Revealing COVID-19 Transmission by SARS-CoV-2 Genome Sequencing and Agent Based Modelling
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Abstract
Community transmission of the new coronavirus SARS-CoV-2 is a major public health concern that remains difficult to assess. We present a genomic survey of SARS-CoV-2 from a during the first 10 weeks of COVID-19 activity in New South Wales, Australia. Transmission events were monitored prospectively during the critical period of implementation of national control measures. SARS-CoV-2 genomes were sequenced from 209 patients diagnosed with COVID-19 infection between January and March 2020. Only a quarter of cases appeared to be locally acquired and genomic-based estimates of local transmission rates were concordant with predictions from a computational agent-based model. This convergent assessment indicates that genome sequencing provides key information to inform public health action and has improved our understanding of the COVID-19 evolution from outbreak to epidemic.
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SciScore for 10.1101/2020.04.19.048751: (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 SARS-CoV-2 genome sequencing: We undertook SARS-CoV-2 WGS using an existing amplicon-based Illumina sequencing approach29,30. WGSsuggested: NoneAmplicons were then pooled equally, purified and quantified before Nextera XT library preparation and multiplex sequencing on an Illumina iSeq or MiniSeq (150 cycle flow cell)31. MiniSeqsuggested: NoneDemultiplexed reads were quality trimmed using Trimmomatic (sliding window of 4, minimum read quality score of 20, leading/trailing quality … SciScore for 10.1101/2020.04.19.048751: (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 SARS-CoV-2 genome sequencing: We undertook SARS-CoV-2 WGS using an existing amplicon-based Illumina sequencing approach29,30. WGSsuggested: NoneAmplicons were then pooled equally, purified and quantified before Nextera XT library preparation and multiplex sequencing on an Illumina iSeq or MiniSeq (150 cycle flow cell)31. MiniSeqsuggested: NoneDemultiplexed reads were quality trimmed using Trimmomatic (sliding window of 4, minimum read quality score of 20, leading/trailing quality of 5)32. Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)Briefly, reads were mapped to the reference SARS-CoV-2 genome (NCBI GenBank accession MN908947) using BWA-mem version 0.7.17, with unmapped reads discarded. BWA-memsuggested: (Sniffles, RRID:SCR_017619)The quality of GISAID genomes was evaluated using QUAST, with sequences retained only if they were >28,000-bp in length and contained <0.05% missing bases (n=1,985 reference genomes). QUASTsuggested: (QUAST, RRID:SCR_001228)The GISAID and NSW genomes were aligned with MAFFT v7.402 (FFT-NS-2, progressive method)35. MAFFTsuggested: (MAFFT, RRID:SCR_011811)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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