Sequencing and genetic characterization of two strains Paramushir virus obtained from the Tyuleniy Island in the Okhotsk Sea (2015)

Safonova, Marina V.; Shchelkanov, M. Yu.; Khafizov, K.; Matsvay, Alina D.; Ayginin, Andrey A.; Dolgova, Anna; Щелканов, Е. М.; Pimkina, Ekaterina V.; Speranskaya, A.S.; Галкина, И. В.; Dedkov, Vladimir G.

doi:10.1016/j.ttbdis.2018.11.004

“…uriae . For example, Avalon virus, closely related to Paramushir virus [33], has been found at the Great island, Newfoundland, Canada [29], along the coast of Brittany, France [34], and now in the northern part of Sweden. As noted earlier, there are also indications of movement between the northern and southern circumpolar regions.…”

Section: Resultsmentioning

confidence: 99%

Circumpolar diversification of theIxodes uriaetick virome

Pettersson

¹

,

Ellström

²

,

Ling

³

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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“…Two experiments studying Noroviruses included amplification with 14 and 22 primer pairs, respectively [137,138]. Finally, sequencing of the Paramurshir virus genome was conducted with a set of 60 PCR reactions and additional Sanger sequencing to cover the unamplified fragments [139].…”

Section: Target Amplificationmentioning

confidence: 99%

“…Apparently, sometimes amplification, as described above, overloads laboratory workflow with numerous reactions and mandatory normalization of the products' concentrations. There is always room for error, e.g., primers failing to anneal to targets due to unmatching primer sequences (particularly in rapidly mutating viruses [139]). It is also important to consider the costs of primer synthesis and reagents, along with the amount of labor required for setting up multiple reactions per each sample [140].…”

Section: Target Amplificationmentioning

confidence: 99%

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Kiselev

¹

,

Matsvay

²

,

Абрамов

³

et al. 2020

Viruses

Self Cite

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Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.

show abstract

“…uriae. For example, Avalon virus, closely related to Paramushir virus [34], has been found at the Great island, Newfoundland, Canada [29], along the coast of Brittany, France [35], and now in the northern part of Sweden. As noted earlier, there are also indications of movement between the northern and southern circumpolar regions.…”

Section: Plos Pathogensmentioning

confidence: 99%

Circumpolar diversification of the Ixodes uriae tick virome

Pettersson

¹

,

Ellström

²

,

Ling

³

et al. 2020

View full text Add to dashboard Cite

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 provide evidence for virus dispersal within and between the circumpolar regions. In marked contrast, our phylogenetic analysis revealed no movement of the Ix. uriae tick hosts between the same locations. Combined, these data suggest that migratory birds are responsible for the movement of viruses at both local and global scales.

show abstract

Sequencing and genetic characterization of two strains Paramushir virus obtained from the Tyuleniy Island in the Okhotsk Sea (2015)

Cited by 13 publications

References 28 publications

Circumpolar diversification of theIxodes uriaetick virome

Circumpolar diversification of theIxodes uriaetick virome

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Circumpolar diversification of the Ixodes uriae tick virome

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