Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2
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Abstract
The emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions.
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SciScore for 10.1101/2020.06.26.173203: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources To identify iSNV sites, paired-end metatranscriptomic coronaviridae-like short read data were mapped to the reference genome (EPI_ISL_402119) using BWA aln (v.0.7.16) with default parameters [20]. BWAsuggested: (BWA, RRID:SCR_010910)The duplicated reads were detected and marked using Picard MarkDuplicates (v. 2.10.10) (http://broadinstitute.github.io/picard). Picardsuggested: (Picard, RRID:SCR_006525)The variable sites of each sample were identified using the variant caller LoFreq with default filters and the cut-off of 5% minor allele frequency. LoFreqsuggested: (LoFreq, RRID:SCR_013054)The … SciScore for 10.1101/2020.06.26.173203: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources To identify iSNV sites, paired-end metatranscriptomic coronaviridae-like short read data were mapped to the reference genome (EPI_ISL_402119) using BWA aln (v.0.7.16) with default parameters [20]. BWAsuggested: (BWA, RRID:SCR_010910)The duplicated reads were detected and marked using Picard MarkDuplicates (v. 2.10.10) (http://broadinstitute.github.io/picard). Picardsuggested: (Picard, RRID:SCR_006525)The variable sites of each sample were identified using the variant caller LoFreq with default filters and the cut-off of 5% minor allele frequency. LoFreqsuggested: (LoFreq, RRID:SCR_013054)The identified iSNVs were then annotated using the SnpEff (v.2.0.5) with default settings [21]. SnpEffsuggested: (SnpEff, RRID:SCR_005191)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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