The virome investigation of the globally endangered Eld's deer (Rucervus eldii) on Hainan Island, China

More than 60% of emerging (re-emerging) infectious diseases worldwide are caused by animal-derived pathogens, of which 71% are of wild animal origin. It is important to obtain insight into the viral pathogens present in the wildlife reservoir from a public health perspective. Based on next-generation sequencing (NGS), we report a metagenomic viral survey of Eld's deer ( Rucervus eldii ) (n = 33) in Bangxi Provincial Nature Reserve in Hainan Province. We collected 33 nasal swabs, 33 anal swabs, and 9 tick bite wound swabs and combined them into 5 pools according to the type of swabs. The metagenomic analysis showed that there were differences in the 5pools of viral reads, but the overall viral reads were closely related to mammals. We amplified and obtained the complete genomes of novel papillomaviruses (PV) and circoviruses (CV) in Eld's deer, PsPV-HMU-1 and PsaCV-HMU-1. The novel PV and CV genomic structure revealed that it was consistent with that of the known mammalian PV and CV. The L1 of PsPV-HMU-1 and the rep of PsaCV-HMU-1 showed less than 77.20% and 45.43% amino acid homology with the closest viruses, respectively. The positive rate of PV carried by Eld's deer is relatively high. Multiple Eld's deer with positive nase or anal swabs, accompanied by positive swabs from tick bites and wounds, indicate that insect bites may be closely related viral infection. This study helps us monitor Eld's deer viral diseases and understand the genetic diversity and evolutionary history of FV and CV carried by Eld's deer.