Abstract
Background:
Ticks are important vectors for a wide range of pathogens, including viruses, bacteria, and protozoa, that impact both humans and animals. Recent advances in metagenomic sequencing have established it as a powerful tool for uncovering the microbial diversity within ticks, enabling the discovery of previously unrecognized pathogens.

Aim:
This study aimed to enrich the pathogen database for Tarim red deer in southern Xinjiang and provide experimental data to aid in the diagnosis, prevention, control, and treatment of viral diseases in Tarim red deer.

Methods:
Metagenomic sequencing was employed to analyze the viral species carried by ticks parasitizing the red tarim deer. Additionally, ELISA based antibody testing was conducted on 195 red deer samples from four farms M01, M02, M03, and M04 to detect antibodies against the Orf virus.

Results:
Next generation sequencing was used to obtain partial sequences of viruses and bacteria, with further analysis focusing on viruses with higher abundance, such as mule deer pox virus and Orf virus. Serological testing for Orf virus antibodies in 195 red deer samples identified 7 positive cases, resulting in a positivity rate of 3.59% (7/195). Positivity rates were 5.26% (4/76) and 6.12% (3/49) for farms M02 and M04, respectively, whereas no seropositive individuals were identified at farms M01 and M03.

Conclusion:
This study expands the current knowledge of tick borne pathogens in southern Xinjiang by identifying diverse viral species associated with tick-infested Tarim red deer. The findings confirm the presence of Orf virus in red deer populations, particularly on farms M02 and M04. These results underscore the importance of ongoing surveillance efforts and offer valuable insights into the diversity and geographical distribution of tick-associated viruses within the arid and semi arid ecosystems of southern Xinjiang.

Key words: Ticks; Red deer; mNGS; Tick-borne pathogens; Orf virus.