Extensive conservation of prokaryotic ribosomal binding sites in known and novel picobirnaviruses

Krishnamurthy, Siddharth R.; Wang, David

doi:10.1016/j.virol.2018.01.006

Cited by 96 publications

(106 citation statements)

References 31 publications

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“…Importantly, these viruses did not form a monophyletic group, but were distributed throughout genogroup 1. This pattern is typical of the Picobirnaviridae that show limited host structure in the RdRp phylogeny (Figure 4), and is compatible with the idea that these are in fact bacterial-associated viruses (Krishnamurthy & Wang, 2018). The RdRp segments (segment 2) were predicted to have one ORF, consistent with other members of this family.…”

Section: Resultssupporting

confidence: 82%

Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

Mahar

Shī

Hall

et al. 2019

Preprint

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Ectoparasites play an important role in virus transmission among vertebrates. However, little is known about the extent and composition of viruses that pass between invertebrates and vertebrates. In Australia, flies and fleas support the mechanical transmission of viral biological controls against wild rabbits - rabbit haemorrhagic disease virus (RHDV) and myxoma virus. We compared virome structure and composition in rabbits and these associated ectoparasites, sequencing total RNA from multiple tissues and gut contents of wild rabbits, fleas collected from these rabbits, and flies trapped sympatrically. Meta-transcriptomic analyses identified 50 novel viruses from multiple RNA virus families. Rabbits and their ectoparasites were characterised by markedly different viromes: although viral contigs from six virus families/groups were found in both rabbits and ectoparasites, none were vertebrate-associated. A novel calicivirus and picornavirus detected in rabbit caecal content were vertebrate-specific: the newly detected calicivirus was distinct from known rabbit caliciviruses, while the novel picornavirus clustered with the Sapeloviruses. Several Picobirnaviridae were also identified, falling in diverse phylogenetic positions suggestive of an association with co-infecting bacteria. The remaining viruses found in rabbits, and all those from ectoparasites, were likely associated with invertebrates, plants and co-infecting endosymbionts. While no full genomes of vertebrate-associated viruses were detected in ectoparasites, suggestive of major barriers to biological transmission with active replication, small numbers of reads from rabbit astrovirus, RHDV and other lagoviruses were present in flies. This supports the role of flies in the mechanical transmission of RHDV and implies that they may assist the spread of astroviruses.

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Section: Resultssupporting

confidence: 82%

Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

Mahar

Shī

Hall

et al. 2019

Preprint

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“…In the absence of evidence of actual infection, the word "associated" is usually added to the potential host name to emphasize that the organism may or may not be the actual host. As a case in point, it has been recently suggested that dsRNA viruses of the family Picobirnaviridae, which for three decades were considered to infect eukaryotes [5], might instead replicate in bacteria that populate the enteric tract of animals [10]. Thus, utmost caution should be exercised when assigning viruses to potential hosts.…”

Section: Pan Troglodytesmentioning

confidence: 99%

Smacoviridae: a new family of animal-associated single-stranded DNA viruses

Varsani

Krupovìč

2018

Arch Virol

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Smacoviruses have small (∼2.3-2.9 kb), circular single-stranded DNA genomes encoding rolling circle replication-associated proteins (Rep) and unique capsid proteins. Although smacoviruses are prevalent in faecal matter of various vertebrates, including humans, none of these viruses have been cultured thus far. Smacoviruses display ∼45% genome-wide sequence diversity, which is very similar to that found within other families of circular Rep-encoding single-stranded (CRESS) DNA viruses, including members of the families Geminiviridae (46% diversity) and Genomoviridae (47% diversity). Here, we announce the creation of a new family Smacoviridae and describe a sequence-based taxonomic framework which was used to classify 83 smacovirus genomes into 43 species within six new genera, Bovismacovirus (n=3), Cosmacovirus (n=1), Dragsmacovirus (n=1), Drosmacovirus (n=3), Huchismacovirus (n=7), and Porprismacovirus (n=28). As in the case of genomoviruses, the species demarcation is based on the genome-wide pairwise identity, whereas genera are established based on the Rep amino acid sequence identity coupled with strong phylogenetic support. A similar sequence-based taxonomic framework should guide the classification of an astonishing diversity of other uncultured and currently unclassified CRESS DNA viruses discovered by metagenomic approaches.

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“…No known prokaryotic viruses are classified in branch 2, but it has been proposed that the picobirnaviruses, for which no hosts have been reliably identified, actually are prokaryotic viruses. This proposal is based on the conspicuous conservation of functional, bacterium-type, ribosome-binding sites (Shine-Dalgarno sequences) in picobirnavirus genomes (107,108). Should that be the case, viruses of prokaryotes might be lurking among totiviruses as well.…”

Section: Evolution Of the 5 Major Branches Of Rna Viruses And Reconstmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Wolf

Kazlauskas

Iranzo

et al. 2018

mBio

429

333

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Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (ϩ) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (Ϫ) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from ϩRNA viruses on at least two independent occasions, whereas ϪRNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of ϩRNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy. IMPORTANCE The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.

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Extensive conservation of prokaryotic ribosomal binding sites in known and novel picobirnaviruses

Cited by 96 publications

References 31 publications

Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

Smacoviridae: a new family of animal-associated single-stranded DNA viruses

Origins and Evolution of the Global RNA Virome

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