Epidemiology, clinical characteristics, and virologic features of COVID-19 patients in Kazakhstan: A nation-wide retrospective cohort study
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SciScore for 10.1101/2021.01.06.20249091: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The retrospective cohort study was approved by the Research Ethics Board of Semey Medical University as an anonymized epidemiological study, for which the requirement for informed consent was waived due to the pandemic state and urgent need to collect and analyze data. Randomization Virus genome sequencing and bioinformatics: Nasopharyngeal swabs were collected from 53 randomly selected symptomatic patients, who had a positive SARS-CoV-2 PCR test and were hospitalized in the capital city, Nur-Sultan between 22 March and 9 May (Fig 1B). Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
… SciScore for 10.1101/2021.01.06.20249091: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The retrospective cohort study was approved by the Research Ethics Board of Semey Medical University as an anonymized epidemiological study, for which the requirement for informed consent was waived due to the pandemic state and urgent need to collect and analyze data. Randomization Virus genome sequencing and bioinformatics: Nasopharyngeal swabs were collected from 53 randomly selected symptomatic patients, who had a positive SARS-CoV-2 PCR test and were hospitalized in the capital city, Nur-Sultan between 22 March and 9 May (Fig 1B). Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sequences were aligned to the Wuhan reference using MAFFT 9, the alignment checked for discrepancies and ends trimmed manually to match the reference, followed by reconstruction of a maximum likelihood phylogeny in IQTREE 10 using the GTR + F + I model and ultrafast bootstrap option with 1,000 replicates. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Statistical analyses were performed using IBM SPSS V.23 and R V.3.6.3. SPSSsuggested: (SPSS, RRID:SCR_002865)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:Our study has several limitations. First, our cohort represents only a third of all COVID-19 cases confirmed by PCR in March-April in Kazakhstan. Second, the quality of our dataset is largely dependent on the quality of the medical record data, which were collected in emergency settings by clinicians and which could have increased data heterogeneity. Third, some data, such as laboratory findings for CRP, were only available for a subset of participants, while other data, such as D-dimer levels and information on clinical outcomes or complications were available for <40% of patients within the comparison groups and were excluded from the analyses. Fourth, death reporting may have been delayed or more deaths may have occurred after April 30, resulting in under-estimation of mortality. Fifth, laboratory confirmation of COVID-19 was done using a commercially available PCR supplied centrally to all testing sites, but we were unable to access data on the intra- and inter-laboratory performance of this test. Sixth, our genomic analysis was limited to a qualitative assessment and cannot fully recapitulate the country-wide SARS-CoV-2 diversity due to the small sample size and geographic constraints. To conclude, we are hopeful that these clinical and virologic data on COVID-19 will help shape public health policies and therapeutic and vaccine interventions in Kazakhstan. Our findings could ultimately be applicable to other neighbouring countries that are similar in their ethnic and so...
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04627194 Active, not recruiting Characteristics of COVID-19 Patients in Kazakhstan in Early … 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.
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