Correction of Daily Positivity Rates for contribution of various test protocols being used in a pandemic
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Abstract
Daily positivity rate (DPR) is a popular metric to judge the prevalence of an infection in the population and the testing response to it as a single number. It has been widely implicated in predicting future course of the SARS CoV-2 pandemic in India. With increasing use of multiple testing protocols with varying sensitivity and specificity in various proportions, the naïve calculation loses meaning particularly during comparison between states/countries with large daily variations in contribution of different testing protocols to the testing response. We propose an adjustment to the naïve DPR based on the testing parameters and the relative proportional use of each such protocol. Such a correction has become essential for comparing testing response of Indian states from Jun 2020 – Aug 2020 because of steep variations in testing protocol in certain states.
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SciScore for 10.1101/2020.08.25.20181347: (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: 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 fraction of PCRs that were employed as a follow-up to negative RATs was only 1.02%, which gives certain validity to our initial assumption and dilutes the extent of the limitation. From the data of PCR follow-ups, extrapolating to all RAT negative cases, we also managed to estimate an independent measure of sensitivity of RAT …
SciScore for 10.1101/2020.08.25.20181347: (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: 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 fraction of PCRs that were employed as a follow-up to negative RATs was only 1.02%, which gives certain validity to our initial assumption and dilutes the extent of the limitation. From the data of PCR follow-ups, extrapolating to all RAT negative cases, we also managed to estimate an independent measure of sensitivity of RAT (assuming their specificity is almost 1). This estimated yielded an average sensitivity of 0.29, varying from 0.06 to 0.59 among districts. The extrapolation of RAT False Negatives was done as: The sensitivity of RAT was estimated as follows: When corrected for measured sensitivity of RAT (assuming its specificity = 1), the true positivity can be evaluated to be around 23.86%. Similar data was available for Karnataka from Jun 25 to Aug 5 2020 [6], which revealed a similar story of dismal RT-PCR follow-ups to negative RATs. It was found that among the total tests (n = 979,329) done in Karnataka during this period, RATs (n = 290,085) constitute 29.6% of them, of whom at net 12.87% turned out positive (this is the measured DPR for RATs). Of the RATs that turned out negative (n = 252,726), only a meagre 5.6% (n = 14,209) were followed-up with an RT-PCR, though better than Delhi but not significant enough to come out as a major limitation. Similar analysis for the total RT-PCRs (n = 689,244) of whom 140,889 turned out positive, gave a net positivity rate (here: measured) of 20.44%. Similar sensitivity was estimated (as in equations {5} and {6}) to yield a...
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.
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