Meta-transcriptomic sequencing reveals divergent RNA viruses in geckos

Geckos are generally small, predominantly nocturnal reptiles, with several species commonly found close to human habitations. However, little is known about viral diversity in geckos. Using meta-transcriptomic sequencing we identified four novel RNA viruses - provisionally denoted Gecko astrovirus, Gecko parechovirus, Gecko reptillovirus, and Gecko hartmanivirus - in geckos sampled in October 2019 from Hainan Province, China. The presence of these viruses was confirmed by reverse transcription (RT)-PCR. Phylogenetic analyses revealed that these viruses were most closely related to those identified in various gecko species from China and Australia, such that they represent gecko-specific lineages, yet were also genetically distinct, with amino acid sequence identities to their closest relatives ranging from 38.6 % to 74.2 %. A co-phylogeny analysis revealed a complex interplay between long-term virus-host co-divergence and more recent host jumping, which differed in frequency among groups. In sum, we demonstrate the presence of four novel gecko-associated RNA viruses, expanding our understanding of viral diversity in these common animal species.