Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data
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RESEARCH ARTICLE
Open Access
Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data Xiaofeng Xu1†, Jinlong Bei2,3†, Yibo Xuan1, Jiayuan Chen4, Defu Chen4, Stephen C. Barker5, Samuel Kelava5, Xiaoai Zhang2,3, Shan Gao4* and Ze Chen1*
Abstract Background: In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)—evolutionarily related to MGTV—were reported. Results: In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China’s Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia. Conclusions: To the best of our knowledge, this is the first study in which 5′ and 3′ sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography. Keywords: MGTV, JMTV, Full-length genome, 5′ sRNA, 3′ sRNA
Background Next generation sequencing (NGS) technologies have been widely applied to virus and viroid discovery in plants and animals. Compared to other NGS based methods, the small RNA sequencing (sRNA-seq) based * Correspondence: [email protected]; [email protected] † Xiaofeng Xu and Jinlong Bei contributed equally to this work. 4 College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, People’s Republic of China 1 Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, People’s Republic of China Full list of author information is available at the end of the article
method simplifies virus detection and has several other advantages [1]. The sRNA-seq based method was originally used for viral detection and identification in plants [2] and in invertebrates [3]. Although the sRNA-seq based method does not perform as well in the detection of mammalian viruses as in the detection of plant or invertebrate viruses, we still detected eight mammalian viruses: human papillomavirus type 18 (HPV-18) [4], hepatitis
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