A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions.
Identifieur interne : 000321 ( Main/Exploration ); précédent : 000320; suivant : 000322A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions.
Auteurs : May S. Soliman [Égypte] ; May Abdelfattah [Égypte] ; Soad M N. Aman [Égypte] ; Lamyaa M. Ibrahim [Égypte] ; Ramy K. Aziz [Égypte]Source :
- Omics : a journal of integrative biology [ 1557-8100 ] ; 2020.
Abstract
The novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is causing an unprecedented pandemic, threatening planetary health, society, and economy. Genomic surveillance continues to be a critical effort toward tracking the virus and containing its spread, and more genomes from diverse geographical areas and different time points are needed to provide an appropriate representation of the virus evolution. In this study, we report the successful assembly of one single gapless, unambiguous contiguous sequence representing the complete viral genome from a nasopharyngeal swab of an infected health care worker in Cairo, Egypt. The sequence has all typical features of SARS-CoV-2 genomes, with no protein-disrupting mutations. However, three mutations are worth highlighting and future tracking: a synonymous mutation causing a rare spike S813I variation and two less frequent ones leading to an A41V variation in NSP3, encoded by ORF1a (ORF1a A895V), and a Q677H variation in the spike protein. Both affected proteins, S and NSP3, are relevant to vaccine and drug development. Although the genome, named CU_S3, belongs to the prevalent global genotype, marked by the D614G spike variation, the combined variations in the spike proteins and ORF1a do not co-occur in any of the 197,000 genomes reported to date. Future studies will assess the biological, pathogenic, and epidemiological implications of this set of genetic variations. This line of research is needed to inform vaccine and therapeutic innovation to stem the COVID-19 pandemic.
DOI: 10.1089/omi.2020.0194
PubMed: 33253058
Affiliations:
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Although the genome, named CU_S3, belongs to the prevalent global genotype, marked by the D614G spike variation, the combined variations in the spike proteins and ORF1a do not co-occur in any of the 197,000 genomes reported to date. Future studies will assess the biological, pathogenic, and epidemiological implications of this set of genetic variations. 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Genomic surveillance continues to be a critical effort toward tracking the virus and containing its spread, and more genomes from diverse geographical areas and different time points are needed to provide an appropriate representation of the virus evolution. In this study, we report the successful assembly of one single gapless, unambiguous contiguous sequence representing the complete viral genome from a nasopharyngeal swab of an infected health care worker in Cairo, Egypt. The sequence has all typical features of SARS-CoV-2 genomes, with no protein-disrupting mutations. However, three mutations are worth highlighting and future tracking: a synonymous mutation causing a rare spike S813I variation and two less frequent ones leading to an A41V variation in NSP3, encoded by ORF1a (ORF1a A895V), and a Q677H variation in the spike protein. Both affected proteins, S and NSP3, are relevant to vaccine and drug development. Although the genome, named CU_S3, belongs to the prevalent global genotype, marked by the D614G spike variation, the combined variations in the spike proteins and ORF1a do not co-occur in any of the 197,000 genomes reported to date. Future studies will assess the biological, pathogenic, and epidemiological implications of this set of genetic variations. This line of research is needed to inform vaccine and therapeutic innovation to stem the COVID-19 pandemic.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Soliman</LastName><ForeName>May S</ForeName><Initials>MS</Initials><AffiliationInfo><Affiliation>Clinical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>AbdelFattah</LastName><ForeName>May</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Clinical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Cairo University Pediatric Hospital, Cairo, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Aman</LastName><ForeName>Soad M N</ForeName><Initials>SMN</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ibrahim</LastName><ForeName>Lamyaa M</ForeName><Initials>LM</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Aziz</LastName><ForeName>Ramy K</ForeName><Initials>RK</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>11</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>OMICS</MedlineTA><NlmUniqueID>101131135</NlmUniqueID><ISSNLinking>1536-2310</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">genomic epidemiology</Keyword><Keyword MajorTopicYN="N">high-throughput sequencing</Keyword><Keyword MajorTopicYN="N">pandemic</Keyword><Keyword MajorTopicYN="N">replicase</Keyword><Keyword MajorTopicYN="N">spike protein</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>11</Month><Day>30</Day><Hour>17</Hour><Minute>11</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>12</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>12</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33253058</ArticleId><ArticleId IdType="doi">10.1089/omi.2020.0194</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Égypte</li></country></list><tree><country name="Égypte"><noRegion><name sortKey="Soliman, May S" sort="Soliman, May S" uniqKey="Soliman M" first="May S" last="Soliman">May S. Soliman</name></noRegion><name sortKey="Abdelfattah, May" sort="Abdelfattah, May" uniqKey="Abdelfattah M" first="May" last="Abdelfattah">May Abdelfattah</name><name sortKey="Abdelfattah, May" sort="Abdelfattah, May" uniqKey="Abdelfattah M" first="May" last="Abdelfattah">May Abdelfattah</name><name sortKey="Aman, Soad M N" sort="Aman, Soad M N" uniqKey="Aman S" first="Soad M N" last="Aman">Soad M N. Aman</name><name sortKey="Aziz, Ramy K" sort="Aziz, Ramy K" uniqKey="Aziz R" first="Ramy K" last="Aziz">Ramy K. Aziz</name><name sortKey="Aziz, Ramy K" sort="Aziz, Ramy K" uniqKey="Aziz R" first="Ramy K" last="Aziz">Ramy K. Aziz</name><name sortKey="Ibrahim, Lamyaa M" sort="Ibrahim, Lamyaa M" uniqKey="Ibrahim L" first="Lamyaa M" last="Ibrahim">Lamyaa M. Ibrahim</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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