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Article ; 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.
Keywords	covid19
Publisher	biorxiv
Document type	Article ; Online
DOI	10.1101/2020.02.07.937862
Database	COVID19

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Article ; Online: Birnavirus VP4 processing endopeptidase

Gorbalenya, A. E. / Mundt, Egbert

2015

Keywords	Text ; ddc:610
Language	English
Publishing date	2015-07-09
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; 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.
Keywords	covid19
Publisher	Elsevier; PMC
Document type	Article ; Online
DOI	10.1016/b978-012374410-4.00712-3
Database	COVID19

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

Gorbalenya, A E

Advances in experimental medicine and biology

2001 Volume 494, Page(s) 1–17

MeSH term(s)	Animals ; Genome, Viral ; Humans ; Nidovirales/chemistry ; Nidovirales/genetics ; Polyproteins/metabolism ; RNA, Viral/biosynthesis ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	Polyproteins ; RNA, Viral ; Viral Proteins
Language	English
Publishing date	2001
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
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Article: Non-canonical inteins.

Gorbalenya, A E

Nucleic acids research

1998 Volume 26, Issue 7, Page(s) 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 term(s)	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
Chemical Substances	Peptide Library ; Serine (452VLY9402) ; Adenosine Triphosphatases (EC 3.6.1.-) ; Cysteine (K848JZ4886) ; Alanine (OF5P57N2ZX)
Language	English
Publishing date	1998-04-01
Publishing country	England
Document type	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
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Article ; 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 Volume 165, Issue 6, Page(s) 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.
Language	English
Publishing date	2020-03-23
Publishing country	Austria
Document type	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
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Article: 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.
Keywords	public health ; taxonomy ; terminology ; tissue tropism ; virology
Language	English
Dates of publication	2020-03
Size	p. 793-797.
Publishing place	Springer Vienna
Document type	Article
Note	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
Database	NAL-Catalogue (AGRICOLA)

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Article: 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 Volume 3, Issue 7, Page(s) 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 term(s)	Amino Acid Sequence ; Conserved Sequence ; Deoxyribonucleases/chemistry ; Deoxyribonucleases/genetics ; Histidine ; Introns ; Molecular Sequence Data ; RNA Splicing ; Sequence Alignment ; Zinc/metabolism ; Zinc Fingers
Chemical Substances	Histidine (4QD397987E) ; Deoxyribonucleases (EC 3.1.-) ; Zinc (J41CSQ7QDS)
Language	English
Publishing date	1994-07
Publishing country	United States
Document type	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
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Article ; 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 Volume 165, Issue 3, Page(s) 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 term(s)	Enterovirus/classification ; Humans ; Rhinovirus/classification ; Terminology as Topic
Language	English
Publishing date	2019-12-26
Publishing country	Austria
Document type	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
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Article ; Online: PCR assays for detection of human astroviruses: In silico evaluation and design, and in vitro application to samples collected from patients in the Netherlands.

Nijhuis, R H T / Sidorov, I A / Chung, P K / Wessels, E / Gulyaeva, A A / de Vries, J J / Claas, E C J / Gorbalenya, A E

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2018 Volume 108, Page(s) 83–89

Abstract: Background: Human astroviruses (HAstV) comprise three phylogenetically compact and non-adjacent groups of species including classical HAstV (HAstV-C) and the novel ones (HAstV-VA/HMO and HAstV-MLB). Of these, HAstV-C is known to be responsible for ... ...

Abstract	Background: Human astroviruses (HAstV) comprise three phylogenetically compact and non-adjacent groups of species including classical HAstV (HAstV-C) and the novel ones (HAstV-VA/HMO and HAstV-MLB). Of these, HAstV-C is known to be responsible for gastroenteritis while the novel HAstV are associated with cases of neurological disorders. Accurate detection of all known variants by (real-time) PCR is challenging because of the high intra- and intergroup genetic divergence of HAstV. Objectives: To evaluate published HAstV PCR assays in silico, design de novo real-time PCR assays that can detect and discriminate three groups of HAstV, and apply those to patient samples to analyse the prevalence of HAstV in stool and cerebrospinal fluid (CSF) specimens. Study design: In silico evaluation of published PCR assays and design of real-time PCR assays for detection of different subsets of HAstV was conducted within a common computational framework that used all astrovirus full genome sequences from GenBank. The newly designed real-time PCR assays were evaluated in vitro and applied to faecal samples (collected in January-May 2016) and cerebrospinal fluid specimens (2010-2016) from patients in the Netherlands. Results: Quantitative in silico evaluation of published PCRs is provided. The newly designed real-time PCR assays can reliably assign all available HAstV genome sequences to one of the three phylogenetic groups in silico, and differentiate among HAstV-specific controls in vitro. A total of 556 samples were tested using these PCR assays. Fourteen fecal samples (2.5%) tested positive for HAstV, 3 of which could be identified as the novel HAstV-MLB variants. No novel HAstV were found in CSF specimens. Conclusion: Newly designed real-time PCR assays with improved detection of all known HAstV allowed the first-time identification of novel astroviruses from stool samples in the Netherlands.
MeSH term(s)	Astroviridae Infections/cerebrospinal fluid ; Astroviridae Infections/epidemiology ; Feces/virology ; Gastroenteritis/virology ; Genome, Viral ; Genotype ; Humans ; Mamastrovirus/classification ; Mamastrovirus/isolation & purification ; Meningitis/epidemiology ; Meningitis/virology ; Netherlands/epidemiology ; Phylogeny ; Prevalence ; Real-Time Polymerase Chain Reaction/standards ; Sequence Analysis, DNA
Language	English
Publishing date	2018-09-13
Publishing country	Netherlands
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2018.09.007
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