Genomic characterization and the prevalence of a novel copiparvovirus in wild sika deer (Cervus nippon) in Japan

• Novel parvovirus strains were obtained from wild sika deer in japan. • Nine deer parvovirus strains shared 91.4–99.7% identity over the near-full genome. • The strains were closest to copiparvovirus strains, with only 44.7–60.7% identity. • The strains were a putative new species within the genus copiparvovirus . • The DNA prevalence was 15% (31/206), with the region-dependent distribution (0–67%). A preliminary metagenomic analysis of the virome of wild sika deer ( Cervus nippon ) blood in Japan resulted in the identification of a novel parvovirus. The virus was closest, but only 44.7–60.7% identical to 17 reported strains belonging to the genus Copiparvovirus within the subfamily Parvovirinae, over the near-entire genomic sequence. The sika deer copiparvovirus DNA was detected in 15% (31/206) of sika deer captured in 7 prefectures of Japan, and a region-dependent prevalence of 0–66.7% was noted, with a biased distribution in the southern part of Japan. The observed biased distribution of sika deer copiparvovirus may be due to the habitat density of deer and the number of ticks, which might play a role in the transmission of the virus.