Virome of Rhipicephalus ticks by metagenomic analysis in Guangdong, southern China

Abstract

Tick-borne viruses (TBVs) have increasingly caused a global public health concern. This study collected Rhipicephalus ticks in Guangdong, southern China to identify RNA viruses. Meta-transcriptome analysis revealed the virome in Rhipicephalus ticks, resulting in the discovery of 10 viruses, including Lihan tick virus, Brown dog tick phlebovirus 1 and 2 in the family Phenuiviridae, Mivirus and Wuhan tick virus 2 in the family Chuviridae, Wuhan tick virus 1 in the family Rhabdoviridae, bovine hepacivirus in the family Flaviviridae, Guangdong tick quaranjavirus (GTQV) in the family Orthomyxoviridae, Guangdong tick orbivirus (GTOV) in the family Reoviridae, and Guangdong tick Manly virus (GTMV) of an unclassified family. Phylogenetic analysis showed that most of these TBVs were genetically related to the strains in countries outside China, and GTQV, GTOV, and GTMV may represent novel viral species. These findings provided evidence of the long-distance spread of these TBVs in Guangdong, southern China, suggesting the necessity and importance of TBV surveillance.

Diversity Analysis of Tick-Borne Viruses from Hedgehogs and Hares in Qingdao, China

“…Our results showed that there were large numbers of viruses of the Phenuiviridae , Iflaviridae , Nairoviridae , and Chuviridae in the five species of ticks in Qingdao. Our research revealed the diversity and abundance of viruses carried by different tick species ( 26 , 27 ), which enriches the viral diversity of ticks in China.…”

“…The discovered viruses were classified based on nucleotide and amino acid identities (Table S3). If the nucleotide identity of a new virus species with the whole genome of the reference virus strain is less than 80% or the amino acid identity with the RNA-dependent RNA polymerase (RdRp) domain of a known virus is less than 90%, the virus is defined as a new virus ( 27 ). All new viruses were named “Qingdao tick” (QDT), followed by the names of common viruses classified by them in this study.…”

Impact of nanopore-based metagenome sequencing on tick-borne virus detection

“…Tick-associated phleboviruses identified in the pools include Brown dog tick phlebovirus 2 (BDTP2), phlebovirus Strandja, tick phlebovirus Anatolia, and Lesvos virus ( Table 1 ). Strandja and Anatolia phleboviruses were mainly reported in Rhipicephalus ticks from Bulgaria and Turkey (Emanet et al, 2019 ; Ohlendorf et al, 2019 ), while BDTP2 appears widespread, detected in China, and Trinidad and Tobago as well as the Balkans (Sameroff et al, 2019 ; Bratuleanu et al, 2022 ; Guo et al, 2022 ). Lesvos virus was originally reported from Hae.…”

“…BTV3 and tick phleboviruses appear to be a ubiquitous virus in Anatolia, having been detected in various tick species (Dinçer et al, 2017 ; Brinkmann et al, 2018 ; Emanet et al, 2019 ; Ergünay et al, 2020 ). Tick phleboviruses are also widely distributed in Asia, Europe, and America (Ohlendorf et al, 2019 ; Sameroff et al, 2019 ; Bratuleanu et al, 2022 ; Guo et al, 2022 ). As vertebrate in vivo experiments failed to propagate these viruses, they are currently considered non-virulent residents of the tick virome (Emanet et al, 2019 ).…”

Extensive diversity of RNA viruses in ticks revealed by metagenomics in northeastern China

“…Therefore, it is necessary to conduct routine surveillance of tick-borne viruses. The tick viromes have been analyzed in several provinces, including Heilongjiang, Liaoning, Hebei, Henan, Yunnan and Guangdong in China [23][24][25][26][27][28], revealing a large number of novel RNA viruses of vertebrate and invertebrate hosts. These studies also suggest that the viromes are significantly affected by the tick species and geographical location.…”