Genomic characterization of a novel SARS-CoV-2
Identifieur interne : 001020 ( Pmc/Curation ); précédent : 001019; suivant : 001021Genomic characterization of a novel SARS-CoV-2
Auteurs : Rozhgar A. Khailany [Iraq] ; Muhamad Safdar [Pakistan] ; Mehmet Ozaslan [Turquie]Source :
- Gene Reports [ 2452-0144 ] ; 2020.
Abstract
A new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with human to human transmission and extreme human sickness has been as of late announced from the city of Wuhan in China. Our objectives were to mutation analysis between recently reported genomes at various times and locations and to characterize the genomic structure of SARS-CoV-2 using bioinformatics programs. Information on the variation of viruses is of considerable medical and biological impacts on the prevention, diagnosis, and therapy of infectious diseases. To understand the genomic structure and variations of the SARS-CoV-2. The study analyzed 95 SARS-CoV-2 complete genome sequences available in GenBank, National MicrobiologyData Center (NMDC) and NGDC Genome Warehouse from December-2019 until 05 of April-2020. The genomic signature analysis demonstrates that a strong association between the time of sample collection, location of sample and accumulation of genetic diversity. We found 116 mutations, the three most common mutations were 8782C>T in ORF1ab gene, 28144T>C in ORF8 gene and 29095C>T in the N gene. The mutations might affect the severity and spread of the SARS-CoV-2. The finding heavily supports an intense requirement for additional prompt, inclusive investigations that combine genomic detail, epidemiological information and graph records of the clinical features of patients with COVID-19.
Url:
DOI: 10.1016/j.genrep.2020.100682
PubMed: 32300673
PubMed Central: 7161481
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Khailany</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Biology, College of Science, University of Salahaddin-Erbil, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of Biology, College of Science, University of Salahaddin-Erbil</wicri:regionArea></affiliation></author><author><name sortKey="Safdar, Muhamad" sort="Safdar, Muhamad" uniqKey="Safdar M" first="Muhamad" last="Safdar">Muhamad Safdar</name><affiliation wicri:level="1"><nlm:aff id="af0010">Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100, Pakistan</nlm:aff><country xml:lang="fr">Pakistan</country><wicri:regionArea>Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100</wicri:regionArea></affiliation></author><author><name sortKey="Ozaslan, Mehmet" sort="Ozaslan, Mehmet" uniqKey="Ozaslan M" first="Mehmet" last="Ozaslan">Mehmet Ozaslan</name><affiliation wicri:level="1"><nlm:aff id="af0015">Department of Biology, Gaziantep University, 27310 Gaziantep, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Biology, Gaziantep University, 27310 Gaziantep</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">32300673</idno><idno type="pmc">7161481</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161481</idno><idno type="RBID">PMC:7161481</idno><idno type="doi">10.1016/j.genrep.2020.100682</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">001020</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001020</idno><idno type="wicri:Area/Pmc/Curation">001020</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001020</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genomic characterization of a novel SARS-CoV-2</title><author><name sortKey="Khailany, Rozhgar A" sort="Khailany, Rozhgar A" uniqKey="Khailany R" first="Rozhgar A." last="Khailany">Rozhgar A. Khailany</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Biology, College of Science, University of Salahaddin-Erbil, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of Biology, College of Science, University of Salahaddin-Erbil</wicri:regionArea></affiliation></author><author><name sortKey="Safdar, Muhamad" sort="Safdar, Muhamad" uniqKey="Safdar M" first="Muhamad" last="Safdar">Muhamad Safdar</name><affiliation wicri:level="1"><nlm:aff id="af0010">Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100, Pakistan</nlm:aff><country xml:lang="fr">Pakistan</country><wicri:regionArea>Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100</wicri:regionArea></affiliation></author><author><name sortKey="Ozaslan, Mehmet" sort="Ozaslan, Mehmet" uniqKey="Ozaslan M" first="Mehmet" last="Ozaslan">Mehmet Ozaslan</name><affiliation wicri:level="1"><nlm:aff id="af0015">Department of Biology, Gaziantep University, 27310 Gaziantep, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Biology, Gaziantep University, 27310 Gaziantep</wicri:regionArea></affiliation></author></analytic><series><title level="j">Gene Reports</title><idno type="eISSN">2452-0144</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with human to human transmission and extreme human sickness has been as of late announced from the city of Wuhan in China. Our objectives were to mutation analysis between recently reported genomes at various times and locations and to characterize the genomic structure of SARS-CoV-2 using bioinformatics programs. Information on the variation of viruses is of considerable medical and biological impacts on the prevention, diagnosis, and therapy of infectious diseases. To understand the genomic structure and variations of the SARS-CoV-2. The study analyzed 95 SARS-CoV-2 complete genome sequences available in GenBank, National MicrobiologyData Center (NMDC) and NGDC Genome Warehouse from December-2019 until 05 of April-2020. The genomic signature analysis demonstrates that a strong association between the time of sample collection, location of sample and accumulation of genetic diversity. We found 116 mutations, the three most common mutations were 8782C>T in ORF1ab gene, 28144T>C in ORF8 gene and 29095C>T in the N gene. The mutations might affect the severity and spread of the SARS-CoV-2. