Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences
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Abstract
The SARS-CoV-2 disease, first detected in Wuhan, China, in December 2019 has become a global pandemic and is causing an unprecedented burden on health care systems and the economy globally. While the travel history of index cases may suggest the origin of infection, phylogenetic analysis of isolated strains from these cases and contacts will increase the understanding and link between local transmission and other global populations. The objective of this analysis was to provide genomic data on the first six cases of SARS-CoV-2 in The Gambia and to determine the source of infection. This ultimately provide baseline data for subsequent local transmission and contribute genomic diversity information towards local and global data. Our analysis has shown that the SARS-CoV-2 virus identified in The Gambia are of European and Asian origin and sequenced data matched patients’ travel history. In addition, we were able to show that two COVID-19 positive cases travelling in the same flight had different strains of SARS-CoV-2. Although whole genome sequencing (WGS) data is still limited in sub-Saharan Africa, this approach has proven to be a highly sensitive, specific and confirmatory tool for SARS-CoV-2 detection.
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SciScore for 10.1101/2020.10.26.354969: (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 Of the 6 cases sequenced, 4 were male; 2 females, there was one death, two recoveries and two active cases. Table 2: Resources
Software and Algorithms Sentences Resources Of the 451 samples screened by rRT-PCR, ten were confirmed as SARS-CoV-2 cases and 5 as indeterminate cases (positive for the screening gene and negative for the SARS-CoV-2 confirmatory gene) For WGS, four SARS-CoV-2 confirmed cases, one indeterminate case and one negative case were processed Table 1. WGSsuggested: NoneThe pool was run at a final concentration of 10 pM on an Illumina … SciScore for 10.1101/2020.10.26.354969: (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 Of the 6 cases sequenced, 4 were male; 2 females, there was one death, two recoveries and two active cases. Table 2: Resources
Software and Algorithms Sentences Resources Of the 451 samples screened by rRT-PCR, ten were confirmed as SARS-CoV-2 cases and 5 as indeterminate cases (positive for the screening gene and negative for the SARS-CoV-2 confirmatory gene) For WGS, four SARS-CoV-2 confirmed cases, one indeterminate case and one negative case were processed Table 1. WGSsuggested: NoneThe pool was run at a final concentration of 10 pM on an Illumina MiSeq instrument using MiSeq V3 reagent kit. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Fig 1 summarised the steps involved in sequencing using for both Nanopore and Illumina platform. Nanoporesuggested: NoneSARS-CoV-2 novel Coronavirus bioinformatics protocol; SAMTOOLS). SAMTOOLSsuggested: (SAMTOOLS, RRID:SCR_002105)Similarly, 250 bp paired end Illumina reads were quality checked using FASTQC ( FASTQCsuggested: (FastQC, RRID:SCR_014583)18 Reads with only a minimum Phred score of 30 were included in our downstream analysis. Phredsuggested: (Phred, RRID:SCR_001017)Filtered reads were then mapped to the Wuhan-Hu-1 reference genomes (accession number MN908947.3) using BWA-mem (0.7.17-r1188). BWA-memsuggested: (Sniffles, RRID:SCR_017619)Phylogenetic analysis for Illumina and Nanopore platform: Prank (v140603) was used to generate a multiple alignment of all the samples including some available reference genomes around the globe (Downloaded from RefSeq). Pranksuggested: (prank, RRID:SCR_017228)RefSeqsuggested: (RefSeq, RRID:SCR_003496)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 rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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SciScore for 10.1101/2020.04.30.070771: (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 Of the 6 cases sequenced, 4 were male; 2 female, there was one death, two recoveries and two active cases. Table 2: Resources
Software and Algorithms Sentences Resources Of the 451 samples screened by rRT-PCR, ten were confirmed as SARS-CoV-2 cases and 5 as indeterminate cases (positive for the screening gene and negative for the SARS-CoV-2 confirmatory gene) For WGS, four SARS-CoV-2 confirmed cases, one indeterminate case and one negative case were processed (Table 1). WGSsuggested: NoneResults from OddPub: We did not detect open data. We also did not …
SciScore for 10.1101/2020.04.30.070771: (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 Of the 6 cases sequenced, 4 were male; 2 female, there was one death, two recoveries and two active cases. Table 2: Resources
Software and Algorithms Sentences Resources Of the 451 samples screened by rRT-PCR, ten were confirmed as SARS-CoV-2 cases and 5 as indeterminate cases (positive for the screening gene and negative for the SARS-CoV-2 confirmatory gene) For WGS, four SARS-CoV-2 confirmed cases, one indeterminate case and one negative case were processed (Table 1). WGSsuggested: NoneResults 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 rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
-