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.
Highlights
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)
We identified a new MGTV strain Yunnan2016 detected in Amblyomma testudinarium ticks [17] and aimed to achieve the following research goals: (1) establish a method to generate the full-length genome sequence of an RNA virus using sRNA-seq data; (2) determine the feasibility of using the sRNA-seq based method in the detection of viruses in a small tick; and (3) provide a high-quality and well-curated reference genome for future studies on MGTV, Jingmen tick virus (JMTV), Kindia tick virus (KITV) and Guangxi tick virus (GXTV)
Using VirusDetect (Refer to Methods), MGTV was detected in A. testudinarium ticks (SRA: SRP084097) but not in D. nuttalli, D. niveus or D. silvarum (SRA: SRP178347) ticks that were used as negative controls
Summary
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). Compared to other NGS based methods, the small RNA sequencing (sRNA-seq) based. To the best of our knowledge, there are no previous studies of virus detection in ticks using the sRNA-seq based method until the detection of the DNA segment of ASFV [6]. High-depth sRNA-seq data was used to detect a DNA segment of ASFV, the coverage of the ASFV reference genome was still very low. This suggested that the sRNA-seq based method does not perform as well in the detection of DNA viruses as it does in the detection of RNA viruses
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