Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations
Identifieur interne : 000742 ( Main/Exploration ); précédent : 000741; suivant : 000743Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations
Auteurs : Meriem Laamarti [Maroc] ; Tarek Alouane [Maroc] ; Souad Kartti [Maroc] ; M. W. Chemao-Elfihri [Maroc] ; Mohammed Hakmi [Maroc] ; Abdelomunim Essabbar [Maroc] ; Mohamed Laamarti [Maroc] ; Haitam Hlali [Maroc] ; Houda Bendani [Maroc] ; Nassma Boumajdi [Maroc] ; Oussama Benhrif [Maroc] ; Loubna Allam [Maroc] ; Naima El Hafidi [Maroc] ; Rachid El Jaoudi [Maroc] ; Imane Allali [Maroc] ; Nabila Marchoudi [Maroc] ; Jamal Fekkak [Maroc] ; Houda Benrahma [Maroc] ; Chakib Nejjari [Maroc] ; Saaid Amzazi [Maroc] ; Lahcen Belyamani [Maroc] ; Azeddine Ibrahimi [Maroc]Source :
- PLoS ONE [ 1932-6203 ] ; 2020.
Descripteurs français
- KwdFr :
- Betacoronavirus (classification), Betacoronavirus (génétique), Betacoronavirus (isolement et purification), Chine (MeSH), Glycoprotéine de spicule des coronavirus (composition chimique), Glycoprotéine de spicule des coronavirus (génétique), Génome viral (MeSH), Humains (MeSH), Infections à coronavirus (anatomopathologie), Infections à coronavirus (virologie), Pandémies (MeSH), Phylogenèse (MeSH), Pneumopathie virale (anatomopathologie), Pneumopathie virale (virologie), Polyprotéines (MeSH), Protéines virales (composition chimique), Protéines virales (génétique), Structure tertiaire des protéines (MeSH), Variation génétique (MeSH), Évolution moléculaire (MeSH).
- MESH :
- anatomopathologie : Infections à coronavirus, Pneumopathie virale.
- composition chimique : Betacoronavirus, Glycoprotéine de spicule des coronavirus, Protéines virales.
- génétique : Betacoronavirus, Glycoprotéine de spicule des coronavirus, Protéines virales.
- isolement et purification : Betacoronavirus.
- virologie : Infections à coronavirus, Pneumopathie virale.
- Chine, Génome viral, Humains, Pandémies, Phylogenèse, Polyprotéines, Structure tertiaire des protéines, Variation génétique, Évolution moléculaire.
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- Betacoronavirus (classification), Betacoronavirus (genetics), Betacoronavirus (isolation & purification), COVID-19 (MeSH), China (MeSH), Coronavirus Infections (pathology), Coronavirus Infections (virology), Evolution, Molecular (MeSH), Genetic Variation (MeSH), Genome, Viral (MeSH), Humans (MeSH), Pandemics (MeSH), Phylogeny (MeSH), Pneumonia, Viral (pathology), Pneumonia, Viral (virology), Polyproteins (MeSH), Protein Structure, Tertiary (MeSH), SARS-CoV-2 (MeSH), Spike Glycoprotein, Coronavirus (chemistry), Spike Glycoprotein, Coronavirus (genetics), Viral Proteins (chemistry), Viral Proteins (genetics).
- MESH :
- chemical , chemistry : Spike Glycoprotein, Coronavirus, Viral Proteins.
- chemical , genetics : Spike Glycoprotein, Coronavirus, Viral Proteins.
- chemical : Polyproteins.
- geographic : China.
- classification : Betacoronavirus.
- genetics : Betacoronavirus.
- isolation & purification : Betacoronavirus.
- pathology : Coronavirus Infections, Pneumonia, Viral.
- virology : Coronavirus Infections, Pneumonia, Viral.
- COVID-19, Evolution, Molecular, Genetic Variation, Genome, Viral, Humans, Pandemics, Phylogeny, Protein Structure, Tertiary, SARS-CoV-2.
