251 lines
21 KiB
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251 lines
21 KiB
XML
<document ID-DOI="10.1038/s41564-020-0695-z" ID-GBIF-Dataset="feda4f71-b2b9-48cd-923f-a077d7c4dc77" ID-PMC="PMC7095448" ID-PubMed="32123347" ID-Zenodo-Dep="3725837" checkinTime="1585060652100" checkinUser="plazi" docAuthor="Gorbalenya, Alexander E., Baker, Susan C., Baric, Ralph S., de Groot, Raoul J., Drosten, Christian, Gulyaeva, Anastasia A., Haagmans, Bart L., Lauber, Chris, Leontovich, Andrey M., Neuman, Benjamin W., Penzar, Dmitry, Perlman, Stanley, Poon, Leo L. M., Samborskiy, Dmitry V., Sidorov, Igor A., Sola, Isabel & Ziebuhr, John" docDate="2020" docId="0382878DFFFBE849B570FDD812D497E2" docLanguage="en" docName="natureMicrobiology.s41564-020-0695-z.pdf" docOrigin="Nature Microbiology 5" docStyle="DocumentStyle{}" docTitle="Coronaviridae Study" docType="treatment" docVersion="8" lastPageNumber="537" masterDocId="FFBBFFF5FFFBE848B501FFCB177B920C" masterDocTitle="The species Severe acute respiratory syndromerelated coronavirus: classifying 2019 - nCoV and naming it SARS-CoV- 2" masterLastPageNumber="544" masterPageNumber="536" pageNumber="536" updateTime="1668137197998" updateUser="ExternalLinkService">
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<mods:titleInfo>
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<mods:title>The species Severe acute respiratory syndromerelated coronavirus: classifying 2019 - nCoV and naming it SARS-CoV- 2</mods:title>
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<mods:namePart>Gorbalenya, Alexander E.</mods:namePart>
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<mods:namePart>Baker, Susan C.</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Baric, Ralph S.</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>de Groot, Raoul J.</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Drosten, Christian</mods:namePart>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Gulyaeva, Anastasia A.</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Haagmans, Bart L.</mods:namePart>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Lauber, Chris</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Leontovich, Andrey M.</mods:namePart>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Neuman, Benjamin W.</mods:namePart>
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Penzar, Dmitry</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Perlman, Stanley</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Poon, Leo L. M.</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Samborskiy, Dmitry V.</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Sidorov, Igor A.</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Sola, Isabel</mods:namePart>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Ziebuhr, John</mods:namePart>
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<mods:title>Nature Microbiology</mods:title>
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<mods:date>2020</mods:date>
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<mods:number>2020-03-22</mods:number>
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<mods:number>5</mods:number>
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<treatment ID-DOI="http://doi.org/10.5281/zenodo.3728366" ID-GBIF-Taxon="163283670" ID-Zenodo-Dep="3728366" LSID="urn:lsid:plazi:treatment:0382878DFFFBE849B570FDD812D497E2" httpUri="http://treatment.plazi.org/id/0382878DFFFBE849B570FDD812D497E2" lastPageId="1" lastPageNumber="537" pageId="0" pageNumber="536">
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<emphasis bold="true" box="[113,1250,531,562]" pageId="0" pageNumber="536">
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<taxonomicName authority="Study" authorityName="Study" box="[113,388,531,562]" family="Coronaviridae" kingdom="Viruses" order="Nidovirales" pageId="0" pageNumber="536" rank="family">Coronaviridae Study</taxonomicName>
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Group of the International Committee on Taxonomy of Viruses*
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</emphasis>
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</heading>
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</paragraph>
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<subSection pageId="0" pageNumber="536" type="abstract">
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<paragraph blockId="0.[113,1475,601,961]" pageId="0" pageNumber="536">
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<emphasis bold="true" pageId="0" pageNumber="536">
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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
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<taxonomicName authority="Study" authorityName="Study" box="[159,375,657,681]" family="Coronaviridae" kingdom="Viruses" order="Nidovirales" pageId="0" pageNumber="536" rank="family">
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<emphasis bold="true" box="[159,307,657,681]" italics="true" pageId="0" pageNumber="536">Coronaviridae</emphasis>
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Study
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</taxonomicName>
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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
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<taxonomicName box="[863,1011,685,709]" family="Coronaviridae" kingdom="Viruses" order="Nidovirales" pageId="0" pageNumber="536" rank="family">
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<emphasis bold="true" box="[863,1011,685,709]" italics="true" pageId="0" pageNumber="536">Coronaviridae</emphasis>
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</taxonomicName>
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, has assessed the placement of the human
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</emphasis>
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</heading>
