Genomic insights into early SARS-CoV-2 strains isolated in Reunion Island
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Abstract
The relative isolation of many island communities provides some protection from the COVID-19 pandemic, as imported cases can be limited and traced effectively. Until recently, this was true for the population of the French overseas department, Reunion Island, where only limited numbers of autochthonous cases were observed prior to August 2020. Since the report of the first case of COVID-19, contact tracing has been carried out for each new case identified in Reunion Island to identify transmission and clusters. To contribute to the public health response and understand the diffusion of SARS-Cov-2 strains in Reunion Island, we established in-house genome sequencing capability in Reunion using Oxford nanopore technology (MinION) as an inexpensive option for genomic typing of SARS-CoV-2 lineages on the island, and cross-validated typing results between viral isolation methods and different sequencing technologies. The results of our work during the early phase of the epidemics are presented herein.
Article Summary Line
The COVID-19 pandemic has had an unprecedented impact on the global community. Here we provide epidemiological and genomic details of the early stages of the pandemic on Reunion Island.
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SciScore for 10.1101/2021.01.21.21249623: (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. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Viral isolation and production: SARS-CoV-2 strains were isolated in the African green monkey kidney cell line, Vero E6. Vero E6suggested: RRID:CVCL_XD71)When cell density reached approximately 80%, cells were rinsed once with MEM medium supplemented with 2% FBS, then 50 to 100 µl of SARS-CoV-2-positive swab specimen was mixed with 2 mL MEM 2% FBS and layered on the Vero cell monolayer. Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVC…SciScore for 10.1101/2021.01.21.21249623: (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. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Viral isolation and production: SARS-CoV-2 strains were isolated in the African green monkey kidney cell line, Vero E6. Vero E6suggested: RRID:CVCL_XD71)When cell density reached approximately 80%, cells were rinsed once with MEM medium supplemented with 2% FBS, then 50 to 100 µl of SARS-CoV-2-positive swab specimen was mixed with 2 mL MEM 2% FBS and layered on the Vero cell monolayer. Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)Software and Algorithms Sentences Resources Briefly, cells were cultured in a 25 cm2 flask containing 5 ml of Eagle medium (MEM: Gibco/Invitrogen, Carlsbad, CA, USA) supplemented with 5% heat-inactivated fetal bovine serum (FBS), 2 mmol/L L-Glutamine, 1 mmol/L sodium pyruvate, 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.5 µg/mL of Amphotericin B (PAN Biotech, Aidenbach, Germany), at 37°C under a 5% CO2 atmosphere. Gibco/Invitrogensuggested: NoneNanopore (MinION) Sequencing and Analysis: Genomes were sequenced from viruses originally infecting four independent patients. MinIONsuggested: (MinION, RRID:SCR_017985)Geneious v9.1.8[13] was used to inspect and curate mapped sequence data. Geneioussuggested: (Geneious, RRID:SCR_010519)Sequencing was performed on the MiSeq platform, with 1 * 170 bp single end reads. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Sequences were quality trimmed and adapters removed using Trimmomatic v0.39. Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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 scite Reference Check: We found no unreliable references.
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