Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals

Janowski, Andrew B.; Krishnamurthy, Siddharth R.; Lim, Efrem S.; Zhao, Guoyan; Brenchley, Jason M.; Barouch, Dan H.; Thakwalakwa, Chrissie; Manary, Mark J.; Holtz, Lori R.; Wang, David

doi:10.1016/j.virol.2017.01.010

Cited by 18 publications

(30 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Within Branch 3, the phylogenetically compact alphavirus supergroup is embedded within the radiation of diverse virus groups including the well-known tombusviruses and nodaviruses, along with several newcomers discovered via metaviromics, such as the “statovirus”, “weivirus”, “yanvirus”, and “zhaovirus” groups (14, 80, 81) (Figure 4A). Our RdRp analysis revealed remarkable phylogenetic heterogeneity within and among these groups and split “tombus-like viruses” into 5 lineages with distinct evolutionary affinities (groups ‘Uncl.…”

Section: Resultsmentioning

confidence: 99%

“…Plant tombusviruses (and members of closely related plant virus genera), the only group of “tombus-like viruses” that was available at the time of previous analyses (7, 21), now form but a small twig deep within the large assemblage we refer to as tombusviruses. Tombusviruses are affiliated with “statoviruses” (80) and a subset of unclassified viruses from invertebrate holobionts rather than with flaviviruses (Figure 4A). Flaviviruses now form a separate clade within Branch 3, the flavivirus supergroup that includes members of four recognized flaviviral genera (Pegivirus, Hepacivirus, Flavivirus, and Pestivirus), the newly discovered “jingmenviruses” with segmented genomes (38) and a variety of unclassified, extremely divergent “flavi-like viruses” of animals and plants.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

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%

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

“…Plant tombusviruses (and members of closely related plant virus genera), representing the only group of "tombus-like viruses" that was available at the time of previous analyses (7,21), now form but a small twig deep within the large assemblage that we refer to as tombusviruses. Tombusviruses are affiliated with "statoviruses" (80) and with a subset of unclassified viruses from invertebrate holobionts rather than with flaviviruses ( Fig. 4A).…”

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

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

“…The International Committee on Taxonomy of Viruses has approved formal classification of viruses characterized solely by metagenomics 10 . The rapid advances in metaviromics have substantially expanded the known diversity of RNA viruses, yielding vast amounts of sequences for comprehensive studies on RNA virus evolution [11][12][13][14][15][16][17] .…”

mentioning

confidence: 99%

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

et al. 2020

View full text Add to dashboard Cite

RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.

show abstract

Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals

Cited by 18 publications

References 50 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

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

Contact Info

Product

Resources

About