Twenty five new viruses associated with the Drosophilidae (Diptera)

Webster, Claire L.; Longdon, Ben; Lewis, Samuel H.; Obbard, Darren J.

doi:10.1101/041665

Cited by 24 publications

(58 citation statements)

References 76 publications

(95 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Members of this group have a similar genomic structure with two ORFs spanning 3 to 4.2 kb. This group includes viruses and viral sequences described in other acarine species like the deer tick (Ixodes scapularis) and the American dog tick (Dermacentor variabilis) (Harvey et al 2019;Levin et al 2016;Levin et al 2019;Pettersson et al 2017;Sadeghi et al 2018;Shi et al 2016;Webster et al 2016) and not much information about their incidence and replication in a specific host has been reported. Nevertheless, given the mentioned similarities and the replicative activity of these viruses (see below), these V. destructor associated viruses could define a new family of +ssRNA viruses infecting invertebrates.…”

Section: New Viruses Associated To V Destructormentioning

confidence: 99%

Identification of new viruses specific to the honey bee mite Varroa destructor

Herrero

Coll

et al. 2019

Preprint

View full text Add to dashboard Cite

Large-scale colony losses among managed Western honey bees have become a serious threat to the beekeeping industry in the last decade. There are multiple factors contributing to these losses but the impact of Varroa destructor parasitism is by far the most important, along with the contribution of some pathogenic viruses vectored by the mite. So far, more than 20 viruses have been identified infecting the honey bee, most of them RNA viruses. They may be maintained either as covert infections or causing severe symptomatic infections, compromising the viability of the colony. In silico analysis of available transcriptomic data obtained from mites collected in the USA and Europe as well as additional investigation with new samples collected locally allowed the description of three novel RNA viruses. Our results showed that these viruses were widespread among samples and that they were present in the mites and in the bees but with differences in the relative abundance and prevalence. However, we have obtained strong evidence showing that these three viruses were able to replicate in the mite, but not in the bee, suggesting that they are selectively infecting the mite. To our knowledge, this is the first demonstration of Varroa-specific viruses, which open the door to future applications that might help controlling the mite through biological control approaches.

show abstract

Section: New Viruses Associated To V Destructormentioning

confidence: 99%

Identification of new viruses specific to the honey bee mite Varroa destructor

Herrero

Coll

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…For example, Shi et al have discovered a large number of new RNA viruses by sequencing samples from invertebrate and vertebrate animals [4,5]. Claire et al have discovered 25 new RNA viruses by sequencing samples associated with different drosophilid [6]. Bolduc et al sequenced RNA viruses from Archaeal and bacterial samples [7].…”

Section: Introductionmentioning

confidence: 99%

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning

Shang

Sun

2020

Preprint

View full text Add to dashboard Cite

ABSTRARCTThe fast accumulation of viral metagenomic data has contributed significantly to new RNA virus discovery. However, the short read size, complex composition, and large data size can all make taxonomic analysis difficult. In particular, commonly used alignment-based methods are not ideal choices for detecting new viral species. In this work, we present a novel hierarchical classification model named CHEER, which can conduct read-level taxonomic classification from order to genus for new species. By combining k-mer embedding-based encoding, hierarchically organized CNNs, and carefully trained rejection layer, CHEER is able to assign correct taxonomic labels for reads from new species. We tested CHEER on both simulated and real sequencing data. The results show that CHEER can achieve higher accuracy than popular alignment-based and alignment-free taxonomic assignment tools. The source code, scripts, and pre-trained parameters for CHEER are available via GitHub: https://github.com/KennthShang/CHEER.

show abstract

“…One of the most powerful ways to identify viruses is to capitalise on the host's own ability to recognise pathogens, for example by sequencing the copious virus-derived small RNAs generated by the antiviral RNAi responses of plants, fungi, nematodes and arthropods (Aguiar et al 2015, Webster et al 2015. This not only demonstrates host recognition of the sequences as viral in origin, but also (if both strands of ssRNA viruses are present) demonstrates viral replication, and can even identify the true host of the virus based on the length distribution and base composition of the small RNAs (compare Webster et al 2016, with Coyle et al 2018).…”

Section: Introductionmentioning

confidence: 99%

A new lineage of segmented RNA viruses infecting animals

Obbard

Shī

Roberts

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera).Here we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single-and doublestranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.

show abstract

Twenty five new viruses associated with the Drosophilidae (Diptera)

Cited by 24 publications

References 76 publications

Identification of new viruses specific to the honey bee mite Varroa destructor

Identification of new viruses specific to the honey bee mite Varroa destructor

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning

A new lineage of segmented RNA viruses infecting animals

Contact Info

Product

Resources

About