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Artikel ; Online: Severe acute respiratory syndrome-related coronavirus - The species and its viruses, a statement of the Coronavirus Study Group

Gorbalenya, A. E.

Abstract: The present outbreak of lower respiratory tract infections, including respiratory distress syndrome, is the third spillover, in only two decades, of an animal coronavirus to humans resulting in a major epidemic. Here, the Coronavirus Study Group (CSG) of ...

Abstract	The present outbreak of lower respiratory tract infections, including respiratory distress syndrome, is the third spillover, in only two decades, of an animal coronavirus to humans resulting in a major epidemic. Here, the Coronavirus Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the official classification of viruses and taxa naming (taxonomy) of the Coronaviridae family, assessed the novelty of the human pathogen tentatively named 2019-nCoV. Based on phylogeny, taxonomy and established practice, the CSG formally recognizes this virus as a sister to severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus and designates it as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To facilitate communication, the CSG further proposes to use the following naming convention for individual isolates: SARS-CoV-2/Isolate/Host/Date/Location. The 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 the entire (virus) species to complement research focused on individual pathogenic viruses of immediate significance. This research will improve our understanding of virus-host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
Schlagwörter	covid19
Verlag	biorxiv
Dokumenttyp	Artikel ; Online
DOI	10.1101/2020.02.07.937862
Datenquelle	COVID19

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Artikel ; Online: Birnavirus VP4 processing endopeptidase

Gorbalenya, A. E. / Mundt, Egbert

2015

Schlagwörter	Text ; ddc:610
Sprache	Englisch
Erscheinungsdatum	2015-07-09
Erscheinungsland	de
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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Artikel ; Online: Phylogeny of Viruses

Gorbalenya, A.E.

Encyclopedia of Virology

Abstract: Biological species, including viruses, change through generations and over time in the process known as evolution. Viruses may evolve at high, uneven, and fluctuating rates among genome sites. The accumulated changes, through either mutation or ... ...

Abstract	Biological species, including viruses, change through generations and over time in the process known as evolution. Viruses may evolve at high, uneven, and fluctuating rates among genome sites. The accumulated changes, through either mutation or recombination with other species, are first fixed in the genome of successful individuals that give rise to genetic lineages. The relationship between biological lineages related by common descent is called ‘phylogeny’. For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. The tree is characterized by a topology, length of branches, shape, and the root position. A complex mathematical apparatus has been developed for phylogeny inference that can evaluate inter-species differences, facilitate tree building and comparison of trees, and assess the fit between data and tree through, typically, computationally intensive calculations. A reconstructed tree is an approximation of the true phylogeny that practically remains unknown. The phylogenetic analysis is used in applied and fundamental virus research, including epidemiology, diagnostics, forensic studies, phylogeography, evolutionary studies, and virus taxonomy. It can provide an evolutionary perspective on variation of any trait that can be measured for a group of viruses.
Schlagwörter	covid19
Verlag	Elsevier; PMC
Dokumenttyp	Artikel ; Online
DOI	10.1016/b978-012374410-4.00712-3
Datenquelle	COVID19

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Artikel: Big nidovirus genome. When count and order of domains matter.

Gorbalenya, A E

Advances in experimental medicine and biology

2001 Band 494, Seite(n) 1–17

Mesh-Begriff(e)	Animals ; Genome, Viral ; Humans ; Nidovirales/chemistry ; Nidovirales/genetics ; Polyproteins/metabolism ; RNA, Viral/biosynthesis ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemische Substanzen	Polyproteins ; RNA, Viral ; Viral Proteins
Sprache	Englisch
Erscheinungsdatum	2001
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Review
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Recommendations for the nomenclature of enteroviruses and rhinoviruses [Erratum: Jun. 2020, v.165(6), p.1515]

Simmonds, P / Gorbalenya, A. E / Harvala, H / Hovi, T / Knowles, N. J / Lindberg, A. M / Oberste, M. S / Palmenberg, A. C / Reuter, G / Skern, T / Tapparel, C / Wolthers, K. C / Woo, P. C. Y / Zell, R

Archives of virology. 2020 Mar., v. 165, no. 3

2020

Abstract: Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and ... ...

Abstract	Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as “coxsackieviruses”, “polioviruses” and “echoviruses”, which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series of recommendations for the nomenclature of EV and RV types and their abbreviations. We believe their adoption will promote greater clarity and consistency in the terminology used in the scientific and medical literature. The recommendations will additionally provide a useful reference guide for journals, other publications and public databases seeking to use standardised terms for the growing multitude of enteroviruses and rhinoviruses described worldwide.
Schlagwörter	public health ; taxonomy ; terminology ; tissue tropism ; virology
Sprache	Englisch
Erscheinungsverlauf	2020-03
Umfang	p. 793-797.
Erscheinungsort	Springer Vienna
Dokumenttyp	Artikel
Anmerkung	NAL-AP-2-clean
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-019-04520-6
Datenquelle	NAL Katalog (AGRICOLA)

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Artikel: Non-canonical inteins.

