Recombinant identification, molecular classification and proposed reference genomes for hepatitis delta virus

Abstract

Hepatitis delta virus (HDV), as a defective sub-virus that co-infects with hepatitis B virus, imposes an emerging global health burden. However, genetic characteristics and molecular classification of HDV remain under investigated. In this study, we have systematically retrieved and analysed a large set of HDV full-length genome sequences and identified novel recombinants. Based on phylogenetic and genetic analyses, we have established an updated classification system for HDV when recombinants were excluded. Furthermore, we have mapped the global distribution of different genotypes and subtypes. Finally, we have compiled a complete set of reference genomes for each subtype and proposed criteria for future identification of novel genotypes and subtypes. Of note, the global distribution map indicates that currently available HDV genetic data remain limited, and thus our proposed classification will likely evolve as future epidemiological data will accumulate. These results will facilitate the future research on the diagnosis, screening, epidemiology, evolution, prevention and clinical management of HDV infection.

Keywords: cRNA; genetic recombination; genotype; hepatitis delta virus; viral RNA; viral genome.

Figure 1

Phylogenetic analysis of 312 hepatitis delta virus (HDV) full‐length antigenomic RNA (cRNA) sequences. The maximum‐likelihood (ML) tree of eight HDV genotypes with subtypes showing the overall classification framework. All original HDV full‐length genomic RNA sequences were transformed to cRNA sequences and standardized to read from 1 to 1678. The tree was reconstructed using the best DNA model, General Time Reversible (GTR) model of evolution with 5 rate categories (G) and invariable sites (I). Potential recombinants were excluded from the tree. Branch support was calculated using 1000 replications, and only bootstrap values >70% are shown. The tree was rooted with woodchuck hepatitis B virus (WHV)

Figure 2

Genetic analysis of 312 hepatitis delta virus (HDV) full‐length antigenomic RNA (cRNA) sequences. Cartoon representation of the identification criteria of HDV novel genotype or subtype. The comparisons of mean intergenotypic and intersubtypic nucleotide similarity and genetic distance were based on 312 HDV full‐length cRNA sequences. Axes show the percentage similarity and genetic distance, respectively. The blue dash line indicates the lowest range of intergenotypic nucleotide similarity and genetic distance, the red dash line indicates the cut‐off range between genotype and subtype, and the green dash line indicates the highest range of intersubtypic nucleotide similarity and genetic distance. The detailed results of calculation were shown in Figure S5A,B

Figure 3

Worldwide distribution of hepatitis delta virus (HDV) genotypes and subtypes. Data were based on HDV full‐length genomic sequences. This map was modified according to the free map templates (http://d-maps.com/carte.php?num_car=13180&lang=en) using Inkscape 0.92.2 software