Identification of Novel Viruses in Amblyomma americanum , Dermacentor variabilis, and Ixodes scapularis Ticks

Abstract

The incidence of tick-borne disease is increasing, driven by rapid geographical expansion of ticks and the discovery of new tick-associated pathogens. The examination of the tick microbiome is essential in order to understand the relationship between microbes and their tick hosts and to facilitate the identification of new tick-borne pathogens. Genomic analyses using unbiased high-throughput sequencing platforms have proven valuable for investigations of tick bacterial diversity, but the examination of tick viromes has historically not been well explored. By performing a comprehensive virome analysis of the three primary tick species associated with human disease in the United States, we gained substantial insight into tick virome diversity and can begin to assess a potential role of these viruses in the tick life cycle.

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

“…In both cases, the scaffolds only encode the polymerase with a Bunyavirus RNA dependent RNA polymerase domain. This genome structure is shared by Hubei myriapoda virus 6 (23) and Ixodes scapularis associated virus 3 (37).…”

Sequence diversity and evolution of an iflavirus family associated with ticks

“…The latter sequence was obtained from a pool of tick species which contained several species of the Metastriata (non-Ixodes hard ticks) or soft ticks species (Argasidae), but no species of the genus Ixodes. Of note, a sequence found in A. americanum in the study of Tokarz et al [5] corresponds to an iflavirus although it was named "dicistrovirus" in this manuscript.…”

“…Communities of microorganisms associated with ticks are attracting a special interest in the context of the growing concern for tick-transmitted diseases [27]. In recent years, there has been a particular interest for viruses associated with ticks, and in particular for the iflavirus family since several tick species appeared to harbour iflavirus-like viral genomes [3,5,9,11,16]. Our study, based on the exploration of assembled transcriptomes, allowed to discover nine new iflavirus genome sequences in ticks, and to perform a phylogenetic study that includes both these new genome sequences and previously published sequences.…”

“…Recently, a complete genome of an iflavirus has also been sequenced in an endemic Australian species, Ixodes holocyclus [9], in a tick species associated with marine birds, Ixodes uriae [10], and in the ISE6 cell line of Ixodes scapularis [11]. These findings illustrate two different strategies to isolate microorganisms, which each have their specific potential and interests: collecting and sequencing large pools of wild individuals (allowing to obtain sequences even for viruses that have a potentially low prevalence, as in [5] and [9]), or investigating well-characterized cell lines (as in [11]). Tick cell lines are an important tool for characterizing or experimenting on the interactions between microorganisms and mammalian systems [12] and have been screened for the presence of microorganisms, including viruses [13,14].…”

“…The discovery of new RNA viruses has rapidly increased in the recent years, and they have appeared to be far more prevalent and diverse than previously expected, especially in invertebrates, which exhibit a large and diverse "virosphere" [2,3]. High throughput transcriptome sequencing (or RNA-Seq) has proven to be a tool of choice to characterize the genomes of these viruses (see [4], [3], and even in ticks [5], [6], as this technique does not require to target known sequences, while allowing to retrieve contigs that may contain full viral genomes given a sufficient coverage and sufficient prevalence of the virus in the analyzed tissues/individuals. Iflaviruses represent a particular group of RNA viruses: members of Picornavirales, they are non-envelopped and have a single strand positive sense non segmented genome of ~9-11 kb -see [7] for a general description.…”