Sequence diversity and evolution of a group of iflaviruses associated with ticks

Abstract

We studied a group of tick-associated viruses with characteristics of members of the family Iflaviridae, a family of viruses frequently found in arthropods. Our aim was to gain insight into the evolutionary dynamics of this group of viruses, which may be linked to the biology of ticks. We explored assembled RNA-Seq data sets for different species of ticks. We identified members of five different iflavirus species, four of them novel, and discovered nine new genome sequences, including variants. Five variants represented a virus species associated with Ixodes ricinus. Unexpectedly, a sequence found in the Ixodes scapularis cell line ISE6 was nearly identical to the sequences of I. ricinus variants, suggesting a contamination of this cell line by I. ricinus material. Analysing patterns of substitutions between these variants, we detected a strong excess of synonymous mutations, suggesting evolution under strong positive selection. The phylogenies of the viruses and of their tick hosts were not congruent, suggesting recurrent host changes across tick genera during their evolution. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.

Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia

“…Sequence reads mapping to family Iflaviridae (1.4% of the total reads) were the second most common virus group after phleboviruses. Sequences longer than 1000 aa detected in pools K1 to K4 showed a high similarity with newly identified Iflavirus HdromIV (97–100% identity) [ 33 ]. Lower similarities (>75%) were found with other iflaviruses, like the Gerbovich virus and Hubei tick virus 1 and 2 ( Figure S2 ).…”

Hazard potential of Swiss Ixodes ricinus ticks: Virome composition and presence of selected bacterial and protozoan pathogens

“…The detected sequences showed approximately 99% identity to Iflavirus IricIV-2 which was already described in a I . ricinus lab strain from Neuchâtel, Switzerland [ 69 ]. Flaviviridae sequences were found in tick samples from six of the ten cantons, first and foremost in GR at three of the four collection time points, followed by ZH, SG and SH.…”

Differential susceptibility of geographically distinct Ixodes ricinus populations to tick-borne encephalitis virus and louping ill virus

“…Another explanation for differences in infection rates observed between the different tick populations could be the presence or absence of specific microorganisms in the ticks [ 53 , 62 , 63 ]. Ticks harbour a plethora of symbiotic microorganisms, from facultative symbionts, tick-specific viruses to human pathogens, and co-infections of these microorganisms are frequently observed [ 64 , 65 ].…”

“…Recent studies discovered the presence of arthropod-specific viruses in ticks [ 63 , 71 , 72 ]. Although their role in pathogen transmission is unknown for ticks, some mosquito-specific viruses can interfere with the transmission of arthropod-borne viruses [ 73 ].…”