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对新疆地区蜱传病毒类群进行调查，本研究利用Illumia深度测序技术对新疆全沟硬蜱体内的病毒小RNA分子进行筛查，从提取的蜱小RNA组份中共测得32,631条病毒特异性读序，77条读序与蜱传黄病毒基因组序列匹配，核苷酸数合计约占病毒基因组的3.8%~2.4%，其中32条读序与国内尚未发现的西伯利亚型蜱传脑炎病毒一致。为对上述结果进行确证，利用RT-PCR对此型病毒核酸进行检测，从蜱总RNA中分别扩增获得病毒包膜基因与基因组3′末端片段，测序比对表明上述片段序列与西伯利亚南部检出病毒高度近似，核苷酸与氨基酸似然率分别为97.2%~95.5%与99.4%~98.3%。综上所述，本研究利用基于深度测序的病毒筛查方法，首次从我国新疆蜱传脑炎疫源地检出西伯利亚型病毒，为下一步针对病毒的分离与流行病学调查提供了重要线索。Abstract: Until the recent emergence/re-emergence of human-pathogenic viruses in ticks, tick-borne viruses have been neglected as causative agents of human disease (particularly in China). To gain insight into the diversity of tick-borne viruses in Xinjiang Uygur Autonomous Region (northwestern China), we conducted illumina deep sequencing-based screening for virus-derived small RNAs in field-collected Ixodes persulcatus ticks. We found 32,631 unique virus-matched reads. In particular, 77 reads mapped to the tick-borne group within the genus of Flavivirus, and covered 3.8–2.4% viral genomes. In addition, 32 unique reads were specific to the Siberian subtype of tick-borne encephalitis viruses (TBEV-Sib) which have never been reported in Chinese TBE loci. We confirmed the potential existence of TBEV-Sib by amplification (using reverse transcription-polymerase chain reaction) of genomic fragments from the envelope gene or 3′ genomic terminus from the pools of examined ticks. Both sequences demonstrated high homology to TBEV-Sib strains attached geographically to southern Siberia with nucleotide identity of 97.2–95.5% and amino-acid identity of 99.4–98.3%, respectively. In conclusion, we report, for the first time, detection of TBEV-Sib in the natural TBE loci of China. These novel data may provide genetic information for further isolation and epidemiologic investigation of TBEV-Sib.