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</paragraph>
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<subSubSection lastPageId="1" lastPageNumber="537" pageId="0" pageNumber="536" type="description">
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<paragraph blockId="0.[113,1475,601,961]" pageId="0" pageNumber="536">
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<emphasis bold="true" pageId="0" pageNumber="536">
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pathogen, tentatively named 2019-nCoV, within the
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<taxonomicName box="[671,819,713,737]" family="Coronaviridae" kingdom="Viruses" order="Nidovirales" pageId="0" pageNumber="536" rank="family">
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<emphasis bold="true" box="[671,819,713,737]" italics="true" pageId="0" pageNumber="536">Coronaviridae</emphasis>
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</taxonomicName>
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. 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
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<emphasis bold="true" box="[510,1091,769,793]" italics="true" pageId="0" pageNumber="536">Severe acute respiratory syndrome-related coronavirus</emphasis>
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, 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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</emphasis>
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</paragraph>
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<paragraph blockId="0.[110,779,1014,1938]" pageId="0" pageNumber="536">
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pon
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<subSection pageId="0" pageNumber="536" type="multiple">U a viral outbreak, it is important to rapidly establish whether the outbreak is caused by a new or a previously known virus (Box 1), as this helps decide which approaches and actions are most appropriate to detect the causative agent, con- trol its transmission and limit potential consequences of the epi- demic. The assessment of virus novelty also has implications for virus naming and, on a different timescale, helps to define research priorities in virology and public health.</subSection>
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</paragraph>
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<paragraph blockId="0.[110,779,1014,1938]" pageId="0" pageNumber="536">
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For many human virus infections such as influenza virus
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<bibRefCitation author="Krammer, F." box="[739,746,1242,1254]" journalOrPublisher="Nat. Rev. Dis. Primers" pageId="0" pageNumber="536" pagination="3" part="4" refId="ref5748" refString="1. Krammer, F. et al. Influenza. Nat. Rev. Dis. Primers 4, 3 (2018)." title="Influenza" type="journal article" year="2018">
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<superScript attach="left" box="[739,746,1242,1254]" fontSize="5" pageId="0" pageNumber="536">1</superScript>
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or norovirus
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<bibRefCitation author="Zheng, D. P." box="[210,217,1270,1282]" journalOrPublisher="Virology" pageId="0" pageNumber="536" pagination="312 - 323" part="346" refId="ref5773" refString="2. Zheng, D. P. et al. Norovirus classification and proposed strain nomenclature. Virology 346, 312 - 323 (2006)." title="Norovirus classification and proposed strain nomenclature" type="journal article" year="2006">
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<superScript attach="left" box="[210,217,1270,1282]" fontSize="5" pageId="0" pageNumber="536">2</superScript>
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infections, well-established and internationally approved methods, standards and procedures are in place to identify and name the causative agents of these infections and report this infor- mation promptly to public health authorities and the general public. In outbreaks involving newly emerged viruses, the situation may be different, and appropriate procedures to deal with these viruses need to be established or refined with high priority.
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</paragraph>
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<paragraph blockId="0.[110,779,1014,1938]" pageId="0" pageNumber="536">
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Here, we present an assessment of the genetic relatedness of the newly identified human coronavirus
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<bibRefCitation box="[483,490,1494,1506]" pageId="0" pageNumber="536" refId="ref5801" refString="3. Wu, A. et al. Genome composition and divergence of the novel">
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<superScript attach="left" box="[483,490,1494,1506]" fontSize="5" pageId="0" pageNumber="536">3</superScript>
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</bibRefCitation>
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, provisionally named 2019- nCoV, to known coronaviruses, and detail the basis for (re)naming this virus severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2), which will be used hereafter. Given the public interest in nam- ing newly emerging viruses and the diseases caused by these viruses in humans, we will give a brief introduction to virus discovery and classification — specifically the virus species concept — and the roles of different bodies, such as the World Health Organization (WHO) and the International Committee on Taxonomy of Viruses (ICTV), in this process. We hope this will help readers to better understand the scientific approach we have taken to arrive at this name, and we will also discuss implications of this analysis and naming decision.
