Genomic reconstruction of the SARS-CoV-2 epidemic in England
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Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
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SciScore for 10.1101/2021.05.22.21257633: (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 We then extracted a sub-alignment from each lineage (following the 01-04-2021 version of PANGOlin for the 17-04-2021 alignment and the 23-04-2021 version of PANGOlin for the 05-05-2021 alignment), and, for each sub-alignment, we inferred a phylogeny via maximum likelihood using FastTree2 version 2.1.11 (Price et al., 2010) with default options and GTR substitution model (Tavaré, 1986). FastTree2suggested: NoneResults from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not …SciScore for 10.1101/2021.05.22.21257633: (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 We then extracted a sub-alignment from each lineage (following the 01-04-2021 version of PANGOlin for the 17-04-2021 alignment and the 23-04-2021 version of PANGOlin for the 05-05-2021 alignment), and, for each sub-alignment, we inferred a phylogeny via maximum likelihood using FastTree2 version 2.1.11 (Price et al., 2010) with default options and GTR substitution model (Tavaré, 1986). FastTree2suggested: NoneResults from OddPub: Thank you for sharing your code.
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.
Results from scite Reference Check: We found no unreliable references.
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