Phylogenetic relatedness and genetic diversity of hepatitis B virus isolates in Eastern India

Abstract

Hepatitis B virus (HBV) has been classified into eight genotypes, and several subgenotypes, distinctly distributed geographically. The genotypes A and D were previously reported to be predominant in India. Recent studies indicated evidence of circulation of genotype C in Eastern part of India. With the aim to confirm the phylogenetic relation and molecular genetic characteristics of the HBV circulating in Kolkata, the most populous city in Eastern India, 11 strains were isolated and the complete genome sequences were analyzed. Phylogenetic analysis determined; three genotype C (adr-serotype) isolates closely related with C1 (Cs) subgenotype references from South East Asia, and three genotype A (adw2-serotype) isolates, related to Asia-variant references of subgenotype A1 (Aa). Whereas, five genotype D (ayw2, ayw3 serotype) isolates were highly divergent; one was related to subgenotype D1, two to subgenotype D3, and the remaining two clustered with a single genotype D isolate from Japan belonging to an unclassified subgenotype. Together, these two isolates differed from HBV D1-D4 subgenotypes by nucleotide differences ranging from 5.0 to 5.49%, probably indicating a new subgenotype, which we designate as D5. All serotype ayw3 of genotype D isolates had specific amino acid substitution Threonine at codon 118 and Methionine at codon 125 in antigenic determinant of surface gene that has not been reported previously in isolates from other parts of India. In conclusion; using the complete genome analyses this study has confirmed circulation of the genotype C in Eastern part of India and demonstrated considerable genotypic heterogeneity of the Indian genotype D.

Occult hepatitis B infection among individuals belonging to the aboriginal Nicobarese tribe of India

“…The forward and reverse sequences collected from the sequencer were checked and manually edited in the electro-pherograms using the SeqScape version 2.5 (Applied Biosystems) and MEGA5 software [12]. Genotyping was performed on the basis of phylogenetic relationship, taking 345 base pair sequences along with representative reference sequences from different sub genotypes as described earlier for hepatitis B virus [13,14]. Phylogenetic grouping using a bootstrap neighbour-joining (NJ) analysis with 1,000 replications was performed using the S gene sequence of HBV isolated from Nicobarese tribes and that of other representative sequences submitted in the NCBI database.…”

Hepatitis B virus taxonomy and hepatitis B virus genotypes

“…However, this is not true for genotype D with subgenotypes D1, D2 and D3 being described as widespread in the world; e.g. D3 was found in Asia (East India) [40] , South Africa [41] and Europe (Serbia) (Stanojevic et al, unpublished results).…”

Identification of Novel D11 Hepatitis B Surface Antigen Subgenotype in Jeddah, Kingdom of Saudi Arabia

“…HBV/C is associated with more severe liver diseases than HBV/ B (Kramvis et al, 2008;Sugauchi et al, 2004;Banerjee et al, 2006;Huy et al, 2006;Sakamoto et al, 2006) while contrary studies reported similarity on the risk of HCC development in either HBV/B or HBV/C infection (Kao et al, 2003;Sumi et al, 2003;Yuen et al, 2003Yuen et al, , 2009. Also, patients infected with HBV/D appear to have a higher incidence of HCC (Chan and Sung, 2006) whereas patients with either HBV/C or HBV/D have a lower response rate to treatment with IFN-α compared to those with HBV/A and HBV/B (Zollner et al, 2001).…”