Detection of spp. in farmed deer (Artiodactyla: Cervidae) using multiplex assays in the Qinghai-Tibet Plateau, China.

Unlabelled: In this study, we investigated the prevalence of in deer from Qilian County, Qinghai Province, China. Blood samples were collected from 69 red deer, 40 white-lipped deer, and 27 sika deer. The detection of spp. has been conducted. The overall prevalence of was 33.6% (46/135). Species-specific prevalence was 50.72% in red deer (35/69), 20.00% in white-lipped deer (8/40), and 11.11% in sika deer (3/27). There were significant differences in the prevalence rates among the different species of deer. The amplicon sequence comparison revealed a high homology of the ruminant-associated spp. Nanopore sequencing further confirmed the results. reads were presented in each of the qPCR-positive samples. Phylogenetic analysis indicated that the sequences detected in deer blood were closely related to ruminant-borne spp. In summary, we reported the prevalence of different deer species in Qinghai, and there were at least one species of ruminant-associated , .

Importance: This is the first report about infections in the deer population from China. We found that there were two species of and an unidentified species of among the unculturing strains carried by these deer populations. We first used Nanopore sequencing to detect from deer blood samples and indicated that Nanopore sequencing is beneficial to detect pathogens due to its advantage of real-time and high sensitivity.