Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses

Abstract

Hepadnaviruses (hepatitis B viruses [HBVs]) are the only animal viruses that replicate their DNA by reverse transcription of an RNA intermediate. Until recently, the known host range of hepadnaviruses was limited to mammals and birds. We obtained and analyzed the first amphibian HBV genome, as well as several prototype fish HBVs, which allow the first comprehensive comparative genomic analysis of hepadnaviruses from four classes of vertebrates. Bluegill hepadnavirus (BGHBV) was characterized from in-house viral metagenomic sequencing. The African cichlid hepadnavirus (ACHBV) and the Tibetan frog hepadnavirus (TFHBV) were discovered using in silico analyses of the whole-genome shotgun and transcriptome shotgun assembly databases. Residues in the hydrophobic base of the capsid (core) proteins, designated motifs I, II, and III, are highly conserved, suggesting that structural constraints for proper capsid folding are key to capsid protein evolution. Surface proteins in all vertebrate HBVs contain similar predicted membrane topologies, characterized by three transmembrane domains. Most striking was the fact that BGHBV, ACHBV, and the previously described white sucker hepadnavirus did not form a fish-specific monophyletic group in the phylogenetic analysis of all three hepadnaviral genes. Notably, BGHBV was more closely related to the mammalian hepadnaviruses, indicating that cross-species transmission events have played a major role in viral evolution. Evidence of cross-species transmission was also observed with TFHBV. Hence, these data indicate that the evolutionary history of the hepadnaviruses is more complex than previously realized and combines both virus-host codivergence over millions of years and host species jumping. IMPORTANCEHepadnaviruses are responsible for significant disease in humans (hepatitis B virus) and have been reported from a diverse range of vertebrates as both exogenous and endogenous viruses. We report the full-length genome of a novel hepadnavirus from a fish and the first hepadnavirus genome from an amphibian. The novel fish hepadnavirus, sampled from bluegills, was more closely related to mammalian hepadnaviruses than to other fish viruses. This phylogenetic pattern reveals that, although hepadnaviruses have likely been associated with vertebrates for hundreds of millions of years, they have also been characterized by species jumping across wide phylogenetic distances. The Hepadnaviridae are characterized by extremely small (3-to 3.3-kbp), partially double-stranded DNA (dsDNA) genomes. The viral particles are spherical, with a diameter of approximately 42 nm, each containing a single copy of the genome covalently linked to the viral reverse transcriptase (RT), which provides DNA polymerase activity (1-3). The hepadnaviruses are unique among animal viruses in that they replicate their DNA by reverse transcription of an RNA intermediate and comprise the only group VII animal virus (dsDNA-RT virus) of the Baltimore system, which classifies viruses according to their genome composit...

Genetic diversity of bat orthohepadnaviruses in China and a proposed new nomenclature

“…Recently a virus found in the white sucker fish (White sucker hepatitis B virus, WSHBV) has also been approved as a new species (White sucker hepatitis B virus), but unassigned to any genus (Hahn et al, 2015). Additionally, two other hepadnaviruses have been identified in fish (Bluegill hepadnavirus, BGHBV) and amphibians (Tibetan frog hepadnavirus, TFHBV), with both showing a high genetic diversity compared with other prototypes, and might represent totally new genus candidates (Dill et al, 2016). Currently viral nomenclature within the family follows the conventional tradition: hepatitis B virus (for avian, primate and chiropteran viruses) or hepatitis virus (for rodent viruses) prefixed by the host English name, e.g., duck hepatitis B virus (DHBV), woolly monkey hepatitis B virus (WMHBV), pomona bat hepatitis B virus (PBHBV), and woodchuck hepatitis virus (WHV).…”

Extensive diversity and evolution of hepadnaviruses in bats in China

“…At present, the family contains two genera -Avihepadnavirus, Orthohepadnavirus-as well as one floating virus, White sucker hepatitis B virus, sampled from a fish (https://talk.ictvonline.org/taxonomy). Recently, two additional hepadnaviruses were identified in fish and frogs and await classification (Dill et al, 2016). Hepadnaviruses possess very small (3.0-3.3 kb) partially dsDNA genomes that exhibit a circular conformation by base pairing in a cohesive overlap between the 5' ends of the two DNA strands (Seeger et al, 2013).…”

Evolutionary biology of human hepatitis viruses

“…33 Endogenous and exogenous viruses distantly related to HBV were detected in reptiles, fish and amphibians. [34][35][36][37] HCV-related viruses were detected in horses in 2012, and evidence for sporadic spill-over infections of the horse-associated viruses into dogs and donkeys was found. [38][39][40][41] Soon afterwards, highly diverse HCV-related viruses were detected in bats and rodents, 42,43 in cattle, 44,45 and in black-and-white colobus monkeys.…”

“…long-term virus-host associations and crossspecies transmission events, such as those projected for other viruses. 29,34,36,119,203,218 Future discoveries of viruses will identify missing links in hepatitis virus evolution and may identify direct ancestors of human hepatitis viruses. Finally, there is an increasing drive towards the elimination of viral hepatitis B and C as aspired by the Word Health Organization.…”