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bioRxiv · 10.1101/831891

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

McNaughton, A.·Revill, P.·Littlejohn, M.·Matthews, P. C.·Ansari, M. A.
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Abstract

Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), thus far characterised. 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. An alignment of these reference sequences and maximum-likelihood phylogenetic trees of the sequences are provided to simplify classification. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level.

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McNaughton, A., Revill, P., Littlejohn, M., Matthews, P. C., Ansari, M. A.. 2019-11-07. Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences. https://doi.org/10.1101/831891

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