Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
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Abstract
The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. The United Kingdom has contributed more than 26,000 sequences to this effort. This volume of data allowed du Plessis et al. to develop a detailed picture of the influxes of virus reaching U.K. shores as the pandemic developed during the first months of 2020 (see the Perspective by Nelson). Before lockdown, high travel volumes and few restrictions on international travel allowed more than 1000 lineages to become established. This accelerated local epidemic growth and exceeded contact tracing capacity. The authors were able to quantify the abundance, size distribution, and spatial range of the lineages that were transmitted. Transmission was highly heterogeneous, favoring some lineages that became widespread and subsequently harder to eliminate. This dire history indicates that rapid or even preemptive responses should have been used as they were elsewhere where containment was successful.
Science , this issue p. 708 ; see also p. 680
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SciScore for 10.1101/2020.10.23.20218446: (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 For each lineage in A (n = 3591), B (n = 8821), B.1 (n = 22,861), B.1.1 (n = 15,616), we estimated an approximately maximum-likelihood tree using the Jukes-Cantor model in FastTree v2.1.10 (41), then collapsed branch lengths shorter than 5×10−6 substitutions per site, which corresponded to distances smaller than one substitution across the whole virus genome, and likely result from nucleotide ambiguity codes in the genome sequences. FastTreesuggested: (FastTree, RRID:SCR_015501)We used a two-state asymmetric discrete trait analysis (DTA) model (51) implemented in BEAST 1.10 (42) to infer … SciScore for 10.1101/2020.10.23.20218446: (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 For each lineage in A (n = 3591), B (n = 8821), B.1 (n = 22,861), B.1.1 (n = 15,616), we estimated an approximately maximum-likelihood tree using the Jukes-Cantor model in FastTree v2.1.10 (41), then collapsed branch lengths shorter than 5×10−6 substitutions per site, which corresponded to distances smaller than one substitution across the whole virus genome, and likely result from nucleotide ambiguity codes in the genome sequences. FastTreesuggested: (FastTree, RRID:SCR_015501)We used a two-state asymmetric discrete trait analysis (DTA) model (51) implemented in BEAST 1.10 (42) to infer ancestral node locations (UK, non-UK) on empirical distributions of 500 time-calibrated trees sampled from each of the posterior tree distributions estimated above. BEASTsuggested: (BEAST, RRID:SCR_010228)We collected this information by mining archived FCO sites, manually retrieving HTML files corresponding to updates to the URLs provided above and available at the Internet Archive (https://archive.org/). Internet Archivesuggested: (Internet Archive, RRID:SCR_001682)Results from OddPub: Thank you for sharing your code and 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.
- No funding statement was detected.
- No protocol registration statement was detected.
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