Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

• Published in: Journal of general virology Vol. 101; no. 3; pp. 271 - 283
• Main Authors: McNaughton, Anna L., Revill, Peter A., Littlejohn, Margaret, Matthews, Philippa C., Ansari, M. Azim
• Format: Journal Article
• Language: English
• Published: England Microbiology Society 01.03.2020
• Subjects: Base Sequence - genetics; Databases, Genetic; DNA, Viral - genetics; Genome, Viral; Genotype; Hepatitis B - virology; Hepatitis B virus - genetics; Humans; Phylogeny; Sequence Analysis, DNA; reference sequences; phylogenetics; HBV; whole genome
• ISSN: 0022-1317; 1465-2099; 1465-2099
• DOI: 10.1099/jgv.0.001387

Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A–I), and a putative 10th genotype (J), characterized thus far. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level. All of the generated data, including the alignments, phylogenies and chosen reference sequences, are available online ( https://doi.org/10.6084/m9.figshare.8851946 ) as a simple open-access resource.