SARS-CoV-2 detection in multi-sample pools in a real pandemic scenario: A screening strategy of choice for active surveillance
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Abstract
The current COVID-19 pandemic has overloaded the diagnostic capacity of laboratories by the gold standard method rRT-PCR. This disease has a high spread rate and almost a quarter of infected individuals never develop symptoms. In this scenario, active surveillance is crucial to stop the virus propagation.
Methods
Between July 2020 and April 2021, 11,580 oropharyngeal swab samples collected in closed and semi-closed institutions were processed for SARS-CoV-2 detection in pools, implementing this strategy for the first time in Córdoba, Argentina. Five-sample pools were constituted before nucleic acid extraction and amplification by rRT-PCR. Comparative analysis of cycle threshold (Ct) values from positive pools and individual samples along with a cost-benefit report of the whole performance of the results was performed.
Results
From 2,314 5-sample pools tested, 158 were classified as positive (6.8%), 2,024 as negative (87.5%), and 132 were categorized as indeterminate (5.7%). The Ct value shift due to sample dilution showed an increase in Ct of 2.6±1.53 cycles for N gene and 2.6±1.78 for ORF1ab gene. Overall, 290 pools were disassembled and 1,450 swabs were analyzed individually. This strategy allowed correctly identifying 99.8% of the samples as positive (7.6%) or negative (92.2%), avoiding the execution of 7,806 rRT-PCR reactions which represents a cost saving of 67.5%.
Conclusion
This study demonstrates the feasibility of pooling samples to increase the number of tests performed, helping to maximize molecular diagnostic resources and reducing the work overload of specialized personnel during active surveillance of the COVID-19 pandemic.
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SciScore for 10.1101/2021.12.23.21266126: (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 not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources From these files, the results were organized and interpreted with Perl scripts and conditional rules in Microsoft Excel and then converted into comma-delimited files. Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)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 limitation …
SciScore for 10.1101/2021.12.23.21266126: (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 not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources From these files, the results were organized and interpreted with Perl scripts and conditional rules in Microsoft Excel and then converted into comma-delimited files. Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)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 limitation of this strategy to test the internal control of each sample, which is required to control the specimen quality, must also be underlined. So, false-negative results may occur if samples are improperly collected, transported, or handled. Hence, negative results obtained by pooled sampling do not preclude SARS-CoV-2 infection and should not be used as the only criteria for treatment or for other social management decisions. The high sensitivity of rRT-PCR assays makes pool testing an efficient system that can be applied for resource optimization when positivity rate is low (e.g., 5% or lower), improving laboratory testing capacities without additional requirements in terms of equipment availability or qualified personnel,[19, 21, 26]. Our results show that the implementation of the strategy of pooling was able to save 67,5% of rRT-PCR reactions in a low viral circulation scenario. The approach of testing in pools was a positive experience that allow expanding sample processing capabilities allowing massive testing and early outbreak detections. Our findings could be taken into account as a strategy to be implemented in a new post-pandemic scenario, with an expected decrease of viral circulation (due to vaccine programs) to carry out large-scale testing in hospitals, care homes, schools, and other closed and semi-closed institutions.
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.
- Thank you for including a protocol registration statement.
Results from scite Reference Check: We found no unreliable references.
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