Genomic surveillance revealed prevalence of unique SARS-CoV-2 variants bearing mutation in the RdRp gene among Nevada patients.
Identifieur interne : 000196 ( Main/Exploration ); précédent : 000195; suivant : 000197Genomic surveillance revealed prevalence of unique SARS-CoV-2 variants bearing mutation in the RdRp gene among Nevada patients.
Auteurs : Paul Hartley ; Richard L. Tillett ; Yanji Xu ; David P. Aucoin ; Joel R. Sevinsky ; Andrew Gorzalski ; Mark C. Pandori ; Erin Buttery ; Holly Hansen ; Michael Picker ; Cyprian C. Rossetto ; Subhash C. VermaSource :
- medRxiv : the preprint server for health sciences ; 2020.
Abstract
BACKGROUND
SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19), which has a wide range of disease manifestations, including relatively mild respiratory illness to severe disease requiring hospitalization. Patients with signs of COVID-19 (fever, coughing, shortness of breath) were tested for the virus by targeting specific SARS-COV-2 genomic loci via RT-PCR using RNA extracted from nasopharyngeal/nasal swabs. However, this testing does not yield genetic information required for identifying viral evolution or variants.
METHODS
We sequenced 200 specimens from positively identified cases in Nevada through our robust protocol for sequencing SARS-CoV-2 genomes directly from patients nasopharyngeal/nasal swabs. This protocol enabled identification of specific nucleotide variants including those for D614G and clade defining mutations. Additionally, these sequences were used to determine the phylogenetic relationships of SARS-CoV-2 genomes of public health importance occurring in the state of Nevada.
RESULTS
Our study reports the finding of a novel variant in the nsp12 (RdRp-RNA dependent RNA Polymerase) protein at residue 323 (314aa of orf1b) to Phenylalanine (F) from Proline (P), present in the original isolate of SARS-CoV-2 (Wuhan-1). This 323F variant is found at a very high frequency in Northern Nevada suggesting for a founder effect. Structural modeling of the RdRP with P323F mutation did not show any significant difference in protein conformation but the phenotypic effect is unknown and an area of active investigation.
DOI: 10.1101/2020.08.21.20178863
PubMed: 32869037
PubMed Central: PMC7457609
Affiliations:
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Sevinsky</name></author><author><name sortKey="Gorzalski, Andrew" sort="Gorzalski, Andrew" uniqKey="Gorzalski A" first="Andrew" last="Gorzalski">Andrew Gorzalski</name></author><author><name sortKey="Pandori, Mark C" sort="Pandori, Mark C" uniqKey="Pandori M" first="Mark C" last="Pandori">Mark C. Pandori</name></author><author><name sortKey="Buttery, Erin" sort="Buttery, Erin" uniqKey="Buttery E" first="Erin" last="Buttery">Erin Buttery</name></author><author><name sortKey="Hansen, Holly" sort="Hansen, Holly" uniqKey="Hansen H" first="Holly" last="Hansen">Holly Hansen</name></author><author><name sortKey="Picker, Michael" sort="Picker, Michael" uniqKey="Picker M" first="Michael" last="Picker">Michael Picker</name></author><author><name sortKey="Rossetto, Cyprian C" sort="Rossetto, Cyprian C" uniqKey="Rossetto C" first="Cyprian C" last="Rossetto">Cyprian C. Rossetto</name></author><author><name sortKey="Verma, Subhash C" sort="Verma, Subhash C" uniqKey="Verma S" first="Subhash C" last="Verma">Subhash C. Verma</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32869037</idno><idno type="pmid">32869037</idno><idno type="doi">10.1101/2020.08.21.20178863</idno><idno type="pmc">PMC7457609</idno><idno type="wicri:Area/Main/Corpus">000203</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000203</idno><idno type="wicri:Area/Main/Curation">000203</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000203</idno><idno type="wicri:Area/Main/Exploration">000203</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genomic surveillance revealed prevalence of unique SARS-CoV-2 variants bearing mutation in the RdRp gene among Nevada patients.</title><author><name sortKey="Hartley, Paul" sort="Hartley, Paul" uniqKey="Hartley P" first="Paul" last="Hartley">Paul Hartley</name></author><author><name sortKey="Tillett, Richard L" sort="Tillett, Richard L" uniqKey="Tillett R" first="Richard L" last="Tillett">Richard L. Tillett</name></author><author><name sortKey="Xu, Yanji" sort="Xu, Yanji" uniqKey="Xu Y" first="Yanji" last="Xu">Yanji Xu</name></author><author><name sortKey="Aucoin, David P" sort="Aucoin, David P" uniqKey="Aucoin D" first="David P" last="Aucoin">David P. Aucoin</name></author><author><name sortKey="Sevinsky, Joel R" sort="Sevinsky, Joel R" uniqKey="Sevinsky J" first="Joel R" last="Sevinsky">Joel R. Sevinsky</name></author><author><name sortKey="Gorzalski, Andrew" sort="Gorzalski, Andrew" uniqKey="Gorzalski A" first="Andrew" last="Gorzalski">Andrew Gorzalski</name></author><author><name sortKey="Pandori, Mark C" sort="Pandori, Mark C" uniqKey="Pandori M" first="Mark C" last="Pandori">Mark C. Pandori</name></author><author><name sortKey="Buttery, Erin" sort="Buttery, Erin" uniqKey="Buttery E" first="Erin" last="Buttery">Erin Buttery</name></author><author><name sortKey="Hansen, Holly" sort="Hansen, Holly" uniqKey="Hansen H" first="Holly" last="Hansen">Holly Hansen</name></author><author><name sortKey="Picker, Michael" sort="Picker, Michael" uniqKey="Picker M" first="Michael" last="Picker">Michael Picker</name></author><author><name sortKey="Rossetto, Cyprian C" sort="Rossetto, Cyprian C" uniqKey="Rossetto C" first="Cyprian C" last="Rossetto">Cyprian C. Rossetto</name></author><author><name sortKey="Verma, Subhash C" sort="Verma, Subhash C" uniqKey="Verma S" first="Subhash C" last="Verma">Subhash C. Verma</name></author></analytic><series><title level="j">medRxiv : the preprint server for health sciences</title><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"><p><b>BACKGROUND</b></p><p>SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19), which has a wide range of disease manifestations, including relatively mild respiratory illness to severe disease requiring hospitalization. Patients with signs of COVID-19 (fever, coughing, shortness of breath) were tested for the virus by targeting specific SARS-COV-2 genomic loci via RT-PCR using RNA extracted from nasopharyngeal/nasal swabs. However, this testing does not yield genetic information required for identifying viral evolution or variants.