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

Abstract

The data described in this manuscript, including the genotype alignments (fasta format), consensus sequences and phylogenetic trees (newick format), are available in an open access format on Figshare (

Analysis of Hepatitis B Virus Genotype D in Greenland Suggests the Presence of a Novel Quasi-Subgenotype

“…Phylogenetic analysis circumvents the use of genetic distance as a sole metric for sub-/geno-type naming. Further, while genetic distances between the Greenland taxa and subgenotypes D1 and D2 (3.1 and 3.2%, respectively) are within what McNaughton et al ( 2020 ) cites as the majority of genotype D pairwise distance (i.e., 2–4%, compared to the typical subgenotype divergence of 3–8%), they are also distinctly monophyletic across our methods. Here, we present our inference of 39 Greenland HBV/D taxa as a newly characterized quasi-subgenotype exemplified by this topologically independent lineage.…”

“…As observed in this study, the Greenland HBV clade is well-resolved and clusters completely separately with high confidence by aLRT-SH and posterior probability, and is unique to the geographic region of Greenland. However, in keeping with the suggestion of McNaughton et al ( 2020 ), the Greenland clade may be considered a quasi-subgenotype due to its monophyletic clustering following maximum-likelihood analysis but with a genetic distance separating it from D2 and D1 of ~3%. Based on tree topology, this quasi-subgenotype clusters most closely with HBV subgenotype D2.…”

“…It is a well-known observation that subgenotype D1 shows intergroup divergence with D2 <4–7.5% divergence agreed upon as the definition of an HBV subgenotype (Yousif and Kramvis, 2013 ; McNaughton et al, 2020 ). The justification for classifying D1 and D2 as subgenotypes is based upon well-resolved phylogenetic clustering, supported by high bootstrap values (>85–90%), different serological subtypes, and different geographic distribution (Yousif and Kramvis, 2013 ).…”

“…Precedent sorting of genotype identity is calculated by a distance-based sequence threshold of 8% (Okamoto et al, 1988 ; Zhou and Holmes, 2007 ; Locarnini et al, 2013 ; Araujo, 2015 ; Lin and Kao, 2015 ; Littlejohn et al, 2016 ). Subgenotypes are traditionally assigned based on a 4–7.5% threshold across the full genome (McNaughton et al, 2020 ), though new phylogenetic inference methods to determine subgenotype have been suggested (Yin et al, 2019 ). McNaughton et al ( 2020 ) notes that all genotypes have subgenotype sequence divergence rates of 3–8%, with the exception of genotype D, which is 2–4%, indicating a lack of long evolutionary branches separating well-defined clades.…”

“…Subgenotypes are traditionally assigned based on a 4–7.5% threshold across the full genome (McNaughton et al, 2020 ), though new phylogenetic inference methods to determine subgenotype have been suggested (Yin et al, 2019 ). McNaughton et al ( 2020 ) notes that all genotypes have subgenotype sequence divergence rates of 3–8%, with the exception of genotype D, which is 2–4%, indicating a lack of long evolutionary branches separating well-defined clades. Recent suggestions for HBV taxonomic nomenclature include assigning the term “quasi-subgenotype” to a lineage that does not meet the criteria nor clearly belongs to a defined subgenotype based on <4% nucleotide divergence among complete genomes following detailed phylogenetic analysis (Pourkarim et al, 2010 ).…”