The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Alexander E Gorbalenya - One of the best experts on this subject based on the ideXlab platform.
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the species severe acute respiratory syndrome related coronavirus classifying 2019 ncov and naming it sars cov 2
Nature microbiology, 2020Co-Authors: Alexander E GorbalenyaAbstract:The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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Phylogeny of nidoviruses in comparison to the Tree of life (ToL).
2013Co-Authors: Chris Lauber, Eric J. Snijder, Phan Thi Nga, Jelle J. Goeman, Maria Del Carmen Parquet, Kouichi Morita, Alexander E GorbalenyaAbstract:Bayesian phylogenies of nidoviruses (A) and ToL (B) are drawn to a common scale of 0.1 amino acid substitutions per position. Major lineages are indicated by vertical bars and names; arteri: Arteriviridae, mesoni: Mesoniviridae, roni: Roniviridae, toro: Torovirinae, corona: Coronavirinae. Rooting was according to either (A) domain-specific outgroups [10] or (B) as described [66]. Posterior probability support values and fixed basal branch points (*) are indicated. The nidovirus and ToL alignments include, respectively, three enzymes and 56 single-gene protein families, 604 and 3336 columns, 2.95% and 2.8% gaps. For further details on the nidovirus tree see [10].
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the severe acute respiratory syndrome coronavirus replicative protein nsp9 is a single stranded rna binding subunit unique in the rna virus world
Proceedings of the National Academy of Sciences of the United States of America, 2004Co-Authors: Marie-pierre Egloff, Helene Dutartre, Eric J. Snijder, Corinne Rancurel, Alexander E Gorbalenya, Christian Cambillau, Valerie Campanacci, Francois Ferron, Sonia Longhi, Bruno CanardAbstract:The recently identified etiological agent of the severe acute respiratory syndrome (SARS) belongs to Coronaviridae (CoV), a family of viruses replicating by a poorly understood mechanism. Here, we report the crystal structure at 2.7-A resolution of nsp9, a hitherto uncharacterized subunit of the SARS-CoV replicative polyproteins. We show that SARS-CoV nsp9 is a single-stranded RNA-binding protein displaying a previously unreported, oligosaccharide/oligonucleotide fold-like fold. The presence of this type of protein has not been detected in the replicative complexes of RNA viruses, and its presence may reflect the unique and complex CoV viral replication/transcription machinery.
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a comparative sequence analysis to revise the current taxonomy of the family coronaviridae
Archives of Virology, 2003Co-Authors: J M Gonzalez, Alexander E Gorbalenya, Paulino Gomezpuertas, Dave Cavanagh, Luis EnjuanesAbstract:The Coronaviridae family, comprising the Coronavirus and Torovirus genera, is part of the Nidovirales order that also includes two other families, Arteriviridae and Roniviridae. Based on genetic and serological relationships, groups 1, 2 and 3 were previously recognized in the Coronavirus genus. In this report we present results of comparative sequence analysis of the spike (S), envelope (E), membrane (M), and nucleoprotein (N) structural proteins, and the two most conserved replicase domains, putative RNA-dependent RNA polymerase (RdRp) and RNA helicase (HEL), aimed at a revision of the Coronaviridae taxonomy. The results of pairwise comparisons involving structural and replicase proteins of the Coronavirus genus were consistent and produced percentages of sequence identities that were distributed in discontinuous clusters. Inter-group pairwise scores formed a single cluster in the lowest percentile. No homologs of the N and E proteins have been found outside coronaviruses, and the only (very) distant homologs of S and M proteins were identified in toroviruses. Intragroup sequence conservation was higher, although for some pairs, especially those from the most diverse group 1, scores were close or even overlapped with those from the intergroup comparisons. Phylogenetic analysis of six proteins using a neighbor-joining algorithm confirmed three coronavirus groups. Comparative sequence analysis of RdRp and HEL domains were extended to include arterivirus and ronivirus homologs. The pairwise scores between sequences of the genera Coronavirus and Torovirus (22-25% and 21-25%) were found to be very close to or overlapped with the value ranges (12 to 22% and 17 to 25%) obtained for interfamily pairwise comparisons, but were much smaller than values derived from pairwise comparisons within the Coronavirus genus (63-71% and 59-67%). Phylogenetic analysis confirmed toroviruses and coronaviruses to be separated by a large distance that is comparable to those between established nidovirus families. Based on comparison of these scores with those derived from analysis of separate ranks of several multi-genera virus families, like the Picornaviridae, a revision of the Coronaviridae taxonomy is proposed. We suggest the Coronavirus and Torovirus genera to be re-defined as two subfamilies within the Coronavirdae or two families within Nidovirales, and the current three informal coronavirus groups to be converted into three genera within the Coronaviridae.
