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Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

Authors
  • Xu, Xiaofeng1
  • Bei, Jinlong2, 3
  • Xuan, Yibo1
  • Chen, Jiayuan4
  • Chen, Defu4
  • Barker, Stephen C.5
  • Kelava, Samuel5
  • Zhang, Xiaoai2, 3
  • Gao, Shan4
  • Chen, Ze1
  • 1 Hebei Normal University, Shijiazhuang, Hebei, 050024, People’s Republic of China , Shijiazhuang (China)
  • 2 Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, People’s Republic of China , Guangzhou (China)
  • 3 Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, People’s Republic of China , Guangzhou (China)
  • 4 Nankai University, Tianjin, Tianjin, 300071, People’s Republic of China , Tianjin (China)
  • 5 The University of Queensland, Brisbane, QLD, 4072, Australia , Brisbane (Australia)
Type
Published Article
Journal
BMC Genomics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Sep 16, 2020
Volume
21
Issue
1
Identifiers
DOI: 10.1186/s12864-020-07060-5
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundIn 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.ResultsIn 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.ConclusionsTo 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.

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