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Gene Rep</journal-id><journal-id journal-id-type="iso-abbrev">Gene Rep</journal-id><journal-title-group><journal-title>Gene Reports</journal-title></journal-title-group><issn pub-type="epub">2452-0144</issn><publisher><publisher-name>Elsevier Inc.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">32300673</article-id><article-id pub-id-type="pmc">7161481</article-id><article-id pub-id-type="publisher-id">S2452-0144(20)30096-0</article-id><article-id pub-id-type="doi">10.1016/j.genrep.2020.100682</article-id><article-id pub-id-type="publisher-id">100682</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Genomic characterization of a novel SARS-CoV-2</article-title></title-group><contrib-group><contrib contrib-type="author" id="au0005"><name><surname>Khailany</surname><given-names>Rozhgar A.</given-names></name><email>rozhgar.mohammed@su.edu.krd</email><xref rid="af0005" ref-type="aff">a</xref><xref rid="cr0005" ref-type="corresp">⁎</xref></contrib><contrib contrib-type="author" id="au0010"><name><surname>Safdar</surname><given-names>Muhamad</given-names></name><xref rid="af0010" ref-type="aff">b</xref></contrib><contrib contrib-type="author" id="au0015"><name><surname>Ozaslan</surname><given-names>Mehmet</given-names></name><xref rid="af0015" ref-type="aff">c</xref></contrib></contrib-group><aff id="af0005"><label>a</label>Department of Biology, College of Science, University of Salahaddin-Erbil, Iraq</aff><aff id="af0010"><label>b</label>Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100, Pakistan</aff><aff id="af0015"><label>c</label>Department of Biology, Gaziantep University, 27310 Gaziantep, Turkey</aff><author-notes><corresp id="cr0005"><label>⁎</label>Corresponding author at: Department of Biology, College of Science, University of Salahaddin-Erbil, Erbil 44001, Iraq. <email>rozhgar.mohammed@su.edu.krd</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>16</day><month>4</month><year>2020</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>6</month><year>2020</year></pub-date><pub-date pub-type="epub"><day>16</day><month>4</month><year>2020</year></pub-date><volume>19</volume><fpage>100682</fpage><lpage>100682</lpage><history><date date-type="received"><day>26</day><month>3</month><year>2020</year></date><date date-type="rev-recd"><day>5</day><month>4</month><year>2020</year></date><date date-type="accepted"><day>13</day><month>4</month><year>2020</year></date></history><permissions><copyright-statement>© 2020 Elsevier Inc. All rights reserved.</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>Elsevier Inc.</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract id="ab0005"><p>A new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with human to human transmission and extreme human sickness has been as of late announced from the city of Wuhan in China. Our objectives were to mutation analysis between recently reported genomes at various times and locations and to characterize the genomic structure of SARS-CoV-2 using bioinformatics programs. Information on the variation of viruses is of considerable medical and biological impacts on the prevention, diagnosis, and therapy of infectious diseases. To understand the genomic structure and variations of the SARS-CoV-2. The study analyzed 95 SARS-CoV-2 complete genome sequences available in GenBank, National MicrobiologyData Center (NMDC) and NGDC Genome Warehouse from December-2019 until 05 of April-2020. The genomic signature analysis demonstrates that a strong association between the time of sample collection, location of sample and accumulation of genetic diversity. We found 116 mutations, the three most common mutations were 8782C>T in ORF1ab gene, 28144T>C in ORF8 gene and 29095C>T in the N gene. The mutations might affect the severity and spread of the SARS-CoV-2. The finding heavily supports an intense requirement for additional prompt, inclusive investigations that combine genomic detail, epidemiological information and graph records of the clinical features of patients with COVID-19.</p></abstract><abstract abstract-type="author-highlights" id="ab0010"><title>Highlights</title><p><list list-type="simple" id="l0005"><list-item id="li0005"><label>•</label><p id="p0005">Genomic mutations identification of SARS-CoV-2 in COVID-19 patients</p></list-item><list-item id="li0010"><label>•</label><p id="p0010">Genetic variations in recently sequenced SARS-CoV-2</p></list-item><list-item id="li0015"><label>•</label><p id="p0015">Most common mutations are three in SARS-CoV-2</p></list-item></list></p></abstract><kwd-group id="ks0005"><title>Keywords</title><kwd>SARS-CoV-2</kwd><kwd>Genomic characterization</kwd><kwd>Mutation</kwd><kwd>COVID-19</kwd></kwd-group><kwd-group id="ks0010"><title>Abbreviations</title><kwd>SARS-CoV-2, severe acute respiratory syndrome coronavirus 2</kwd><kwd>COVID-19, Coronavirus disease 2019</kwd><kwd>NGDC, National Genomics Data Center</kwd><kwd>NMDC, National Microbiology Data Center</kwd><kwd>WHO, World Health Organization</kwd><kwd>EMBOSS, The European Molecular Biology Open Software Suite</kwd><kwd>BLAST, Basic Local Alignment Search Tool</kwd><kwd><italic>UTR</italic>, Untranslated region</kwd><kwd>CDC, Centers of Disease Control and Prevention</kwd><kwd>MERS, Middle East Respiratory Syndrome</kwd><kwd>NCBI, National Center for Biotechnology Information</kwd><kwd>NSP, nonstructural protein</kwd><kwd>ORF, Open Reading Frame</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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