Abstract
In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (
Url:
DOI: 10.1371/journal.pone.0240345
PubMed: 33170902
PubMed Central: 7654798
Affiliations:
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Le document en format XML
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last="Bendani">Houda Bendani</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Boumajdi, Nassma" sort="Boumajdi, Nassma" uniqKey="Boumajdi N" first="Nassma" last="Boumajdi">Nassma Boumajdi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Benhrif, Oussama" sort="Benhrif, Oussama" uniqKey="Benhrif O" first="Oussama" last="Benhrif">Oussama Benhrif</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Allam, Loubna" sort="Allam, Loubna" uniqKey="Allam L" first="Loubna" last="Allam">Loubna Allam</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="El Hafidi, Naima" sort="El Hafidi, Naima" uniqKey="El Hafidi N" first="Naima" last="El Hafidi">Naima El Hafidi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="El Jaoudi, Rachid" sort="El Jaoudi, Rachid" uniqKey="El Jaoudi R" first="Rachid" last="El Jaoudi">Rachid El Jaoudi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Allali, Imane" sort="Allali, Imane" uniqKey="Allali I" first="Imane" last="Allali">Imane Allali</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Marchoudi, Nabila" sort="Marchoudi, Nabila" uniqKey="Marchoudi N" first="Nabila" last="Marchoudi">Nabila Marchoudi</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Anoual Laboratory of Radio-Immuno Analysis, Casablanca, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Anoual Laboratory of Radio-Immuno Analysis, Casablanca</wicri:regionArea></affiliation></author><author><name sortKey="Fekkak, Jamal" sort="Fekkak, Jamal" uniqKey="Fekkak J" first="Jamal" last="Fekkak">Jamal Fekkak</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Anoual Laboratory of Radio-Immuno Analysis, Casablanca, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Anoual Laboratory of Radio-Immuno Analysis, Casablanca</wicri:regionArea></affiliation></author><author><name sortKey="Benrahma, Houda" sort="Benrahma, Houda" uniqKey="Benrahma H" first="Houda" last="Benrahma">Houda Benrahma</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca</wicri:regionArea></affiliation></author><author><name sortKey="Nejjari, Chakib" sort="Nejjari, Chakib" uniqKey="Nejjari C" first="Chakib" last="Nejjari">Chakib Nejjari</name><affiliation wicri:level="1"><nlm:aff id="aff005"><addr-line>International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca</wicri:regionArea></affiliation></author><author><name sortKey="Amzazi, Saaid" sort="Amzazi, Saaid" uniqKey="Amzazi S" first="Saaid" last="Amzazi">Saaid Amzazi</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Belyamani, Lahcen" sort="Belyamani, Lahcen" uniqKey="Belyamani L" first="Lahcen" last="Belyamani">Lahcen Belyamani</name><affiliation wicri:level="1"><nlm:aff id="aff006"><addr-line>Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Ibrahimi, Azeddine" sort="Ibrahimi, Azeddine" uniqKey="Ibrahimi A" first="Azeddine" last="Ibrahimi">Azeddine Ibrahimi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">33170902</idno><idno type="pmc">7654798</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7654798</idno><idno type="RBID">PMC:7654798</idno><idno type="doi">10.1371/journal.pone.0240345</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000261</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000261</idno><idno type="wicri:Area/Pmc/Curation">000260</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000260</idno><idno type="wicri:Area/Pmc/Checkpoint">000050</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000050</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:33170902</idno><idno type="wicri:Area/PubMed/Corpus">000081</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000081</idno><idno type="wicri:Area/PubMed/Curation">000080</idno><idno 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xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Alouane, Tarek" sort="Alouane, Tarek" uniqKey="Alouane T" first="Tarek" last="Alouane">Tarek Alouane</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Kartti, Souad" sort="Kartti, Souad" uniqKey="Kartti S" first="Souad" last="Kartti">Souad Kartti</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Chemao Elfihri, M W" sort="Chemao Elfihri, M W" uniqKey="Chemao Elfihri M" first="M. W." last="Chemao-Elfihri">M. W. Chemao-Elfihri</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Hakmi, Mohammed" sort="Hakmi, Mohammed" uniqKey="Hakmi M" first="Mohammed" last="Hakmi">Mohammed Hakmi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Essabbar, Abdelomunim" sort="Essabbar, Abdelomunim" uniqKey="Essabbar A" first="Abdelomunim" last="Essabbar">Abdelomunim Essabbar</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Laamarti, Mohamed" sort="Laamarti, Mohamed" uniqKey="Laamarti M" first="Mohamed" last="Laamarti">Mohamed