Objective To investigate the species and positive rates of viruses carried by ticks and rodents in northern Xinjiang Uygur Autonomous Region (Xinjiang), so as to provide reference for prevention and control of related diseases, China. Methods Questing ticks were collected using the drag-flag and human landing collection methods in 11 counties (cities/districts) in northern Xinjiang from 2013 to 2024. Nocturnal rodents were captured using 5-meter line trapping method with medium-sized plate clamps, while Rhombomys opimus and Spermophilusundulatus were captured using bow-shaped clamps. RNAs were extracted from the brain, lungs, liver, spleen, kidneys, and intestines of rodents and ticks and prepared into cDNAs. Sequencing was conducted using 454 high-throughput, Illumina HiSeq 2500, and Illumina NovaSeq 3000. The sequences were assembled and spliced using Trinity 2.5, followed by alignment and annotation with the basic local alignment search tool (BLAST). Based on the sequence information, specific primers were designed for targeted viruses, and viral nucleic acids were detected using reverse-transcription PCR (RT-PCR). Results High-throughput sequencing was performed on 4 076 ticks in 42 groups, establishing 23 sequencing libraries. Twenty-four viruses in 12 families and 10 unclassified viruses were identified. Among them, Dermacentor nuttalli, Hyalomma asiaticum,and Hy. scupense carried 33, 24, and 10 viruses, respectively. RT-PCR was performed on 56 042 ticks in 596 groups, detecting 14, 12, and 10 viruses in D. nuttalli, Hy. asiaticum, and Hy. scupense, respectively. Significant zoonotic pathogens were found in ticks of 5 species in 4 families, including Crimean-Congo hemorrhagic fever virus (CCHFV), Guertu virus (GTV), Dhori virus (DHOV), Bole tick virus 1 (BLTV 1), and Tacheng tick virus 5 (TCTV 5). The positive rates in D. nuttalli, Hy. asiaticum, and Hy. scupense were 1.46%, 5.00%, and 6.25% for CCHFV; 11.04%, 15.00%, and 18.75% for GTV; 3.31%, 9.46%, and 0.00% for TAMV; 11.16%, 20.27%, and 66.67% for BLTV1; and 12.10%, 23.00%, and 12.50% for TCTV 5. High-throughput sequencing was performed on 125 tissue samples from 25 rodents, establishing 113 sequencing libraries. Fifty-five species in 23 families and 4 unclassified viruses were identified. Among them, Meriones meridianus, Cricetulus migratorius, Mus musculus, Dipus sagitta, and R. opimus carried 45, 13, 7, 6, and 5 viruses, respectively. RT-PCR was performed on 1 092 rodents in 153 groups, with positive results of CCHFV and GTV in R. opimus, Me. meridianus, and S. undulatus. The positive rates in R. opimus, Me. meridianus, and S. undulatus were 6.50%, 9.09%, and 9.09% for CCHFV; 16.00%, 18.18%, and 20.00% for GTV. The positive rate of CCHFV in D. sagitta was 25.00%. Significant zoonotic viruses included TAMV, BLTV 1, rat hepatitis virus (RHV), and encephalomyocarditis virus (EMCV).ConclusionThere are abundant viruses carried by ticks and rodents in northern Xinjiang, including CCHFV, GTV, TAMV, TCTV 5, and BLTV 1, which are capable of infecting both humans and animals.