Gorbalenya, A E

Nucleic acids research

1998 Band 26, Heft 7, Seite(n) 1741–1748

Abstract: Previous analyses have shown that inteins (protein splicing elements) employ two structural organizations: the 'canonical' Nintein-Dod-inteinC found in dozens of inteins and a 'non-canonical' Nintein-inteinC described in two inteins, where Nintein at the ...

Abstract	Previous analyses have shown that inteins (protein splicing elements) employ two structural organizations: the 'canonical' Nintein-Dod-inteinC found in dozens of inteins and a 'non-canonical' Nintein-inteinC described in two inteins, where Nintein at the N-terminus and inteinC at the C-terminus are conserved domains involved in self-splicing and Dod is the Dod DNA endonuclease (DNase). In this study, four non-canonical inteins, each with unique structural features, have been identified using alignment-based Hidden Markov Models. A Nintein-inteinC intein, carrying an unprecedented replacement of the N-terminal catalytic Cys(Ser) by Ala, is described in a putative ATPase encoded by Methanococcus jannaschii . Three replicative proteins of Synechocystis spp. contain inteins with the organizations: (i) Nintein minus X minus inteinC over Dod, where X is an uncharacterized domain and Dod DNase is located in an alternative open reading frame (ORF) being embedded between two novel CG and YK domains; (ii) Nintein-HN-inteinC, where HN stands for phage-like DNase from the EX1H-HX3H family; (iii) Nintein>\|<inteinC, where >\|< indicates that the intein domains are associated with a disrupted host protein encoded by two spatially separated ORFs. The expression of some of these newly identified inteins may affect the intein hosts. The variety of structural forms of inteins could have evolved through invasion of self-splicing proteases by different mobile DNases or the departure of mobile DNases from canonical inteins.
Mesh-Begriff(e)	Adenosine Triphosphatases/biosynthesis ; Adenosine Triphosphatases/chemistry ; Adenosine Triphosphatases/genetics ; Alanine ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Consensus Sequence ; Conserved Sequence ; Cyanobacteria/enzymology ; Cyanobacteria/genetics ; Cysteine ; Databases as Topic ; Methanococcus/enzymology ; Methanococcus/genetics ; Molecular Sequence Data ; Open Reading Frames ; Peptide Library ; Protein Splicing ; Sequence Alignment ; Sequence Homology, Amino Acid ; Serine
Chemische Substanzen	Peptide Library ; Serine (452VLY9402) ; Adenosine Triphosphatases (EC 3.6.1.-) ; Cysteine (K848JZ4886) ; Alanine (OF5P57N2ZX)
Sprache	Englisch
Erscheinungsdatum	1998-04-01
Erscheinungsland	England
Dokumenttyp	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	0305-1048 ; 0301-5610
ISSN	0305-1048 ; 0301-5610
DOI	10.1093/nar/26.7.1741
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Correction to: Recommendations for the nomenclature of enteroviruses and rhinoviruses.

Simmonds, P / Gorbalenya, A E / Harvala, H / Hovi, T / Knowles, N J / Lindberg, A M / Oberste, M S / Palmenberg, A C / Reuter, G / Skern, T / Tapparel, C / Wolthers, K C / Woo, P C Y / Zell, R

Archives of virology

2020 Band 165, Heft 6, Seite(n) 1515

Abstract: Unfortunately, one of the affiliations of author "A. E. Gorbalenya" was missed in original version. The affiliation is updated here. ...

Abstract	Unfortunately, one of the affiliations of author "A. E. Gorbalenya" was missed in original version. The affiliation is updated here.
Sprache	Englisch
Erscheinungsdatum	2020-03-23
Erscheinungsland	Austria
Dokumenttyp	Journal Article ; Published Erratum
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-020-04558-x
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family.

Gorbalenya, A E

Protein science : a publication of the Protein Society

1994 Band 3, Heft 7, Seite(n) 1117–1120

Abstract: A new family of protein domains consisting of 50-80 amino acid residues is described. It is composed of nearly 40 members, including domains encoded by plastid and phage group I introns; mitochondrial, plastid, and bacterial group II introns; eubacterial ...