</p></div><div type="abstract" xml:lang="en"><p><b>METHODS</b></p><p>We sequenced 200 specimens from positively identified cases in Nevada through our robust protocol for sequencing SARS-CoV-2 genomes directly from patients nasopharyngeal/nasal swabs. This protocol enabled identification of specific nucleotide variants including those for D614G and clade defining mutations. Additionally, these sequences were used to determine the phylogenetic relationships of SARS-CoV-2 genomes of public health importance occurring in the state of Nevada.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Our study reports the finding of a novel variant in the nsp12 (RdRp-RNA dependent RNA Polymerase) protein at residue 323 (314aa of orf1b) to Phenylalanine (F) from Proline (P), present in the original isolate of SARS-CoV-2 (Wuhan-1). This 323F variant is found at a very high frequency in Northern Nevada suggesting for a founder effect. Structural modeling of the RdRP with P323F mutation did not show any significant difference in protein conformation but the phenotypic effect is unknown and an area of active investigation.</p></div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32869037</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Aug</Month><Day>26</Day></PubDate></JournalIssue><Title>medRxiv : the preprint server for health sciences</Title><ISOAbbreviation>medRxiv</ISOAbbreviation></Journal><ArticleTitle>Genomic surveillance revealed prevalence of unique SARS-CoV-2 variants bearing mutation in the RdRp gene among Nevada patients.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">2020.08.21.20178863</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1101/2020.08.21.20178863</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19), which has a wide range of disease manifestations, including relatively mild respiratory illness to severe disease requiring hospitalization. Patients with signs of COVID-19 (fever, coughing, shortness of breath) were tested for the virus by targeting specific SARS-COV-2 genomic loci via RT-PCR using RNA extracted from nasopharyngeal/nasal swabs. However, this testing does not yield genetic information required for identifying viral evolution or variants.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">We sequenced 200 specimens from positively identified cases in Nevada through our robust protocol for sequencing SARS-CoV-2 genomes directly from patients nasopharyngeal/nasal swabs. This protocol enabled identification of specific nucleotide variants including those for D614G and clade defining mutations. Additionally, these sequences were used to determine the phylogenetic relationships of SARS-CoV-2 genomes of public health importance occurring in the state of Nevada.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Our study reports the finding of a novel variant in the nsp12 (RdRp-RNA dependent RNA Polymerase) protein at residue 323 (314aa of orf1b) to Phenylalanine (F) from Proline (P), present in the original isolate of SARS-CoV-2 (Wuhan-1). This 323F variant is found at a very high frequency in Northern Nevada suggesting for a founder effect. Structural modeling of the RdRP with P323F mutation did not show any significant difference in protein conformation but the phenotypic effect is unknown and an area of active investigation.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hartley</LastName><ForeName>Paul</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Tillett</LastName><ForeName>Richard L</ForeName><Initials>RL</Initials></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Yanji</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>AuCoin</LastName><ForeName>David P</ForeName><Initials>DP</Initials></Author><Author ValidYN="Y"><LastName>Sevinsky</LastName><ForeName>Joel R</ForeName><Initials>JR</Initials></Author><Author ValidYN="Y"><LastName>Gorzalski</LastName><ForeName>Andrew</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Pandori</LastName><ForeName>Mark C</ForeName><Initials>MC</Initials></Author><Author ValidYN="Y"><LastName>Buttery</LastName><ForeName>Erin</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Hansen</LastName><ForeName>Holly</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Picker</LastName><ForeName>Michael</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Rossetto</LastName><ForeName>Cyprian C</ForeName><Initials>CC</Initials></Author><Author ValidYN="Y"><LastName>Verma</LastName><ForeName>Subhash C</ForeName><Initials>SC</Initials><Identifier Source="ORCID">0000-0002-0492-6578</Identifier></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>P20 GM103440</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U54 GM104944</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType 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Rossetto</name><name sortKey="Sevinsky, Joel R" sort="Sevinsky, Joel R" uniqKey="Sevinsky J" first="Joel R" last="Sevinsky">Joel R. Sevinsky</name><name sortKey="Tillett, Richard L" sort="Tillett, Richard L" uniqKey="Tillett R" first="Richard L" last="Tillett">Richard L. Tillett</name><name sortKey="Verma, Subhash C" sort="Verma, Subhash C" uniqKey="Verma S" first="Subhash C" last="Verma">Subhash C. Verma</name><name sortKey="Xu, Yanji" sort="Xu, Yanji" uniqKey="Xu Y" first="Yanji" last="Xu">Yanji Xu</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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