Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients
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Abstract
The novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5’/3’ UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (Δ21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.
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SciScore for 10.1101/2020.09.04.282616: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources DNA Polymerase I Large Klenow Fragment (BioLabs) was used for generating double stranded cDNA. BioLabssuggested: (Tulip Biolabs, RRID:SCR_013654)Normalized libraries were pooled into a single library for sequencing on MiSeq. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)All genomes were deposited at EMBL-EBI under the BioProject: PRJEB37722 All genomes were deposited at EMBL-EBI under the BioProject: PRJEB37722 BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Results from OddPub:…
SciScore for 10.1101/2020.09.04.282616: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources DNA Polymerase I Large Klenow Fragment (BioLabs) was used for generating double stranded cDNA. BioLabssuggested: (Tulip Biolabs, RRID:SCR_013654)Normalized libraries were pooled into a single library for sequencing on MiSeq. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)All genomes were deposited at EMBL-EBI under the BioProject: PRJEB37722 All genomes were deposited at EMBL-EBI under the BioProject: PRJEB37722 BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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SciScore for 10.1101/2020.09.04.282616: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement L AND CONSENT TO PARTICIPATE 266 The study was approved by the Ethical Committee of the University Hospital Institute Méditerranée 267 Infection (N°: 2020-016). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources DNA Polymerase I 230 Large Klenow Fragment (BioLabs) was used for generating double stranded cDNA. BioLabssuggested: (Tulip Biolabs, RRID:SCR_013654)Normalized libraries 239 were pooled into a single library for … SciScore for 10.1101/2020.09.04.282616: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement L AND CONSENT TO PARTICIPATE 266 The study was approved by the Ethical Committee of the University Hospital Institute Méditerranée 267 Infection (N°: 2020-016). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources DNA Polymerase I 230 Large Klenow Fragment (BioLabs) was used for generating double stranded cDNA. BioLabssuggested: (Tulip Biolabs, RRID:SCR_013654)Normalized libraries 239 were pooled into a single library for sequencing on MiSeq. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)All genomes were deposited at EMBL- 253 EBI under the BioProject: PRJEB37722 254 ABBREVIATIONS 255 BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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