Laamarti</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Hlali, Haitam" sort="Hlali, Haitam" uniqKey="Hlali H" first="Haitam" last="Hlali">Haitam Hlali</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Bendani, Houda" sort="Bendani, Houda" uniqKey="Bendani H" first="Houda" last="Bendani">Houda Bendani</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Boumajdi, Nassma" sort="Boumajdi, Nassma" uniqKey="Boumajdi N" first="Nassma" last="Boumajdi">Nassma Boumajdi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Benhrif, Oussama" sort="Benhrif, Oussama" uniqKey="Benhrif O" first="Oussama" last="Benhrif">Oussama Benhrif</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Allam, Loubna" sort="Allam, Loubna" uniqKey="Allam L" first="Loubna" last="Allam">Loubna Allam</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="El Hafidi, Naima" sort="El Hafidi, Naima" uniqKey="El Hafidi N" first="Naima" last="El Hafidi">Naima El Hafidi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="El Jaoudi, Rachid" sort="El Jaoudi, Rachid" uniqKey="El Jaoudi R" first="Rachid" last="El Jaoudi">Rachid El Jaoudi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Allali, Imane" sort="Allali, Imane" uniqKey="Allali I" first="Imane" last="Allali">Imane Allali</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Marchoudi, Nabila" sort="Marchoudi, Nabila" uniqKey="Marchoudi N" first="Nabila" last="Marchoudi">Nabila Marchoudi</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Anoual Laboratory of Radio-Immuno Analysis, Casablanca, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Anoual Laboratory of Radio-Immuno Analysis, Casablanca</wicri:regionArea></affiliation></author><author><name sortKey="Fekkak, Jamal" sort="Fekkak, Jamal" uniqKey="Fekkak J" first="Jamal" last="Fekkak">Jamal Fekkak</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Anoual Laboratory of Radio-Immuno Analysis, Casablanca, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Anoual Laboratory of Radio-Immuno Analysis, Casablanca</wicri:regionArea></affiliation></author><author><name sortKey="Benrahma, Houda" sort="Benrahma, Houda" uniqKey="Benrahma H" first="Houda" last="Benrahma">Houda Benrahma</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca</wicri:regionArea></affiliation></author><author><name sortKey="Nejjari, Chakib" sort="Nejjari, Chakib" uniqKey="Nejjari C" first="Chakib" last="Nejjari">Chakib Nejjari</name><affiliation wicri:level="1"><nlm:aff id="aff005"><addr-line>International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca</wicri:regionArea></affiliation></author><author><name sortKey="Amzazi, Saaid" sort="Amzazi, Saaid" uniqKey="Amzazi S" first="Saaid" last="Amzazi">Saaid Amzazi</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Belyamani, Lahcen" sort="Belyamani, Lahcen" uniqKey="Belyamani L" first="Lahcen" last="Belyamani">Lahcen Belyamani</name><affiliation wicri:level="1"><nlm:aff id="aff006"><addr-line>Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author><author><name sortKey="Ibrahimi, Azeddine" sort="Ibrahimi, Azeddine" uniqKey="Ibrahimi A" first="Azeddine" last="Ibrahimi">Azeddine Ibrahimi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco</addr-line></nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Betacoronavirus (classification)</term><term>Betacoronavirus (genetics)</term><term>Betacoronavirus (isolation & purification)</term><term>COVID-19 (MeSH)</term><term>China (MeSH)</term><term>Coronavirus Infections (pathology)</term><term>Coronavirus Infections (virology)</term><term>Evolution, Molecular (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome, Viral (MeSH)</term><term>Humans (MeSH)</term><term>Pandemics (MeSH)</term><term>Phylogeny (MeSH)</term><term>Pneumonia, Viral (pathology)</term><term>Pneumonia, Viral (virology)</term><term>Polyproteins (MeSH)</term><term>Protein Structure, Tertiary (MeSH)</term><term>SARS-CoV-2 (MeSH)</term><term>Spike Glycoprotein, Coronavirus (chemistry)</term><term>Spike Glycoprotein, Coronavirus (genetics)</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Betacoronavirus (classification)</term><term>Betacoronavirus (génétique)</term><term>Betacoronavirus (isolement et purification)</term><term>Chine (MeSH)</term><term>Glycoprotéine de spicule des coronavirus (composition chimique)</term><term>Glycoprotéine de spicule des coronavirus (génétique)</term><term>Génome viral (MeSH)</term><term>Humains (MeSH)</term><term>Infections à coronavirus (anatomopathologie)</term><term>Infections à coronavirus (virologie)</term><term>Pandémies (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Pneumopathie virale (anatomopathologie)</term><term>Pneumopathie virale (virologie)</term><term>Polyprotéines (MeSH)</term><term>Protéines virales (composition chimique)</term><term>Protéines virales (génétique)</term><term>Structure tertiaire des protéines (MeSH)</term><term>Variation génétique (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Spike Glycoprotein, Coronavirus</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Spike