Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study

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1. Version published to 10.1016/s0140-6736(22)00017-4

   Jan 1, 2022
2. 

   ScreenIT

   Dec 23, 2021

   SciScore for 10.1101/2021.12.21.21268116: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethical approval: Ethical approval was obtained from the Human Research Ethics Committee (Medical) of University of the Witwatersrand for the collection of COVID-19 case and test data as part of essential communicable disease surveillance (M160667), and for the DATCOV surveillance programme (M2010108).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: The Delta variant was identified by genome sequencing.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Statistical analysis: Analysis was performed using Stata 14.1® (StataCorp LP, College Station, US).	StataCorp suggested: …

   SciScore for 10.1101/2021.12.21.21268116: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethical approval: Ethical approval was obtained from the Human Research Ethics Committee (Medical) of University of the Witwatersrand for the collection of COVID-19 case and test data as part of essential communicable disease surveillance (M160667), and for the DATCOV surveillance programme (M2010108).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: The Delta variant was identified by genome sequencing.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Statistical analysis: Analysis was performed using Stata 14.1® (StataCorp LP, College Station, US).	StataCorp suggested: (Stata, RRID:SCR_012763)

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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: We detected the following sentences addressing limitations in the study:

   This study has a number of limitations. Firstly, SGTF infections were only identifiable using the TaqPath PCR and only for specimens with high viral loads (Ct≤30) and therefore the number of SGTF infections is underestimated and biased towards geographic regions where this assay was more commonly used. Secondly, SGTF identified on PCR was used as a proxy for Omicron variant detection. However, SGTF may also identify the Alpha variant and occur sporadically in other variants and therefore some infections may have been misclassified as Omicron. However, we only used SGTF as a proxy for Omicron after 1 October 2021 and genome data generated by NGS-SA has not identified the Alpha variant in South Africa since August 2021 and at its peak Alpha variant was only detected in 6% of samples in May 2021 13. In addition, Omicron has recently been classified into three sub-lineages, one (BA.2 ) of which does not contain the Δ69-70 deletion and which therefore will not be identifiable by the SGTF. Genome data from November 2021, showed that of 881 Omicron sequences, 872 (99.0%) were BA.1, 1 (0.1%) was BA.2 and 8 (0.9%) were BA.313. Ongoing sequencing will enable definitive classification of the Omicron variant for future severity analyses. Thirdly, our analysis was conducted in the early phase of the fourth wave after the emergence of Omicron when numbers were small, patients with milder symptoms were more likely to be admitted, and there may be a lag in hospitalisations and severe outcome...

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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 10.1101/2021.12.21.21268116 on medRxiv

   Dec 21, 2021