Bioinformatic curation and alignment of genotyped hepatitis B virus (HBV) sequence data from the GenBank public database

Abstract

Background Hepatitis B virus (HBV) DNA sequence data from thousands of samples are present in the public sequence databases. No publicly available, up-to-date, multiple sequence alignments, containing full-length and subgenomic fragments per genotype, are available. Such alignments are useful in many analysis applications, including data-mining and phylogenetic analyses.ResultsBy issuing a query, all HBV sequence data from the GenBank public database was downloaded (67,893 sequences). Full-length and subgenomic sequences, which were genotyped by the submitters (30,852 sequences), were placed into a multiple sequence alignment, for each genotype (genotype A: 5868 sequences, B: 4630, C: 7820, D: 8300, E: 2043, F: 985, G: 189, H: 108, I: 23), according to the results of offline BLAST searches against a custom reference library of full-length sequences. Further curation was performed to improve the alignment.Conclusions The algorithm described in this paper generates, for each of the nine HBV genotypes, multiple sequence alignments, which contain full-length and subgenomic fragments. The alignments can be updated as new sequences become available in the online public sequence databases. The alignments are available at http://hvdr.bioinf.wits.ac.za/alignments.

Identification of hepatitis B virus genotype I in Thailand

“…Sequences were merged with reference sequence alignments including 29 complete HBV genotype I genomes obtained from a comprehensive alignment generated from the Genbank database on 13 February 2018 (version 1.0 alignment from Bell et al), plus eight additional published complete genome sequences in BioEdit v7.2.5 . Neighbor‐joining HBV phylogenetic trees were generated as previously described, and trees were visualized using FigTree software (version 1.4.2; A. Rambaut, Institute of Evolutionary Biology, University of Edinburgh, Scotland).…”

“…Recombinant analysis was completed using Simplot (version 3.5.1) using a window of 400 basepairs (bp), step size of 20 bp, GapStrip on, 100 reps, Kimura two‐parameter, T/t 2.0, and neighbor‐joining settings. Genetic distances were calculated in BioEdit with complete genotype A to H reference strain sequence alignments generated from the Genbank database on 26 June 2017 (version 0.4 alignment from Bell et al).…”

“…Accurate diagnosis of HBV is a critical initial step in caring for patients with HBV and preventing new transmissions; however, the diversity of HBV sequences presents a challenge for diagnostic tests . It has been estimated that HBV was first introduced into the human population approximately 33 600 years ago, and since then it has evolved to nine unique genotypes (A‐I) and a growing list of more than 30 subgenotypes . This diversity is largely driven by the error‐prone viral reverse transcription polymerase, which lacks proofreading abilities and intergenotypic recombination .…”

“…HBV genotypes and subgenotypes are unevenly distributed, with each HBV genotype predominating in unique regions of the world . In particular, HBV genotype I (HBV‐I) has been found in China, India, Laos, and Vietnam, with 39 unique sequences confirmed cases in Asia to date . In addition to these cases, HBV‐I strains have also been sequenced from Vietnamese immigrants living in Canada and France, indicating that a more widespread distribution may exist for HBV‐I outside of the Asia.…”

“…2 It has been estimated that HBV was first introduced into the human population approximately 33 600 years ago, 3 and since then it has evolved to nine unique genotypes (A-I) and a growing list of more than 30 subgenotypes. [4][5][6] This diversity is largely driven by the error-prone viral reverse transcription polymerase, which lacks proofreading abilities and intergenotypic recombination. 6,7 HBV genotypes and subgenotypes are unevenly distributed, with each HBV genotype predominating in unique regions of the world.…”