Glycoprotein, Coronavirus</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Polyproteins</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term></keywords><keywords scheme="MESH" qualifier="anatomopathologie" xml:lang="fr"><term>Infections à coronavirus</term><term>Pneumopathie virale</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Betacoronavirus</term><term>Glycoprotéine de spicule des coronavirus</term><term>Protéines virales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Betacoronavirus</term><term>Glycoprotéine de spicule des coronavirus</term><term>Protéines virales</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="pathology" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term><term>Pneumopathie virale</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" xml:lang="en"><term>COVID-19</term><term>Evolution, Molecular</term><term>Genetic Variation</term><term>Genome, Viral</term><term>Humans</term><term>Pandemics</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term><term>SARS-CoV-2</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Chine</term><term>Génome viral</term><term>Humains</term><term>Pandémies</term><term>Phylogenèse</term><term>Polyprotéines</term><term>Structure tertiaire des protéines</term><term>Variation génétique</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (<ext-link ext-link-type="uri" xlink:href="http://covid-19.medbiotech.ma">http://covid-19.medbiotech.ma</ext-link>) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Enjuanes, Ld" uniqKey="Enjuanes L">LD Enjuanes</name></author><author><name sortKey="Cavanagh, K" uniqKey="Cavanagh K">K Cavanagh</name></author><author><name sortKey="Holmes, Mmc" uniqKey="Holmes M">MMC Holmes</name></author><author><name sortKey="Lai, H" uniqKey="Lai H">H Lai</name></author><author><name sortKey="Laude, P" uniqKey="Laude P">P Laude</name></author><author><name sortKey="Masters, P" uniqKey="Masters P">P Masters</name></author><author><name sortKey="Van Regenmortel, M H V" uniqKey="Van Regenmortel M">M. H. 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uniqKey="Laamarti M" first="Meriem" last="Laamarti">Meriem Laamarti</name></noRegion><name sortKey="Allali, Imane" sort="Allali, Imane" uniqKey="Allali I" first="Imane" last="Allali">Imane Allali</name><name sortKey="Allam, Loubna" sort="Allam, Loubna" uniqKey="Allam L" first="Loubna" last="Allam">Loubna Allam</name><name sortKey="Alouane, Tarek" sort="Alouane, Tarek" uniqKey="Alouane T" first="Tarek" last="Alouane">Tarek Alouane</name><name sortKey="Amzazi, Saaid" sort="Amzazi, Saaid" uniqKey="Amzazi S" first="Saaid" last="Amzazi">Saaid Amzazi</name><name sortKey="Belyamani, Lahcen" sort="Belyamani, Lahcen" uniqKey="Belyamani L" first="Lahcen" last="Belyamani">Lahcen Belyamani</name><name sortKey="Bendani, Houda" sort="Bendani, Houda" uniqKey="Bendani H" first="Houda" last="Bendani">Houda Bendani</name><name sortKey="Benhrif, Oussama" sort="Benhrif, Oussama" uniqKey="Benhrif O" first="Oussama" last="Benhrif">Oussama Benhrif</name><name sortKey="Benrahma, Houda" sort="Benrahma, Houda" uniqKey="Benrahma H" first="Houda" last="Benrahma">Houda Benrahma</name><name sortKey="Boumajdi, Nassma" sort="Boumajdi, Nassma" uniqKey="Boumajdi N" first="Nassma" last="Boumajdi">Nassma Boumajdi</name><name sortKey="Chemao Elfihri, M W" sort="Chemao Elfihri, M W" uniqKey="Chemao Elfihri M" first="M. W." last="Chemao-Elfihri">M. W. Chemao-Elfihri</name><name sortKey="El Hafidi, Naima" sort="El Hafidi, Naima" uniqKey="El Hafidi N" first="Naima" last="El Hafidi">Naima El Hafidi</name><name sortKey="El Jaoudi, Rachid" sort="El Jaoudi, Rachid" uniqKey="El Jaoudi R" first="Rachid" last="El Jaoudi">Rachid El Jaoudi</name><name sortKey="Essabbar, Abdelomunim" sort="Essabbar, Abdelomunim" uniqKey="Essabbar A" first="Abdelomunim" last="Essabbar">Abdelomunim Essabbar</name><name sortKey="Fekkak, Jamal" sort="Fekkak, Jamal" uniqKey="Fekkak J" first="Jamal" last="Fekkak">Jamal Fekkak</name><name sortKey="Hakmi, Mohammed" sort="Hakmi, Mohammed" uniqKey="Hakmi M" first="Mohammed" last="Hakmi">Mohammed Hakmi</name><name sortKey="Hlali, Haitam" sort="Hlali, Haitam" uniqKey="Hlali H" first="Haitam" last="Hlali">Haitam Hlali</name><name sortKey="Ibrahimi, Azeddine" sort="Ibrahimi, Azeddine" uniqKey="Ibrahimi A" first="Azeddine" last="Ibrahimi">Azeddine Ibrahimi</name><name sortKey="Kartti, Souad" sort="Kartti, Souad" uniqKey="Kartti S" first="Souad" last="Kartti">Souad Kartti</name><name sortKey="Laamarti, Mohamed" sort="Laamarti, Mohamed" uniqKey="Laamarti M" first="Mohamed" last="Laamarti">Mohamed Laamarti</name><name sortKey="Marchoudi, Nabila" sort="Marchoudi, Nabila" uniqKey="Marchoudi N" first="Nabila" last="Marchoudi">Nabila Marchoudi</name><name sortKey="Nejjari, Chakib" sort="Nejjari, Chakib" uniqKey="Nejjari C" first="Chakib" last="Nejjari">Chakib Nejjari</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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