Analysis of the full‐length genomes of novel hepatitis B virus subgenotypes C11 and C12 in Papua, Indonesia

Abstract

Two novel subgenotypes (C6 and D6) of hepatitis B virus (HBV) were identified recently in Papua, a multiethnic area of Indonesia. To characterize further the HBV strains in Papua, serum samples collected from 59 viremic subjects (44 males and 15 females; mean age: 30.0 ± 15.5 years) among indigenous inhabitants in Papua, were subjected to phylogenetic analysis of an 1.6-kb partial sequence. Forty-five samples (76%) had genotype C HBV (HBV/C) [C5 (n = 1), C6 (n = 40), and unclassifiable (n = 4)], while seven samples (12%) were HBV/D [D1 (n = 1) and D6 (n = 6)] and six samples (10%) were HBV/B [B2 (n = 1), B3 (n = 3), B7 (n = 1), and B8 (n = 1)]; the remaining sample possessed B3 and C6. An analysis of the full-length sequence of the four HBV/C isolates (NMB09122, NMB09124, NMB09075, and MRK89073) that were unclassifiable into any of the 10 known HBV/C subgenotypes (C1-C10) showed no significant evidence of recombination. Over the entire genome, the NMB09122 and NMB09124 isolates shared 99.8% identity and segregated into a cluster with a bootstrap value of 100%, differing from HBV/C1-HBV/C10 by 3.8-6.9% (mean, ≥4.0%), indicating that NMB09122 and NMB09124 can be classified into a novel subgenotype within genotype C (tentatively designated C11). The NMB09075 and MRK89073 isolates were 97.4% identical to each other and differed from known HBV/C isolates, including the C11 strains, by 4.0-7.2% (mean, ≥4.5%) over the entire genome, indicating that NMB09075 and MRK89703 can be classified into another novel HBV/C subgenotype (C12). The distribution of C11 and C12 seemed to be associated with particular language speakers in Papua.

The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients

“…To detect HBV sequences in our samples, we aligned all short reads from whole-genome sequencing against a comprehensive list (n = 73) of HBV reference genomes (genotype A-I and a strain of Woolly Monkey HBV) (Supplemental Table 2; Zöllner et al 2006;Mulyanto et al 2011). HBV sequences were not detected in samples from the HBV-negative individual but were clearly present in both tumor and nontumor liver samples from the HBV-positive patients (Fig.…”

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

“…This result in agreement with those demonstrated that HBV/D were predominant in the Middle East (Saudy et al, 2003;Norder et al, 2004;Zekri et al, 2007;El Hadad et al, 2013). In addition, present study revealed the presence of multiple subgenotypes of HBV within genotypes D with the predominant distribution of seemingly indigenous subgenotype D1 as well as a new novel subgenotype, tentatively designated D11in Jeddah which meet the proposed rules for classification (Mulyanto et al, 2011;Norder et al, 2004). The identification of HBV isolates of novel sub genotypes in the present study suggested that further studies with a large number of subjects in previously examined and unexamined areas would lead to discovery of HBV strains genotypes even novel subgenotypes circulating in Saudi Arabia.…”

“…The 2nd round of amplification was performed with an initial 5 min preheating at 95°C, followed by 35 cycles 95°C of denaturing for 30 sec at 95°C, annealing for 30 sec at 55°C and an elongation for 1 min at 72°C, with a final extension period of 10 min at 72°C. All PCR contamination precautions were observed and negative controls using sera from subjects with no HBV markers were included (Mulyanto et al, 2011;El Hadad et al, 2013).…”

Molecular Evolution of Hepatitis Viruses

“…Seven subgenotypes are described at the moment for genotype A, 9 for genotype B (Thedja et al, 2011), 12 for genotype C (Mulyanto et al, 2011), 7 for gebnotype D (Meldal et al, 2009) and 4 for genotype F (Devesa et al, 2008). No subgenotypes have been found at present inside genotypes E, G and H. This fact migh be due to the fact that these genotypes might be more recent than the other ones.…”