Paleovirological screen of 818 vertebrate genomes identifies ancient alpharetrovirus lineage in bats

Alpharetroviruses — a family of pathogens historically associated with leukaemias and tumours in birds — were long considered to have a host range confined to avian species. A study published in PLOS Genetics by Harding, Zhang, De Souza, Nino Barreat, and Katzourakis now challenges that view through a systematic paleovirological analysis of 818 vertebrate genomes.

The team identified CHIRalphaEnv, a lineage of endogenous viral elements that clusters firmly within the alpharetrovirus clade but is found in bat genomes. Endogenous retroviruses arise when a retrovirus integrates into a host germline and is subsequently inherited across generations; their presence in modern genomes serves as a molecular fossil of ancient infections.

The study examines the evolutionary relationships between CHIRalphaEnv and modern alpharetroviruses and considers the distribution of these elements across the bat genomes surveyed. The authors also explore possible functional roles the embedded sequences may play in bat reproduction, a line of inquiry consistent with growing evidence that endogenous retroviruses have been co-opted for host biological functions in multiple mammalian lineages.

The findings extend understanding of alpharetrovirus host range and evolutionary history, and contribute to the broader paleovirology literature on the deep interplay between retroviruses and vertebrate genomes.