Po Tien - One of the best experts on this subject based on the ideXlab platform.
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following the rule formation of the 6 helix bundle of the fusion core from severe acute respiratory syndrome coronavirus spike protein and identification of potent peptide inhibitors
Biochemical and Biophysical Research Communications, 2004Co-Authors: Gengfu Xiao, Yanhui Xu, Fang Yuan, Congyi Zheng, David K Cole, John I Bell, Po TienAbstract:Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) is a newly identified member of Family Coronaviridae. Coronavirus envelope spike protein S is a class I viral fusion protein which is characterized by the existence of two heptad repeat regions (HR1 and HR2) (forming a complex called fusion core). Here we report that by using in vitro bio-engineering techniques, SARS-CoV HR1 and HR2 bind to each other and form a typical 6-helix bundle. The HR2, either as a synthetic peptide or as a GST-fusion polypeptide, is a potent inhibitor of virus entry. The results do show that SARS-CoV follows the general fusion mechanism of class I viruses and this lays the ground for identification of virus fusion/entry inhibitors for this devastating emerging virus.
Bruno Canard - One of the best experts on this subject based on the ideXlab platform.
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the severe acute respiratory syndrome coronavirus replicative protein nsp9 is a single stranded rna binding subunit unique in the rna virus world
Proceedings of the National Academy of Sciences of the United States of America, 2004Co-Authors: Marie-pierre Egloff, Helene Dutartre, Eric J. Snijder, Corinne Rancurel, Alexander E Gorbalenya, Christian Cambillau, Valerie Campanacci, Francois Ferron, Sonia Longhi, Bruno CanardAbstract:The recently identified etiological agent of the severe acute respiratory syndrome (SARS) belongs to Coronaviridae (CoV), a family of viruses replicating by a poorly understood mechanism. Here, we report the crystal structure at 2.7-A resolution of nsp9, a hitherto uncharacterized subunit of the SARS-CoV replicative polyproteins. We show that SARS-CoV nsp9 is a single-stranded RNA-binding protein displaying a previously unreported, oligosaccharide/oligonucleotide fold-like fold. The presence of this type of protein has not been detected in the replicative complexes of RNA viruses, and its presence may reflect the unique and complex CoV viral replication/transcription machinery.
Marie-pierre Egloff - One of the best experts on this subject based on the ideXlab platform.
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the severe acute respiratory syndrome coronavirus replicative protein nsp9 is a single stranded rna binding subunit unique in the rna virus world
Proceedings of the National Academy of Sciences of the United States of America, 2004Co-Authors: Marie-pierre Egloff, Helene Dutartre, Eric J. Snijder, Corinne Rancurel, Alexander E Gorbalenya, Christian Cambillau, Valerie Campanacci, Francois Ferron, Sonia Longhi, Bruno CanardAbstract:The recently identified etiological agent of the severe acute respiratory syndrome (SARS) belongs to Coronaviridae (CoV), a family of viruses replicating by a poorly understood mechanism. Here, we report the crystal structure at 2.7-A resolution of nsp9, a hitherto uncharacterized subunit of the SARS-CoV replicative polyproteins. We show that SARS-CoV nsp9 is a single-stranded RNA-binding protein displaying a previously unreported, oligosaccharide/oligonucleotide fold-like fold. The presence of this type of protein has not been detected in the replicative complexes of RNA viruses, and its presence may reflect the unique and complex CoV viral replication/transcription machinery.
Dave Cavanagh - One of the best experts on this subject based on the ideXlab platform.
