J) and multiple subgenotypes, some of which strongly influence disease outcome and their distribution also correlate with human migration. HBV infection is highly prevalent in India and its diverse population provides an excellent opportunity to study the distinctiveness of HBV, its evolution and disease biology in variegated ethnic groups. The North-East India, having international frontiers on three sides, is one of the most ethnically and linguistically diverse region of the country. Given the paucity of information on molecular epidemiology of HBV in this region, the study aimed to carry out an in-depth genetic characterization of HBV prevailing in North-East state of Tripura. From sera of chronically HBV infected patients biochemical/serological tests, HBV DNA quantification, PCR-amplification, sequencing of PreS/S or full-length HBV genomes were done. HBV genotype/subgenotype determination and sequence variability were assessed by MEGA5-software. The evolutionary divergence times of different HBV subgenotypes were estimated by DNAMLK/PHYLIP program while jpHMM method was used to detect any recombination event in HBV genomes. HBV genotypes D (89.5%), C (6.6%) and A (3.9%) were detected among chronic carriers. While all HBV/A and HBV/C isolates belonged to subgenotype-A1 and C1 respectively, five subgenotypes of HBV/D (D1-D5) were identified including the first detection of rare D4. These non-recombinant Indian D4 (IndD4) formed a distinct phylogenetic clade, had 2.7% nucleotide divergence and recent evolutionary radiation than other global D4. Ten unique amino acids and 9 novel nucleotide substitutions were identified as IndD4 signatures. All IndD4 carried T120 and R129 in ORF-S that may cause immune/vaccine/diagnostic escape and N128 in ORF-P, implicated as compensatory Lamivudine resistance mutation. IndD4 has potential to undermine vaccination programs or anti-viral therapy and its introduction to North-East India is believed to be linked with the settlement of ancient Tibeto-Burman migrants from East-Asia.