B.1.617.2 SARS-CoV-2 (Delta) variant is associated with increased risk of hospitalization and death compared with B.1.1.7 SARS-CoV-2 (Alpha) variant

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   ScreenIT

   Jan 25, 2022

   SciScore for 10.1101/2022.01.21.22268602: (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
   First, we used information from a nationwide network group of laboratories (UNILABS) that performs RT-PCR tests for SARS-CoV-2 using Thermofisher TaqPath assay, targeting three regions of the SARS-CoV-2 genome: ORF1ab, N and S genes.	Thermofisher TaqPath suggested: None
   In case of misclassification (e.g., different classification from WGS and SGTF), we accepted the WGS result as final due to higher accuracy(17).	WGS suggested: None
   Additionally, to optimize the use of controls in periods of B.1.617.2 dominance that resulted in a scarcity of controls for matching, we used a nearest-neighbor …

   SciScore for 10.1101/2022.01.21.22268602: (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
   First, we used information from a nationwide network group of laboratories (UNILABS) that performs RT-PCR tests for SARS-CoV-2 using Thermofisher TaqPath assay, targeting three regions of the SARS-CoV-2 genome: ORF1ab, N and S genes.	Thermofisher TaqPath suggested: None
   In case of misclassification (e.g., different classification from WGS and SGTF), we accepted the WGS result as final due to higher accuracy(17).	WGS suggested: None
   Additionally, to optimize the use of controls in periods of B.1.617.2 dominance that resulted in a scarcity of controls for matching, we used a nearest-neighbor algorithm provided with the “Matchit”(19) CRAN package.	CRAN suggested: (CRAN, RRID:SCR_003005)

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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:

   However, secondary use of administrative data encompasses several limitations. First and foremost, hospital admission data can have delays due to coding processes, which would significantly affect participants diagnosed closer to the end of the study period. As the B.1.617.2 variant has become dominant halfway from the end study, it can be argued that this delay would lead to an underestimation of the number of events in this group and by consequence an underestimation of the HR of death and hospitalization. We have mitigated this factor by extracting data on hospital admissions almost two months after the end of the study period. The selection of samples for WGS and SGTF was independent of the VOC type and severity, e.g., hospitalization or death, making the risk of differential selection bias residual. Our study sample showed a skewness towards younger ages, and this may be explained by the fact that our cases were collected mainly through ambulatory laboratories. At the same time, older (80+) individuals are expected to be more frequently diagnosed by hospital laboratories. While the cumulative risk of hospitalization and death could be underestimated, it is unlikely that the age distribution in the study would bias the variant HR estimates. We cannot exclude residual confounding in the study, our study did not account comorbidities. Patients infected with Delta variant for the same age could be sicker (immunocompromised, higher burden of comorbidities) and that affected t...

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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 10.1101/2022.01.21.22268602v1 on medRxiv

   Jan 23, 2022