Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

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1. Version published to 10.1016/j.xcrm.2022.100583

   Apr 1, 2022
2. 

   ScreenIT

   Oct 10, 2021

   SciScore for 10.1101/2021.10.06.21264641: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethics: Yale University (Connecticut): The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples obtained from clinical partners conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Ethics: Yale University (Connecticut): The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR …

   SciScore for 10.1101/2021.10.06.21264641: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethics: Yale University (Connecticut): The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples obtained from clinical partners conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Ethics: Yale University (Connecticut): The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples obtained from clinical partners conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599).	Human Research Protection Program suggested: None
   Transmissibility estimates: All figures were plotted using RStudio (v 1.4.1106).	RStudio suggested: (RStudio, RRID:SCR_000432)
   The reads were aligned to the Wuhan-Hu-1 reference genomes (GenBank MN908937.3) using BWA-MEM v.	BWA-MEM suggested: (Sniffles, RRID:SCR_017619)
   Adaptor sequences were trimmed, primer sequences were masked, and consensus genomes were called (simple majority >60% frequency) using iVar v1.3.1 (Grubaugh et al., 2019) and SAMtools (Danecek et al., 2021).	iVar suggested: None SAMtools suggested: (SAMTOOLS, RRID:SCR_002105)

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   Results from OddPub: Thank you for sharing your code and data.

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

   An important limitation to our comparative analyses was that sequencing coverage improved in states over time (Figure 1A), and thus there may have been a greater delay in the time to the first sequenced detection for Alpha versus Delta. In addition, due to the uncertainty around the serial interval, we selected an uncertain serial interval approach to explore various possible distributions when calculating Rt (Methods). While Vermont had the highest relative growth rates and mean Rt ratio comparing Delta and Alpha, it also had more variable sequencing coverage due to relatively low case counts (Figure 1A). Variant frequencies based on a relatively small number of sequences likely are driving some of the variability and uncertainty around its Rt estimates (Figure 3A), and therefore results for Vermont should be interpreted more cautiously. For the PCR CT analysis, we necessarily used only confirmed variant sequence data, which represents a fraction of the total PCR CT data and is biased against higher CT values that lack sufficient virus RNA for sequencing. It is also important to be cautious in interpreting CT values among institutes due to differences in the diagnostic PCR test platforms and subsequent CT cut-off values. For this reason, we do not aim to directly compare institutes, but rather sought to establish whether an overall pattern of lower CT values for Delta versus Alpha samples held. Mean CT values can also be influenced by the epidemic trajectory, as discussed pr...

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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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3. 

   Version published to 10.1101/2021.10.06.21264641 on medRxiv

   Oct 7, 2021