Phylogenetic estimates of SARS-CoV-2 introductions into Washington State
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SciScore for 10.1101/2021.04.05.21254924: (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 aligned sequences with MAFFT and identified SARS-CoV-2 lineages using the PANGOLIN (Phylogenetic Assignment of Named Global Outbreak LINeages, github.com/cov-lineages/pangolin) tool.13,14 Our analysis pipeline aimed to accommodate issues with SARS-CoV-2 genetic diversity (relative to the timeframes of transmission and accumulation of viral diversity) that lead to challenges with phylogenetic resolution. 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 …
SciScore for 10.1101/2021.04.05.21254924: (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 aligned sequences with MAFFT and identified SARS-CoV-2 lineages using the PANGOLIN (Phylogenetic Assignment of Named Global Outbreak LINeages, github.com/cov-lineages/pangolin) tool.13,14 Our analysis pipeline aimed to accommodate issues with SARS-CoV-2 genetic diversity (relative to the timeframes of transmission and accumulation of viral diversity) that lead to challenges with phylogenetic resolution. 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: We detected the following sentences addressing limitations in the study:This analysis has several limitations. First, we likely are underestimating the true number of introductions due to incomplete sampling. Phylogenetic results need to be interpreted carefully due to incomplete sampling and phylogenetic uncertainty. Because our sampling coverage was only 6% of confirmed SARS-CoV-2 cases, if we were to sequence more genomes, we would find more introductions. Although GISAID and participating laboratories have facilitated the availability of an unprecedented number of publicly available whole genomes of SARS-CoV-2, within specific geographies, sampling coverage is very low and there is significant over-representation of sequences from certain countries (e.g. the United Kingdom, Australia, and the US). Second, due to length-biased sampling, we were unable to assess temporal variation in downstream clade sizes changed over time. Our findings have several important public health implications. First, our findings highlight the importance of genomic surveillance to monitor for emerging variants in WA and elsewhere in the US due to the high levels of inter- and intra-state transmission of SARS-CoV-2 lineages.25 Monitoring inter- and intra-state transmissions and their origins can be used to determine where public health interventions may be most effective. In addition, we observed that number of both introductions and exports fell within the week of the “Stay Home, Stay Health” order, suggesting that lockdowns may be effective at immediately reducing i...
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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