Monitoring of SARS-CoV-2 B.1.1.7 variant early-phase spreading in South-Moravian Region in the Czech Republic and evaluation of its pathogenicity
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
SARS-CoV-2 emerged in Wuhan, China, in December 2019. Starting in January 2020, over a period of several months, the initial virus (Wuhan-Hu-1/2019; Wu et al. 2020) diverged in a descendant strain carrying D614G amino acid mutation in spike protein. By summer 2020 this novel coronavirus (nCoV) became the most dominant form of the virus circulating worldwide and raised serious international concern. Currently (April 2021), there are 3598 subsequent PANGO branched lineages recognized that carry numerous mutations. To date, the most emerging lineages of SARS-CoV-2 worldwide include B.1.1.7 lineage with a frequency of 48% followed by several dozens of others with frequencies 7.5% or less, such as B.1.351, B.1.1.28, B.1.2, B.1.1.519, P.1, R.1, etc. ( www.nextrain.org , Centers for Disease Control and Prevention; CDC 2020 www.cdc.gov ).
In this study, we monitored the spreading of B.1.1.7 lineage from the early phase of its appearance until it became predominant in the South-Moravian region of the Czech Republic. We measured significantly associated clinical marker (Ct; cycle threshold) correlating with viral load in B.1.1.7 lineage. Interestingly, we found that the spreading of B.1.1.7 strain was associated with a shift in patients average age, as compared to the former predominant lineage. Finally, we calculated the impact of the B.1.1.7 lineage on hospitalization and case fatality of the patients on the intensive care unit in the central South-Moravian faculty hospital.
Article activity feed
-
SciScore for 10.1101/2021.05.24.21257365: (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 The selection of the samples was done randomly. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: We further validated Ct values of wild type and B.1.1.7 lineage with the unpaired Mann-Whitney test. Table 2: Resources
Software and Algorithms Sentences Resources To verify the authenticity of the samples, we performed NFS sequencing of 17 selected samples in collaboration with NRL, CEITEC, and Biogen. Biogensuggested: (Biogen Idec, RRID:SCR_003790)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 Na…
SciScore for 10.1101/2021.05.24.21257365: (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 The selection of the samples was done randomly. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: We further validated Ct values of wild type and B.1.1.7 lineage with the unpaired Mann-Whitney test. Table 2: Resources
Software and Algorithms Sentences Resources To verify the authenticity of the samples, we performed NFS sequencing of 17 selected samples in collaboration with NRL, CEITEC, and Biogen. Biogensuggested: (Biogen Idec, RRID:SCR_003790)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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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: Please consider improving the rainbow (“jet”) colormap(s) used on page 15. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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.
-
-