Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons

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1. Version published to 10.1016/j.medj.2022.03.010

   May 1, 2022
2. 

   ScreenIT

   Jan 28, 2022

   SciScore for 10.1101/2022.01.22.22269660: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Study oversight: The Institutional Review Board from the Yale University Human Research Protection Program determined that obtaining de-identified test results linked to vaccination status 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: 2000031374).
   Sex as a biological variable	The participants included a diversity of ages from 0-5 to > 60, and 55% were female.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Study oversight: The Institutional Review Board from the Yale …

   SciScore for 10.1101/2022.01.22.22269660: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Study oversight: The Institutional Review Board from the Yale University Human Research Protection Program determined that obtaining de-identified test results linked to vaccination status 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: 2000031374).
   Sex as a biological variable	The participants included a diversity of ages from 0-5 to > 60, and 55% were female.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Study oversight: The Institutional Review Board from the Yale University Human Research Protection Program determined that obtaining de-identified test results linked to vaccination status 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: 2000031374).	Human Research Protection Program suggested: None
   For rapid confirmation of the initial suspected Omicron samples with SGTF, we used the NEBNext ARTIC SARS-CoV-2 Companion Kit and sequenced pooled libraries on the Oxford Nanopore Technologies (ONT) MinION.	MinION suggested: (MinION, RRID:SCR_017985)
   The RAMPART application developed by the ARTIC Network was used to monitor the sequencing run until sufficient coverage was reached (https://artic.network/ncov-2019/ncov2019-using-rampart.html)2.	RAMPART suggested: (Rampart, RRID:SCR_016742)
   The ARTIC bioinformatics pipeline was used to generate consensus genomes with fast basecalling done by MinKNOW (https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html).	MinKNOW suggested: None
   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 bases were called with simple majority > 60% frequency using iVar v1.3.14 and SAMtools v1.75.	iVar suggested: None SAMtools suggested: (SAMTOOLS, RRID:SCR_002105)

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   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).

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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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 10.1101/2022.01.22.22269660v1 on medRxiv

   Jan 25, 2022