Abstract	A new family of protein domains consisting of 50-80 amino acid residues is described. It is composed of nearly 40 members, including domains encoded by plastid and phage group I introns; mitochondrial, plastid, and bacterial group II introns; eubacterial genomes and plasmids; and phages. The name "EX1HH-HX3H" was coined for both domain and family. It is based on 2 most prominent amino acid sequence motifs, each encompassing a pair of highly conserved histidine residues in a specific arrangement: EX1HH and HX3H. The "His" motifs often alternate with amino- and carboxy-terminal motifs of a new type of Zn-finger-like structure CX2,4CX29-54[CH]X2,3[CH]. The EX1HH-HX3H domain in eubacterial E2-type bacteriocins and in phage RB3 (wild variant of phage T4) product of the nrdB group I intron was reported to be essential for DNA endonuclease activity of these proteins. In other proteins, the EX1HH-HX3H domain is hypothesized to possess DNase activity as well. Presumably, this activity promotes movement (rearrangement) of group I and group II introns encoding the EX1HH-HX3H domain and other gene targets. In the case of Escherichia coli restrictase McrA and possibly several related proteins, it appears to mediate the restriction of alien DNA molecules.
Mesh-Begriff(e)	Amino Acid Sequence ; Conserved Sequence ; Deoxyribonucleases/chemistry ; Deoxyribonucleases/genetics ; Histidine ; Introns ; Molecular Sequence Data ; RNA Splicing ; Sequence Alignment ; Zinc/metabolism ; Zinc Fingers
Chemische Substanzen	Histidine (4QD397987E) ; Deoxyribonucleases (EC 3.1.-) ; Zinc (J41CSQ7QDS)
Sprache	Englisch
Erscheinungsdatum	1994-07
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.5560030716
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Recommendations for the nomenclature of enteroviruses and rhinoviruses.

Simmonds, P / Gorbalenya, A E / Harvala, H / Hovi, T / Knowles, N J / Lindberg, A M / Oberste, M S / Palmenberg, A C / Reuter, G / Skern, T / Tapparel, C / Wolthers, K C / Woo, P C Y / Zell, R

Archives of virology

2019 Band 165, Heft 3, Seite(n) 793–797

Abstract	Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as "coxsackieviruses", "polioviruses" and "echoviruses", which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series of recommendations for the nomenclature of EV and RV types and their abbreviations. We believe their adoption will promote greater clarity and consistency in the terminology used in the scientific and medical literature. The recommendations will additionally provide a useful reference guide for journals, other publications and public databases seeking to use standardised terms for the growing multitude of enteroviruses and rhinoviruses described worldwide.
Mesh-Begriff(e)	Enterovirus/classification ; Humans ; Rhinovirus/classification ; Terminology as Topic
Sprache	Englisch
Erscheinungsdatum	2019-12-26
Erscheinungsland	Austria
Dokumenttyp	Journal Article
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-019-04520-6
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Evidence for functional significance of the permuted C motif in Co2+-stimulated RNA-dependent RNA polymerase of infectious bursal disease virus

Letzel, T / Mundt, E / Gorbalenya, A.E

Journal of general virology. 2007 Oct., v. 88, pt. 10

2007

Abstract: Segment B of bisegmented infectious bursal disease virus (IBDV) encodes virus protein 1 (VP1), possessing RNA-dependent RNA polymerase (RdRp) activity. This multidomain protein includes an RdRp domain with a non-canonical order of three sequence motifs ... ...

Abstract	Segment B of bisegmented infectious bursal disease virus (IBDV) encodes virus protein 1 (VP1), possessing RNA-dependent RNA polymerase (RdRp) activity. This multidomain protein includes an RdRp domain with a non-canonical order of three sequence motifs forming the active site: C-A-B. The A-B-C order of the motifs, as found in RdRps of the majority of viruses, was converted by relocation (permutation) of motif C to a C-A-B order. Due to the unusual location and unproven significance, the motif was named 'C?'. This motif includes an Ala-Asp-Asn tripeptide that replaces the C motif Gly-Asp-Asp sequence, widely considered a hallmark of RdRps. In this study, functional significance of the C? motif was investigated by using purified His-tagged VP1 mutants with either a double replacement (ADN to GDD) or two single-site mutants (ADD or GDN). All mutants showed a significant reduction of RdRp activity in vitro, in comparison to that of VP1. Only the least-affected GDN mutant gave rise to viable, albeit partially impaired, progeny using a reverse-genetics system. Experiments performed to investigate whether the C motif was implicated in the control of metal dependence revealed that, compared with Mn2+ and Mg2+, Co2+ stimulated RdRp unconventionally. No activity was observed in the presence of several divalent cations. Of two Co2+ salts with Cl- and SO₄²⁻ anions, the former was a stronger stimulant for RdRp. When cell-culture medium was supplemented with 50 micromolar Co2+, an increase in IBDV progeny yield was observed. The obtained results provide evidence that the unusual Co2+ dependence of the IBDV RdRp might be linked to the permuted organization of the motif.
Schlagwörter	Infectious bursal disease virus ; vertebrate viruses ; RNA-directed RNA polymerase ; nucleotide sequences ; viral proteins ; enzyme activity ; protein subunits ; peptides ; amino acid sequences ; in vitro studies ; protein structure ; microbial genetics ; virus replication
Sprache	Englisch
Erscheinungsverlauf	2007-10
Umfang	p. 2824-2833.
Dokumenttyp	Artikel
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
Datenquelle	NAL Katalog (AGRICOLA)

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