Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)

Walker, Peter; Siddell, Stuart G.; Lefkowitz, Elliot J.; Mushegian, Arcady; Dempsey, Donald M.; Dutilh, Bas E.; Harrach, Balázs; Harrison, Robert L.; Hendrickson, R. Curtis; Junglen, Sandra; Knowles, Nick J.; Kropinski, Andrew M.; Krupovìč, Mart; Kuhn, Jens H.; Nibert, Max L.; Rubino, Luisa; Sabanadzovic, Sead; Simmonds, Peter; Varsani, Arvind; Zerbini, F. Murilo; Davison, Andrew J.

doi:10.1007/s00705-019-04306-w

Cited by 327 publications

(266 citation statements)

References 4 publications

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“…As shown herein, small perturbations to the balance of NP availability showcases the fragility of this system and its general lack of robustness. Perhaps it is for this reason that negative-sense RNA viruses show the lowest diversity within the known global virosphere (Walker et al, 2019;Wolf et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…The weighted list of selected genes for each pattern was used to identify enriched gene ontology (GO) annotations (biological process) using Enrichr (Kuleshov et al, 2016). Redundant GO annotations were reduced by eliminating annotations that had > 75% overlap to another GO annotation using the reduce_overlap function from the GOplot package in R (Walker et al, 2019). Final annotations were visualized in R using custom scripts.…”

Section: Gene Set Enrichment Analysismentioning

confidence: 99%

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An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense RNA viruses

Blanco-Melo

Nilsson-Payant

Uhl

et al. 2020

Preprint

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Defective viral genomes and viral antagonists are key determinants of the host antiviral responseThe host response and defective viral genome generation further exasperate NP availability NP is an optimal drug target for the whole phylum of negative-sense RNA viruses SUMMARY Cellular biology has a uniformity not shared amongst viruses. This is perhaps best exemplified by negative-sense RNA viruses that encode their genetic material as a ribonucleoprotein complex composed of genome, RNA-dependent RNA polymerase, and the nucleoprotein. Here we demonstrate that limiting nucleoprotein availability not only universally culminates in a replicative catastrophe for negative-sense RNA viruses, but it results in the production of aberrant genomic material and induction of the interferonbased host defenses. This dynamic illustrates the tremendous stress imposed on negative-sense RNA viruses during replication as genomic products accumulate in an environment that requires an increasing demand on nucleoprotein availability. We show that limiting NP by RNA interference or drug targeting blocks replication and primes neighboring cells through the production of interferon. Together, these results demonstrate that the nucleoprotein represents the Achilles heel of the entire phylum of negative-sense RNA viruses. Here we establish this principle for a diverse collection of human pathogens and propose that the nucleoprotein should be a primary target for the development of future antiviral drugs. Manuscript

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Section: Discussionmentioning

confidence: 99%

Section: Gene Set Enrichment Analysismentioning

confidence: 99%

An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense RNA viruses

Blanco-Melo

Nilsson-Payant

Uhl

et al. 2020

Preprint

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“…species and Rhinovirus A, B, C etc. (Walker et al, 2019). Enterovirus A71 (EVA71) and Coxsackievirus A16 (CVA16) are the major causative pathogen of hand, food and mouth disease (HFMD).…”

Section: Introductionmentioning

confidence: 99%

Involvement of VCP/UFD1/Nucleolin in the viral entry of Enterovirus A species

Yan

Wang

et al. 2020

Virus Research

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A B S T R A C TValosin-containing protein (VCP) plays roles in various cellular activities. Recently, Enterovirus A71 (EVA71) infection was found to hijack the VCP protein. However, the mechanism by which VCP participates in the EVA71 life cycle remains unclear. Using chemical inhibitor, RNA interference and dominant negative mutant, we confirmed that the VCP and its ATPase activity were critical for EVA71 infection. To identify the factors downstream of VCP in enterovirus infection, 31 known VCP-cofactors were screened in the siRNA knockdown experiments. The results showed that UFD1 (ubiquitin recognition factor in ER associated degradation 1), but not NPL4 (NPL4 homolog, ubiquitin recognition factor), played critical roles in infections by EVA71. UFD1 knockdown suppressed the activity of EVA71 pseudovirus (causing single round infection) while it did not affect the viral replication in replicon RNA transfection assays. In addition, knockdown of VCP and UFD1 reduced viral infections by multiple human Enterovirus A serotypes. Mechanistically, we found that knockdown of UFD1 significantly decreased the binding and the subsequent entry of EVA71 to host cells through modulating the levels of nucleolin protein, a coreceptor of EVA71. Together, these data reveal novel roles of VCP and its cofactor UFD1 in the virus entry by EVA71. 3A-3D) . The viral RNA-dependent RNA polymerase https://doi.

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“…The precise taxonomic classification of all organisms undergoes constant drift as new discoveries are made that inform their evolutionary histories. However, in 2018, the International Committee for the Taxonomy of Viruses (ICTV) introduced a shift in the taxonomic designations of all RNA viruses, introducing the realm Riboviria , grouping “all RNA viruses that use cognate RNA-dependent RNA polymerases (RdRps) for replication” (19). In addition to this basal classification, many new taxonomic classifications were defined, or existing taxa reclassified.…”

Section: Introductionmentioning

confidence: 99%

Partial RdRp sequences offer a robust method for Coronavirus subgenus classification

Wilkinson

Joffrin

Lebarbenchon

et al. 2020

Preprint

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9The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic 10 categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, 11subfamily Orthocoronavirinae) represents a major shift in how official classifications are used to 12 designate specific viral lineages. While the newly defined subgenera provide much-needed 13 standardisation for commonly cited viruses of public health importance, no method has been 14 proposed for the assignment of subgenus based on partial sequence data, or for sequences that are 15 divergent from the designated holotype reference genomes. Here, we describe the genetic variation 16 of a partial region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the 17 most used partial sequence loci for both detection and classification of coronaviruses in molecular 18 epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus 19 sequences and examine clade groupings relative to all subgenus holotype sequences. Our 20 phylogenetic analyses are largely coherent with genome-scale analyses based on designated 21 holotype members for each subgenus. Distance measures between sequences form discrete clusters 22 between taxa, offering logical threshold boundaries that can attribute subgenus or indicate 23 sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus 24propose that partial RdRp sequence data of coronaviruses is sufficient for the attribution of 25 subgenus-level taxonomic classifications and we supply the R package, "MyCoV", which provides a 26 method for attributing subgenus and assessing the reliability of the attribution. 27 author/funder. All rights reserved. No reuse allowed without permission.

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Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)

Cited by 327 publications

References 4 publications

An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense RNA viruses

An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense RNA viruses

Involvement of VCP/UFD1/Nucleolin in the viral entry of Enterovirus A species

Partial RdRp sequences offer a robust method for Coronavirus subgenus classification

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