SARS-CoV-2 Genomic Surveillance Reveals Little Spread Between a Large University Campus and the Surrounding Community

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   ScreenIT

   Jul 26, 2021

   SciScore for 10.1101/2021.07.19.21260726: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: Use of residual SARS-CoV-2 positive specimens and collection of student status and on-campus residence were approved by the Institutional Review Board at the University of Michigan (Protocol HUM185966).
   Sex as a biological variable	not detected.
   Randomization	To determine whether the contextual genomes were biasing our results, we generated a total of ten random subsamples of the global data using the schema described above and analyzed the data in the same manner (Figure S2C).
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Analysis of Raw Sequence Reads: We mapped reads to the Wuhan/Hu-1/2019 reference genome (GenBank MN908947.3) …

   SciScore for 10.1101/2021.07.19.21260726: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: Use of residual SARS-CoV-2 positive specimens and collection of student status and on-campus residence were approved by the Institutional Review Board at the University of Michigan (Protocol HUM185966).
   Sex as a biological variable	not detected.
   Randomization	To determine whether the contextual genomes were biasing our results, we generated a total of ten random subsamples of the global data using the schema described above and analyzed the data in the same manner (Figure S2C).
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Analysis of Raw Sequence Reads: We mapped reads to the Wuhan/Hu-1/2019 reference genome (GenBank MN908947.3) with BWA-MEM (Li, 2013).	BWA-MEM suggested: (Sniffles, RRID:SCR_017619)
   We determined consensus sequences with samtools mpileup and iVar 1.2.1.	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   We aligned genomes with MAFFT as implemented in augur.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   We inferred a maximum likelihood phylogeny with IQ-TREE with a GTR model and 1000 ultrafast bootstraps (Nguyen et al., 2015).	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   We used TempEst to fit and plot a root-to-tip regression of divergence over time (Rambaut et al., 2016).	TempEst suggested: (TempEst, RRID:SCR_017304)
   We also performed Bayesian ASR using BEAST 1.10.4 using a fixed tree topology derived from TreeTime (Alpert et al., 2021; Drummond and Rambaut, 2007).	BEAST suggested: (BEAST, RRID:SCR_010228)

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   Results from OddPub: Thank you for sharing your code.

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   There are other important limitations. First, we were not able to access specimens from commercial testing sites, and the number of detected transmission introductions is certainly an underestimate. It is likely that many singletons in our data are in fact linked to a small number of other student cases. It is also possible that there were differential contact patterns between students who obtained testing at Michigan Medicine sites and those who did not. Next, our study is not an epidemiologic investigation with contact tracing and individual behavioral information. It is difficult to reliably assess the effectiveness of any single mitigation measure that was implemented during the fall semester from these data alone. In particular, it is difficult to disentangle whether the lack of spread from students into the community is the result of university and county case identification and isolation measures for students, partitioning of social structures between IHE and the surrounding communities, or a combination of both. Thorough contact tracing investigations of IHE-associated outbreaks with dense genomic surveillance across populations may be able to resolve these questions in greater detail. It is also possible that these dynamics could have played out differently with earlier emergence of a highly transmissible variant, such as B.1.1.7 (Alpert et al., 2021; Washington et al., 2021). This work will be a valuable point of comparison for future studies examining the effects o...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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   Results from scite Reference Check: We found no unreliable references.

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   Version published to 10.1101/2021.07.19.21260726 on medRxiv

   Jul 22, 2021