Genomic characterization of a novel SARS-CoV-2.
Identifieur interne : 000484 ( PubMed/Checkpoint ); précédent : 000483; suivant : 000485Genomic 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.
DOI: 10.1016/j.genrep.2020.100682
PubMed: 32300673
Affiliations:
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Khailany</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, College of Science, University of Salahaddin-Erbil, Iraq.</nlm:affiliation><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of Biology, College of Science, University of Salahaddin-Erbil</wicri:regionArea><wicri:noRegion>University of Salahaddin-Erbil</wicri:noRegion></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:affiliation>Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100</wicri:regionArea><wicri:noRegion>Bahawalpur 63100</wicri:noRegion></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:affiliation>Department of Biology, Gaziantep University, 27310 Gaziantep, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Biology, Gaziantep University, 27310 Gaziantep</wicri:regionArea><wicri:noRegion>27310 Gaziantep</wicri:noRegion></affiliation></author></analytic><series><title level="j">Gene reports</title><idno type="ISSN">2452-0144</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32300673</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">2452-0144</ISSN><JournalIssue CitedMedium="Print"><PubDate><Year>2020</Year><Month>Apr</Month><Day>16</Day></PubDate></JournalIssue><Title>Gene reports</Title><ISOAbbreviation>Gene Rep</ISOAbbreviation></Journal><ArticleTitle>Genomic characterization of a novel SARS-CoV-2.</ArticleTitle><Pagination><MedlinePgn>100682</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.genrep.2020.100682</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>© 2020 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Khailany</LastName><ForeName>Rozhgar A</ForeName><Initials>RA</Initials><AffiliationInfo><Affiliation>Department of Biology, College of Science, University of Salahaddin-Erbil, Iraq.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Research Center, Salahaddin University-Erbil, Iraq.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Safdar</LastName><ForeName>Muhamad</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ozaslan</LastName><ForeName>Mehmet</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biology, Gaziantep University, 27310 Gaziantep, Turkey.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Gene Rep</MedlineTA><NlmUniqueID>101680713</NlmUniqueID><ISSNLinking>2452-0144</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">BLAST, Basic Local Alignment Search Tool</Keyword><Keyword MajorTopicYN="N">CDC, Centers of Disease Control and Prevention</Keyword><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">COVID-19, Coronavirus disease 2019</Keyword><Keyword MajorTopicYN="N">EMBOSS, The European Molecular Biology Open Software Suite</Keyword><Keyword MajorTopicYN="N">Genomic characterization</Keyword><Keyword MajorTopicYN="N">MERS, Middle East Respiratory Syndrome</Keyword><Keyword MajorTopicYN="N">Mutation</Keyword><Keyword MajorTopicYN="N">NCBI, National Center for Biotechnology Information</Keyword><Keyword MajorTopicYN="N">NGDC, National Genomics Data Center</Keyword><Keyword MajorTopicYN="N">NMDC, National Microbiology Data Center</Keyword><Keyword MajorTopicYN="N">NSP, nonstructural protein</Keyword><Keyword MajorTopicYN="N">ORF, Open Reading Frame</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2, severe acute respiratory syndrome coronavirus 2</Keyword><Keyword MajorTopicYN="N">UTR, Untranslated region</Keyword><Keyword MajorTopicYN="N">WHO, World Health Organization</Keyword></KeywordList><CoiStatement>The authors declare that they have no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>03</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>04</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>04</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>4</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32300673</ArticleId><ArticleId IdType="doi">10.1016/j.genrep.2020.100682</ArticleId><ArticleId IdType="pii">S2452-0144(20)30096-0</ArticleId><ArticleId IdType="pii">100682</ArticleId><ArticleId IdType="pmc">PMC7161481</ArticleId></ArticleIdList><pmc-dir>pmcsd</pmc-dir>
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