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</paragraph>
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<paragraph blockId="0.[110,779,1014,1938]" box="[113,661,1856,1882]" pageId="0" pageNumber="536">
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<emphasis bold="true" box="[113,661,1856,1882]" pageId="0" pageNumber="536">Classifying and naming viruses and virus species</emphasis>
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</paragraph>
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<paragraph blockId="0.[110,779,1014,1938]" lastBlockId="0.[810,1475,1020,1938]" pageId="0" pageNumber="536">
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||
Defining the novelty of viruses is one of the topics that virus classification deals with. The classification of RNA viruses needs to consider their inherent genetic variability, which often results in two or more viruses with non-identical but similar genome sequences being regarded as variants of the same virus. This immediately poses the question of how much difference to an existing group is large enough to recognize the candidate virus as a member of a new, distinct group. This question is answered in best practice by evaluating the degree of relatedness of the candidate virus to previously identified viruses infecting the same host or established monophy- letic groups of viruses, often known as genotypes or clades, which may or may not include viruses of different hosts. This is formally addressed in the framework of the official classification of virus taxonomy and is overseen and coordinated by the ICTV
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<superScript attach="left" box="[1343,1350,1326,1338]" fontSize="5" pageId="0" pageNumber="536">4</superScript>
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. Viruses are clustered in taxa in a hierarchical scheme of ranks in which the spe- cies represents the lowest and most populous rank containing the least diverged groups (taxa) of viruses (Box 2). The ICTV maintains a Study Group for each virus family. The Study Groups are respon- sible for assigning viruses to virus species and taxa of higher ranks, such as subgenera, genera and subfamilies. In this context they play an important role in advancing the virus species concept and highlighting its significance
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||
<bibRefCitation author="Gorbalenya, A. E. & Lauber, C. & Siddell, S." box="[1038,1045,1550,1562]" journalOrPublisher="Elsevier" pageId="0" pageNumber="536" refId="ref5887" refString="5. Gorbalenya, A. E., Lauber, C. & Siddell, S. Taxonomy of Viruses, in Reference Module in Biomedical Sciences (Elsevier, 2019) https: // doi. org / 10.1016 / B 978 - 0 - 12 - 801238 - 3.99237 - 7." title="Taxonomy of Viruses" type="book" volumeTitle="Reference Module in Biomedical Sciences" year="2019">
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<superScript attach="left" box="[1038,1045,1550,1562]" fontSize="5" pageId="0" pageNumber="536">5</superScript>
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</bibRefCitation>
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.
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</paragraph>
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<paragraph blockId="0.[810,1475,1020,1938]" pageId="0" pageNumber="536">Virus nomenclature is a formal system of names used to label viruses and taxa. The fact that there are names for nearly all viruses within a species is due to the historical perception of viruses as causative agents of specific diseases in specific hosts, and to the way we usually catalogue and classify newly discovered viruses, which increasingly includes viruses that have not been linked to any known disease in their respective hosts (Box 1). The WHO, an agency of the United Nations, coordinates international public health activities aimed at combating, containing and mitigating the consequences of communicable diseases—including major virus epidemics—and is responsible for naming disease(s) caused by newly emerging human viruses. In doing so, the WHO often takes the traditional approach of linking names of specific diseases to viruses (Box 1) and</paragraph>
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<footnote box="[113,726,1970,1990]" pageId="0" pageNumber="536">
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<paragraph blockId="0.[113,726,1970,1990]" box="[113,726,1970,1990]" pageId="0" pageNumber="536">*A list of authors and their affiliations appears at the end of the paper.</paragraph>
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</footnote>
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<caption ID-DOI="http://doi.org/10.5281/zenodo.3725850" ID-Zenodo-Dep="3725850" httpUri="https://zenodo.org/record/3725850/files/figure.png" pageId="1" pageNumber="537" startId="1.[129,196,1302,1323]" targetBox="[371,1163,841,1275]" targetPageId="1">
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<paragraph pageId="1" pageNumber="537">
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<emphasis bold="true" box="[129,1336,1302,1323]" pageId="1" pageNumber="537">History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses.</emphasis>
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According to the current international classification of diseases
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<bibRefCitation author="World Health Organization" box="[566,580,1329,1341]" pageId="1" pageNumber="537" refId="ref7783" refString="49. ICD- 11 (World Health Organization, 2018)." title="ICD- 11" type="book" year="2018">
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<superScript attach="left" box="[566,580,1329,1341]" fontSize="5" pageId="1" pageNumber="537">49</superScript>
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</bibRefCitation>
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,
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<collectionCode box="[589,642,1330,1350]" pageId="1" pageNumber="537">MERS</collectionCode>
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and
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<collectionCode box="[685,734,1330,1350]" pageId="1" pageNumber="537">SARS</collectionCode>
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are classified as 1D64 and 1D65, respectively.
