Highly diverse posaviruses in swine faeces are aquatic in origin

Hause, Ben M.; Palinski, Rachel; Hesse, Richard; Anderson, Gary A.

doi:10.1099/jgv.0.000461

Cited by 21 publications

(16 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The largest and most coherent of the Branch 2 clades includes the cornerstone of the picornavirus supergroup, the ~826 viruses-strong order Picornavirales (56), expanded with caliciviruses, solinviviruses and a multitude of unclassified viruses infecting invertebrates, vertebrates, fungi, protists and undefined hosts (for viruses discovered by metaviromics) (Figure 3) (11, 14, 17, 57-59). The second largest, deep-branching clade consists of two lineages that include, respectively, +RNA and dsRNA viruses (Figure 3).…”

Section: Resultsmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Dolja¹,

Wolf

Kazlauskas³

et al. 2018

Preprint

118

197

View full text Add to dashboard Cite

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 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 which include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded (ds) RNA viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas -RNA 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 +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, particularly, 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.IMPORTANCEThe 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 what 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.

show abstract

Section: Resultsmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Dolja¹,

Wolf

Kazlauskas³

et al. 2018

Preprint

118

197

View full text Add to dashboard Cite

show abstract

“…The largest and most coherent of the branch 2 clades includes the cornerstone of the picornavirus supergroup, the ϳ826 viruses-strong order Picornavirales (56), expanded with caliciviruses, solinviviruses, and a multitude of unclassified viruses infecting invertebrates, vertebrates, fungi, protists, and undefined hosts (for viruses discovered by metaviromics) ( Fig. 3) (11,14,17,(57)(58)(59). The second largest, deep-branching clade consists of two lineages that include, respectively, ϩRNA and dsRNA viruses ( Fig.…”

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

445

333

View full text Add to dashboard Cite

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.

show abstract

“…Genomic organization is variable with a single polyprotein expressed in all orders except Dicistroviridae where structural and non-structural protein genes are expressed from separate transcripts [ 29 ]. Recently, some highly divergent members of the Picornavirales order have been discovered, including porcine-stool-associated RNA viruses (posaviruses) in the feces of pigs [ 30 – 32 ], fish-stool-associated RNA virus (fisavirus) in the intestinal content of a healthy carp [ 33 ], and human-stool-associated virus (husavirus) [ 34 ].…”

Section: Resultsmentioning

confidence: 99%

“…Phylogenetic analysis based on the amino acid sequence of RdRp indicated that these genomes clustered together with those of posaviruses from pig feces and the transcriptome of an Ascaris suum transcriptome (Fig. 5 b) [ 32 ]. Since an Ascaris suum transcriptome sequence was also grouped into this cluster, pansaviruses may not actually infect the intestinal cells of the giant panda but a nematode species in the gut of these animals, a potential source supported by the clinical record that the diseased giant panda contained ascarids in its intestine.…”

Section: Discussionmentioning

confidence: 99%

“…Since an Ascaris suum transcriptome sequence was also grouped into this cluster, pansaviruses may not actually infect the intestinal cells of the giant panda but a nematode species in the gut of these animals, a potential source supported by the clinical record that the diseased giant panda contained ascarids in its intestine. The possible origin of posaviruses from pigs from aquatic algae has also been postulated based on their similarity to members of the algae infecting Marnaviridae and detection in water from wells on pig farms [ 32 ]. Only one fecal sample from the 25 captive giant pandas was positive for pansavirus, possibly reflecting the different environment in a breeding center relative to the wild.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Virome comparisons in wild-diseased and healthy captive giant pandas

et al. 2017

View full text Add to dashboard Cite

BackgroundThe giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available.MethodsUsing a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals.ResultsThe previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda.ConclusionThis viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-017-0308-0) contains supplementary material, which is available to authorized users.

show abstract

Highly diverse posaviruses in swine faeces are aquatic in origin

Cited by 21 publications

References 19 publications

Origins and Evolution of the Global RNA Virome

Origins and Evolution of the Global RNA Virome

Origins and Evolution of the Global RNA Virome

Virome comparisons in wild-diseased and healthy captive giant pandas

Contact Info

Product

Resources

About