Population dynamics and structural effects at short and long range support the hypothesis of the selective advantage of the G614 SARS-Cov2 spike variant.
Identifieur interne : 000014 ( Main/Exploration ); précédent : 000013; suivant : 000015Population dynamics and structural effects at short and long range support the hypothesis of the selective advantage of the G614 SARS-Cov2 spike variant.
Auteurs : Emiliano Trucchi [Italie] ; Paolo Gratton [Italie] ; Fabrizio Mafessoni [Israël] ; Stefano Motta [Italie] ; Francesco Cicconardi [Royaume-Uni] ; Filippo Mancia [États-Unis] ; Giorgio Bertorelle [Italie] ; Ilda D'Annessa [Italie] ; Daniele Di Marino [Italie]Source :
- Molecular biology and evolution [ 1537-1719 ] ; 2021.
Abstract
SARS-CoV-2 epidemics quickly propagated worldwide, sorting virus genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries or an actual selective advantage could explain the global high frequency reached by some genomic variants. Using statistical analyses, demographic reconstructions, and molecular dynamics simulations, we show that the globally invasive G614 spike variant i) underwent a significant demographic expansion in most countries not explained by stochastic effects nor by overrepresentation in clinical samples; ii) increases the spike S1/S2 furin-like site conformational plasticity (short-range effect), and iii) modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect). Our results support the hypothesis of a selective advantage at the basis of the spread of the G614 variant, which we suggest may be due to structural modification of the spike protein at the S1/S2 proteolytic site, and provides structural information to guide the design of variant-specific drugs.
DOI: 10.1093/molbev/msaa337
PubMed: 33386849
Affiliations:
- Israël, Italie, Royaume-Uni, États-Unis
- Latium, Lombardie, État de New York
- Milan, New York, Rome
- Université Columbia
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Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Chemical Science and Technologies, SCITEC-CNR, Via Mario Bianco 9, Milan</wicri:regionArea><placeName><settlement type="city">Milan</settlement><region nuts="2">Lombardie</region></placeName></affiliation></author><author><name sortKey="Marino, Daniele Di" sort="Marino, Daniele Di" uniqKey="Marino D" first="Daniele Di" last="Marino">Daniele Di Marino</name><affiliation wicri:level="1"><nlm:affiliation>Department of Life and Environmental Science, Marche Polytechnic University, Via Brecce Bianche, Ancona, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Life and Environmental Science, Marche Polytechnic University, Via Brecce Bianche, Ancona</wicri:regionArea><wicri:noRegion>Ancona</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>New York-Marche Structural Biology Center (NY-MaSBiC), Marche Polytechnic University, Via Brecce Bianche, Ancona, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>New York-Marche Structural Biology Center (NY-MaSBiC), Marche Polytechnic University, Via Brecce Bianche, Ancona</wicri:regionArea><wicri:noRegion>Ancona</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular biology and evolution</title><idno type="eISSN">1537-1719</idno><imprint><date when="2021" type="published">2021</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">SARS-CoV-2 epidemics quickly propagated worldwide, sorting virus genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries or an actual selective advantage could explain the global high frequency reached by some genomic variants. Using statistical analyses, demographic reconstructions, and molecular dynamics simulations, we show that the globally invasive G614 spike variant i) underwent a significant demographic expansion in most countries not explained by stochastic effects nor by overrepresentation in clinical samples; ii) increases the spike S1/S2 furin-like site conformational plasticity (short-range effect), and iii) modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect). Our results support the hypothesis of a selective advantage at the basis of the spread of the G614 variant, which we suggest may be due to structural modification of the spike protein at the S1/S2 proteolytic site, and provides structural information to guide the design of variant-specific drugs.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33386849</PMID><DateRevised><Year>2021</Year><Month>01</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2021</Year><Month>Jan</Month><Day>02</Day></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Population dynamics and structural effects at short and long range support the hypothesis of the selective advantage of the G614 SARS-Cov2 spike variant.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">msaa337</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1093/molbev/msaa337</ELocationID><Abstract><AbstractText>SARS-CoV-2 epidemics quickly propagated worldwide, sorting virus genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries or an actual selective advantage could explain the global high frequency reached by some genomic variants. Using statistical analyses, demographic reconstructions, and molecular dynamics simulations, we show that the globally invasive G614 spike variant i) underwent a significant demographic expansion in most countries not explained by stochastic effects nor by overrepresentation in clinical samples; ii) increases the spike S1/S2 furin-like site conformational plasticity (short-range effect), and iii) modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect). Our results support the hypothesis of a selective advantage at the basis of the spread of the G614 variant, which we suggest may be due to structural modification of the spike protein at the S1/S2 proteolytic site, and provides structural information to guide the design of variant-specific drugs.</AbstractText><CopyrightInformation>© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Trucchi</LastName><ForeName>Emiliano</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Department of Life and Environmental Science, Marche Polytechnic University, Via Brecce Bianche, Ancona, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gratton</LastName><ForeName>Paolo</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Rome "Tor Vergata", Via Cracovia, 1, 00133, Roma, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mafessoni</LastName><ForeName>Fabrizio</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Motta</LastName><ForeName>Stefano</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, Milan, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cicconardi</LastName><ForeName>Francesco</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mancia</LastName><ForeName>Filippo</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bertorelle</LastName><ForeName>Giorgio</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Department of Life Sciences and Biotechnology, University of Ferrara, Via Luigi Borsari 46, Ferrara, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>D'Annessa</LastName><ForeName>Ilda</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Institute of Chemical Science and Technologies, SCITEC-CNR, Via Mario Bianco 9, Milan, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Marino</LastName><ForeName>Daniele Di</ForeName><Initials>DD</Initials><AffiliationInfo><Affiliation>Department of Life and Environmental Science, Marche Polytechnic University, Via Brecce Bianche, Ancona, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>New York-Marche Structural Biology Center (NY-MaSBiC), Marche Polytechnic University, Via Brecce Bianche, Ancona, Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2021</Year><Month>01</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">SARS-Cov-2 evolution</Keyword><Keyword MajorTopicYN="N">coalescent-based inference</Keyword><Keyword MajorTopicYN="N">generalized linear mixed models</Keyword><Keyword MajorTopicYN="N">molecular dynamics</Keyword><Keyword MajorTopicYN="N">population dynamics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>07</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>11</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>12</Month><Day>17</Day></PubMedPubDate><PubMedPubDate 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