Putative RNA viral sequences detected in an Ixodes scapularis-derived cell line

Matsuno, Keita; Qiu, Yongjin; Maruyama, Junki; Eguchi, Nao; Nao, Naganori; Kajihara, Masahiro; Yoshii, Kentaro; Sawa, Hirofumi; Takada, Ayato; Sugimoto, Chihiro

doi:10.1016/j.ttbdis.2016.10.005

Cited by 25 publications

(28 citation statements)

References 33 publications

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“…Similarly, Ubmeje virus ( Bunyavirales ) was identified in several libraries from northern Sweden, although it was not abundant (Table 1). Ubmeje virus shared only ∼35.8% and 35.9% amino acid identity to Bronnoya virus and Ixodes scapularis bunyavirus, both previously observed in ixodid ticks [37,38], and which together form a monophyletic group (Figure 1).…”

Section: Resultsmentioning

confidence: 79%

Circumpolar diversification of theIxodes uriaetick virome

Pettersson

Ellström

Ling

et al. 2020

Preprint

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Ticks (order: Ixodida) are a highly diverse and ecologically important group of ectoparasitic blood-feeding organisms. One such species, the seabird tick (Ixodes uriae), is widely distributed around the circumpolar regions of the northern and southern hemispheres. It has been suggested that Ix. uriae spread from the southern to the northern circumpolar region millions of years ago and has remained isolated in these regions ever since. Such a profound biographic subdivision provides a unique opportunity to determine whether viruses associated with ticks exhibit the same evolutionary patterns as their hosts. To test this, we collected Ix. uriae specimens near a Gentoo penguin (Pygoscelis papua) colony at Neko harbour, Antarctica, and from migratory birds - the Razorbill (Alca torda) and the Common murre (Uria aalge) - on Bonden island, northern Sweden. Through meta-transcriptomic next- generation sequencing we identified 16 RNA viruses, seven of which were novel. Notably, we detected the same species, Ronne virus, and two closely related species, Bonden virus and Piguzov virus, in both hemispheres indicating that there have been at least two cross- circumpolar dispersal events. Similarly, we identified viruses discovered previously in other locations several decades ago, including Gadgets Gully virus, Taggert virus and Okhotskiy virus. By identifying the same or closely related viruses in geographically disjunct sampling locations we therefore provide evidence for virus dispersal within and between the circumpolar regions. In marked contrast, our phylogenetic analysis revealed no movement of the Ix. uriae hosts between the same locations. Combined, these data suggest that migratory birds are responsible for the movement of viruses at both the local and global scales.Author summary/ImportanceAs host populations diverge, so may those microorganisms, including viruses, that are dependent on those hosts. To examine this key issue in host-microbial evolution we compared the co-phylogenies of the seabird tick, Ixodes uriae, and their RNA viruses sampled from the far northern and southern hemispheres. Despite the huge geographic distance between them, phylogeographic analysis reveals that the same viruses were found both within and between the northern and southern circumpolar regions, most likely reflecting transfer by virus-infected migratory birds. In contrast, genomic data suggested that the Ix. uriae populations were phylogenetically distinct between the northern and southern hemispheres. This work emphasises the importance of migratory birds and ticks as vectors and sources of virus dispersal and introduction at both the local and global scales.

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Section: Resultsmentioning

confidence: 79%

Circumpolar diversification of theIxodes uriaetick virome

Pettersson

Ellström

Ling

et al. 2020

Preprint

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“…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.…”

Section: Discussionmentioning

confidence: 99%

“…To obtain a comprehensive phylogeny of iflavirus genome sequences associated with ticks, we integrated all the available genome sequences (as detailed in Table 1), comprising sequences already described [3,9,11,16] and the nine sequences newly identified in the present study ( Fig. 1).…”

Section: Phylogenymentioning

confidence: 99%

“…Some iflaviruses have also been identified in ticks, for example in the tick Hyalomma asiaticum and in pools of different tick species [3]. 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]).…”

Section: Introductionmentioning

confidence: 99%

“…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].…”

Section: Introductionmentioning

confidence: 99%

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Sequence diversity and evolution of an iflavirus family associated with ticks

Daveu¹,

Hervet²,

Sigrist³

et al. 2020

Preprint

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We studied a family of iflaviruses, a group of RNA viruses frequently found in arthropods, focusing on viruses associated with ticks. Our aim was to bring insight on the evolutionary dynamics of this group of viruses, which may interact with the biology of ticks. We explored systematically de novo RNA-Seq assemblies available for species of ticks which allowed to identify nine new genomes of iflaviruses. The phylogeny of virus sequences was not congruent with that of the tick hosts, suggesting recurrent host changes across tick genera along evolution. We identified five different variants with a complete or near-complete genome in Ixodes ricinus. These sequences were closely related, which allowed a fine-scale estimation of patterns of substitutions: we detected a strong excess of synonymous mutations suggesting evolution under strong positive selection. ISIV, a sequence found in the ISE6 cell line of Ixodes scapularis, was unexpectedly nearidentical with I. ricinus variants, suggesting a contamination of this cell line by I. ricinus material. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.

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Characterisation of putative novel tick viruses and zoonotic risk prediction

Lin,

Pascall

2024

Ecology and Evolution

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Tick‐associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta‐genomic and ‐transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta‐genomic and ‐transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick‐associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick‐associated viruses using a genome composition‐based machine learning model. We found five high‐risk tick‐associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick‐associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick‐associated diseases.

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Putative RNA viral sequences detected in an Ixodes scapularis-derived cell line

Cited by 25 publications

References 33 publications

Circumpolar diversification of theIxodes uriaetick virome

Circumpolar diversification of theIxodes uriaetick virome

Sequence diversity and evolution of an iflavirus family associated with ticks

Characterisation of putative novel tick viruses and zoonotic risk prediction

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