New HBV subgenotype D9, a novel D/C recombinant, identified in patients with chronic HBeAg‐negative infection in Eastern India

Abstract

Genome diversity is a hallmark of hepatitis B virus (HBV), which allowed its classification into 10 genotypes (A-J) and numerous subgenotypes. Among them, Genotype D is currently segregated into eight subgenotypes (D1-D8). Here, we report the identification and characterization of a novel subgenotype within genotype D of HBV from chronic hepatitis B e antigen (HBeAg)-negative patients of Eastern India. Phylogenetic tree analysis based on complete genome sequences revealed that six of 39 HBV/D isolates formed a distinct cluster supported by high bootstrap value and had nucleotide divergence >4% relative to the known D subgenotypes (D1-D8), justifying their assignment into a new subgenotype (D9). By comparing the amino acid sequences of the four ORFs of HBV/D9 with D1-D8, 36 specific residues, including a unique one (E(112) in the core region), were identified that could be considered as a signature of D9. Further analysis by Simplot, BootScan and jpHMM demonstrated that D9 resulted from a discrete recombination with genotype C over the precore-core region. This type of recombination has not been described previously as all C/D recombinants reported so far possessed genotype C backbones with mosaic fragments derived from HBV/D. Interestingly, compared to other subgenotypes of HBV/D, D9 isolates had a higher frequency of mutations (A1762T and G1764A) in the basal core promoter region that had been implicated in the development of hepatocellular carcinoma. Further investigations are needed to determine the overall prevalence and clinical significance of these newly characterized D9 strains and to assess the impact of inter-genotypic recombination on viral properties.

Unravelling the history of hepatitis B virus genotypes A and D infection using a full-genome phylogenetic and phylogeographic approach

“…With regard to genotype D, previously named ‘D4’, ‘D5’, ‘D6’, ‘D7’, ‘D8’, ‘D9’ were classified as RS-D4, RS-D5, RS-D6, RS-D7, RS-D8, RS-D9, respectively. This was due to the putative recombinant nature of these subgenotypes (Yousif and Kramvis, 2013; Meldal et al, 2009; Ghosh et al, 2013, 2012). …”

“…RS-D4 (formerly ‘D4’) is found in Haiti, the Arctic and Oceania (Yousif and Kramvis, 2013; Norder et al, 2004), RS-D5 (formerly ‘D5’) circulates mainly in indigenous populations in India (Banerjee et al, 2006), RS-D6 (formerly ‘D6’) in Tunisia, Morocco and Madagascar (Kitab et al, 2011; Meldal et al, 2009). RS-D8 and RS-D9 (formerly ‘D8’ and ‘D9’) have been found in Niger (Abdou Chekaraou et al, 2010) and India (Ghosh et al, 2013), respectively. An updated classification of genotype D has been published (Pourkarim et al, 2010; Yousif and Kramvis, 2013; Pourkarim et al, 2014).…”

Epidemiology of HBV subgenotypes D

“…D8 and D9 are recently described genotypes and reported from Niger and India, respectively [20,59]. Subgenotype D8 is a recombination between genotypes D and E and D9 is a novel D/C recombination.…”

“…It seems to be relatively common in Eastern India [20]. Ghosh et al described 13 HBV(+) patients with D5 subgenotype from a primitive tribal community in eastern India (15).…”

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

“…Recently, new HBV subgenotype has been classified and designated as HBV/B3 using the partial sequence of the S gene (Lusida et al, 2008). Also the novel HBV/D9 have been classified from isolates showed recombination between genotype D and C in the pre core/core region, although the pre-S/S ORF didn't possess any unique motif that can distinguish HBV/D9 isolates from the other eight subgenotypes of D. Moreover, the sequencing of only the pre-S/S region that is frequently practiced for defining genotype/subgenotype will lead to their improper classification as subgenotype D3 or D2 (Ghosh et al, 2013). The previous suggestion confirmed by present phylogenetic tree, where pre S/S sequence analysis of HBV/D9 previously revealed that one isolate was belonged to do HBV/D2 while the other was clustered in specific branch.…”