The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads
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SciScore for 10.1101/2022.01.26.22269927: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization Notably, samples are collected randomly from the whole system for whole genome sequencing for surveillance. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell culture: Vero-TMPRSS2 cells were cultured and infected with aliquots of swab specimens as previously described for VeroE6 cells (14). Vero-TMPRSS2suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)VeroE6suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)Software and Algorithms Sentences Resources Sequencing was performed using the Nanopore GridION and reads were basecalled with … SciScore for 10.1101/2022.01.26.22269927: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization Notably, samples are collected randomly from the whole system for whole genome sequencing for surveillance. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell culture: Vero-TMPRSS2 cells were cultured and infected with aliquots of swab specimens as previously described for VeroE6 cells (14). Vero-TMPRSS2suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)VeroE6suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)Software and Algorithms Sentences Resources Sequencing was performed using the Nanopore GridION and reads were basecalled with MinKNOW, and demultiplexed with guppybarcoder that required barcodes at both ends. MinKNOWsuggested: NoneStatistical analysis: Statistical analyses were conducted using GraphPad prism. GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)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).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The limitations of our study include the retrospective nature of data collections which doesn’t allow the collection of baseline serum and respiratory IgG levels. Antibody neutralization assays and quantification of viruses from clinical samples were not conducted as a part of this study nor were Omicron or Delta specific IgG assays. Clinical data was compiled from patients tested and admitted to the Johns Hopkins Health System. It is possible that patients who tested positive in our system then sought additional clinical care, including admission, at a different hospital not affiliated with Johns Hopkins. While this could artificially lower our admission rates, we have no reason to think that this was different in the first half of December, when Delta was predominant, compared to the end of December. In conclusion, we show a significant reduction in disease severity with Omicron when compared to Delta, yet we show that Omicron associates with significant increases in infections of fully and booster vaccinated individuals. It is important to note that admitted patients didn’t show a significant difference in the use of supplementary oxygen, ICU level care, stressing the importance of taking infection control precautions and raising an awareness that Omicron infections should not be underestimated.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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.
Results from scite Reference Check: We found no unreliable references.
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