Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes

Abstract

The increasing prevalence and expanding distribution of tick-borne viruses globally have raised health concerns, but the full repertoire of the tick virome has not been assessed. We sequenced the meta-transcriptomes of 31 different tick species in the Ixodidae and Argasidae families from across mainland China, and identified 724 RNA viruses with distinctive virome compositions among genera. A total of 1,801 assembled and complete or nearly complete viral genomes revealed an extensive diversity of genome architectures of tick-associated viruses, highlighting ticks as a reservoir of RNA viruses. We examined the phylogenies of different virus families to investigate virome evolution and found that the most diverse tick-associated viruses are positive-strand RNA virus families that demonstrate more ancient divergence than other arboviruses. Tick-specific viruses are often associated with only a few tick species, whereas virus clades that can infect vertebrates are found in a wider range of tick species. We hypothesize that tick viruses can exhibit both ‘specialist’ and ‘generalist’ evolutionary trends. We hope that our virome dataset will enable much-needed research on vertebrate-pathogenic tick-associated viruses.

Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses

“…While our findings indicate that phylogenetic distance among mosquitos constrained virus transmission, there are cases of generalist viruses that can infect multiple mosquito species. Hence, counter to earlier ideas, virome compositions are not completely distinct among insect species 7,10,12 . Notably, our results also imply that the host specificity of mosquito-associated viruses exists on a spectrum rather than adhering to a rigid “generalist-specialist” dichotomy 28,33 .…”

“…Some viruses appear to be predominantly associated with particular mosquito species, although sporadic host switching events are frequent, such as the case of Mosquito narna-like virus SC1. This phenomenon of frequent host switching has also been observed in rabies viruses of bats 34 , and in recent metagenomics studies in mammals 6 and ticks 7 . The frequent spillover events, along with the frequent co-infection of viruses within individual mosquitos, are likely to contribute to increased genetic diversity among viruses circulating in mosquito communities.…”

“…Individual animal virome data sets are also valuable for investigating both virus-virus and virus-host interactions 4,6 . Many metagenomics studies have pooled individual insects by species or sampling location [7][8][9][10] . Although pooling is an efficient means to explore viral diversity, it inevitably hinders mechanistic insights into the viral ecology and evolution.…”

Characterisation of putative novel tick viruses and zoonotic risk prediction

“…For instance, some newly discovered tick‐associated viruses (such as the viruses identified in Zhang et al., 2021 and Kong et al., 2022) were not included in the data set. Furthermore, a recent examination of tick metaviromes showed that approximately 70% of the 223 viruses identified in their study had never been previously documented in ticks (Ni et al., 2023). Hence, it is important to acknowledge that some putative novel tick‐associated viruses may have been missed due to the absence of similar viruses for comparison.…”

“…Furthermore, a recent examination of tick metaviromes showed that approximately 70% of the 223 viruses identified in their study had never been previously documented in ticks (Ni et al, 2023).…”