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

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.