Spatial scales, patterns, and positivity trends of SARS-CoV-2 pandemics in mass rapid antigen testing in Slovakia
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Abstract
We study geographical epidemic scales and patterns and positivity trends of SARS-CoV-2 pandemics in mass antigen testing in Slovakia in 2020. The observed test positivity was exponentially distributed with a long scale exponential spatial trend, and its characteristic correlation length was approximately 10 km. Spatial scales also play an important role in test positivity reduction between two consecutive testing rounds. While test positivity decreased in all counties, it increased in individual municipalities with low test positivity in the earlier testing round in a way statistically different from a mean-reversion process. Also, non-residents testing influences the mass testing results as test positivity of non-residents was higher than of residents when testing was offered only in municipalities with the highest positivity in previous rounds. Our results provide direct guidance for pandemic geographical data surveillance and epidemic response management.
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SciScore for 10.1101/2020.12.23.20248808: (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
No key resources detected.
Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The data and its analysis discussed here have systematic limitations. All findings are limited in scope to the epidemiological situation in Slovakia during October-November, and any inference from the data applied to other settings needs to be taken with precaution. The same is true about an inference of infection prevalence from the positivity data as no direct relation between these two factors was established yet. Systematic limitations stem …
SciScore for 10.1101/2020.12.23.20248808: (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
No key resources detected.
Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The data and its analysis discussed here have systematic limitations. All findings are limited in scope to the epidemiological situation in Slovakia during October-November, and any inference from the data applied to other settings needs to be taken with precaution. The same is true about an inference of infection prevalence from the positivity data as no direct relation between these two factors was established yet. Systematic limitations stem from test parameters, testing procedures and test evaluations, see Supplementary material S1.4 for more details. Up to this date there is a lack of scientific validation of the test parameters used on a general population sample dominated by asymptomatic individuals. No test validation was conducted during the mass testing in Slovakia, test results were not confirmed by other laboratory diagnostics, test subjects were often not at room temperature prior to sample collection, the sample collection was performed by volunteer medical personnel that did not receive proper training how to perform the pharangonasal swabs, no specialized training was provided for test evaluation, 20 Euro risk compensation was paid to staff collecting the sample for each positive test. Test parameters (sensitivity and specificity) may be sample dependent as their sensitivity depends on distribution of viral loads in the sample [30]. Areas with fast epidemic growth that are dominated by fresh infections have a higher apparent average viral load in routine PCR t...
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 2. 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.
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