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coronaviridae a review of coronaviruses and toroviruses
2005Co-Authors: Dave CavanaghAbstract:From rags to riches, pauper to princess. Thus did Cinderella progress, literally overnight (well, three nights; Grimm & Grimm http://www.nationalgeographic.com/grimm/index2.html). Coronaviruses were described as being a “virology backwater”, the SARS coronavirus (SARS-CoV; severe acute respiratory syndrome) likened to Cinderella, thrusting coronaviruses from the shadows to the spotlight in early 2003. Understandably, this is the view from a human disease standpoint; coronaviruses in humans are usually considered to be the cause of nothing more serious than the common cold. However, this group of viruses has long had a higher profile in the veterinary science field, most of our knowledge of coronaviruses being based on viruses of domesticated species – plus the mouse (Tab. 1). Most of the 40 000 000 000 chickens in the world annually succumb to infection by avian infectious bronchitis coronavirus (IBV), resulting in reduced production, including mortality. The death toll amongst newborn swine can be 90% when infected with porcine transmissible gastroenteritis coronavirus (TGEV). The names porcine haemagglutinating encephalomyelitis coronavirus (HEV) and porcine epidemic diarrhoea coronavirus (PEDV) tell their own story. Most of the coronaviruses replicate, at least initially, in either or both of the respiratory or enteric tracts (Tab. 1). Within a coronavirus species some variants may have a tropism for the respiratory tract, others for the enteric region, though usually causing pathology in only one of these regions. SARS-CoV might be an exception to this, it appearing to cause pathology in both tracts, although that might be strain dependent. The advent of SARS-CoV served as a reminder of an important aspect that we already knew about coronaviruses, namely that their host range is greater than was often supposed. One of the human coronaviruses, human coronavirus-OC43, is extremely similar genetically to bovine coronavirus (BCoV), suggesting that these viruses might be capable of infecting each other’s recognised host. BCoV, under experimental conditions at least, infects and causes disease in turkeys. Canine enteric coronavirus (CECoV) Coronaviridae: a review of coronaviruses and toroviruses
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a comparative sequence analysis to revise the current taxonomy of the family coronaviridae
Archives of Virology, 2003Co-Authors: J M Gonzalez, Alexander E Gorbalenya, Paulino Gomezpuertas, Dave Cavanagh, Luis EnjuanesAbstract:The Coronaviridae family, comprising the Coronavirus and Torovirus genera, is part of the Nidovirales order that also includes two other families, Arteriviridae and Roniviridae. Based on genetic and serological relationships, groups 1, 2 and 3 were previously recognized in the Coronavirus genus. In this report we present results of comparative sequence analysis of the spike (S), envelope (E), membrane (M), and nucleoprotein (N) structural proteins, and the two most conserved replicase domains, putative RNA-dependent RNA polymerase (RdRp) and RNA helicase (HEL), aimed at a revision of the Coronaviridae taxonomy. The results of pairwise comparisons involving structural and replicase proteins of the Coronavirus genus were consistent and produced percentages of sequence identities that were distributed in discontinuous clusters. Inter-group pairwise scores formed a single cluster in the lowest percentile. No homologs of the N and E proteins have been found outside coronaviruses, and the only (very) distant homologs of S and M proteins were identified in toroviruses. Intragroup sequence conservation was higher, although for some pairs, especially those from the most diverse group 1, scores were close or even overlapped with those from the intergroup comparisons. Phylogenetic analysis of six proteins using a neighbor-joining algorithm confirmed three coronavirus groups. Comparative sequence analysis of RdRp and HEL domains were extended to include arterivirus and ronivirus homologs. The pairwise scores between sequences of the genera Coronavirus and Torovirus (22-25% and 21-25%) were found to be very close to or overlapped with the value ranges (12 to 22% and 17 to 25%) obtained for interfamily pairwise comparisons, but were much smaller than values derived from pairwise comparisons within the Coronavirus genus (63-71% and 59-67%). Phylogenetic analysis confirmed toroviruses and coronaviruses to be separated by a large distance that is comparable to those between established nidovirus families. Based on comparison of these scores with those derived from analysis of separate ranks of several multi-genera virus families, like the Picornaviridae, a revision of the Coronaviridae taxonomy is proposed. We suggest the Coronavirus and Torovirus genera to be re-defined as two subfamilies within the Coronavirdae or two families within Nidovirales, and the current three informal coronavirus groups to be converted into three genera within the Coronaviridae.
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the coronaviridae now comprises two genera coronavirus and torovirus report of the coronaviridae study group
Advances in Experimental Medicine and Biology, 1993Co-Authors: Dave Cavanagh, Luis Enjuanes, M Into, Kathry V Holmes, Marian C. Horzinek, Michael M C Lai, Hube Laude, P G Plagema, Stuart G. SiddellAbstract:At the April 1992, mid-term meeting of the International Committee on Taxonomy of Viruses (ICTV) a proposal from the Coronaviridae Study Group (CSG) to include the torovirus genus in the Coronaviridae was accepted. Following another proposal, the arterivirus genus was removed from the Togaviridae but not assigned to another family. The arteriviruses have some features in common with the Coronaviridae but also have major differences. After much debate, culminating in September 1992, it was decided that the CSG would not recommend inclusion of arterivirus in the Coronaviridae. It was agreed that (a) the nomenclature used for coronavirus genes, mRNAs and polypeptides (Cavanagh et al., 1990) should be used for toroviruses, (b) that the small (about 100 amino acids) membrane-associated protein, which is distinct from the integral membrane glycoprotein M, associated with virions of infectious bronchitis (Liu & Inglis, 1991) and transmissible gastroenteritis (Godet et al., 1992) coronaviruses would be referred to by the acronym sM (lower case 's') and (c) that 'pol' (polymerase) should be used as a working term for gene 1, which comprises open reading frames (ORFs) 1a and 1b in both genera of the Coronaviridae.