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</paragraph>
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</caption>
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<paragraph blockId="1.[113,779,1468,1994]" pageId="1" pageNumber="537">assessing virus novelty by an apparent failure to detect the causative agent using established diagnostic assays.</paragraph>
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Apart from disease, geography and the organism from which a given virus was isolated also dominate the nomenclature, occasionally engraving connections that may be accidental (rather than typical) or even stigmatizing, which should be avoided. Establishing a universal nomenclature for viruses was one of the major tasks of the ICTV when it was founded more than 50 years ago
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<bibRefCitation author="Adams, M. J." box="[660,667,1662,1674]" journalOrPublisher="Arch. Virol." pageId="1" pageNumber="537" pagination="1441 - 1446" part="162" refId="ref5848" refString="4. Adams, M. J. et al. 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Arch. Virol. 162, 1441 - 1446 (2017)." title="50 years of the International Committee on Taxonomy of Viruses: progress and prospects" type="journal article" year="2017">
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<superScript attach="left" box="[660,667,1662,1674]" fontSize="5" pageId="1" pageNumber="537">4</superScript>
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</bibRefCitation>
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. When the species rank was established in the taxonomy of viruses
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<bibRefCitation author="Van Regenmortel, M. H. & Maniloff, J. & Calisher, C." box="[686,693,1690,1702]" journalOrPublisher="Arch. Virol." pageId="1" pageNumber="537" pagination="313 - 314" part="120" refId="ref5942" refString="6. Van Regenmortel, M. H., Maniloff, J. & Calisher, C. The concept of virus species. Arch. Virol. 120, 313 - 314 (1991)." title="The concept of virus species" type="journal article" year="1991">
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<superScript attach="left" box="[686,693,1690,1702]" fontSize="5" pageId="1" pageNumber="537">6</superScript>
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</bibRefCitation>
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, ICTV’s responsibility for naming viruses was shifted to naming and establishing species.
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<taxonomicName authority="Study Groups" authorityName="Study Groups" box="[322,527,1748,1770]" pageId="1" pageNumber="537" rank="species" species="ictv">ICTV Study Groups</taxonomicName>
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may also be involved in virus naming on a case-by-case basis as an extension of their official remit, as well as using the special expertise of their members. As virus species names are often very similar to the name of the founding member of the respective species, they are frequently confused in the literature with names of individual viruses in this species. The species name is italicized, starts with a capital letter and should not be spelled in an abbreviated form
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<bibRefCitation author="The International Code of Virus Classification" box="[471,478,1943,1955]" journalOrPublisher="and Nomenclature" pageId="1" pageNumber="537" publicationUrl="https://talk.ictvonline.org/information/w/ictv-information/383/ictv-code" refId="ref5980" refString="7. ICTV Code. The International Code of Virus Classification and Nomenclature https: // talk. ictvonline. org / information / w / ictv-information / 383 / ictv-code (2018)." title="ICTV Code" type="url" year="2018">
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<superScript attach="right" box="[471,478,1943,1955]" fontSize="5" pageId="1" pageNumber="537">7</superScript>
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; hence the species name
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<emphasis italics="true" pageId="1" pageNumber="537">Severe acute respiratory syndrome-related coronavirus</emphasis>
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. In contrast, this convention does not apply to virus names, hence severe acute respiratory syndrome coronavirus, or SARS-CoV, as it is widely known.
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |