Swab pooling: A new method for large-scale RT-qPCR screening of SARS-CoV-2 avoiding sample dilution
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
To minimize sample dilution effect on SARS-CoV-2 pool testing, we assessed analytical and diagnostic performance of a new methodology, namely swab pooling. In this method, swabs are pooled at the time of collection, as opposed to pooling of equal volumes from individually collected samples. Paired analysis of pooled and individual samples from 613 patients revealed 94 positive individuals. Having individual testing as reference, no false-positives or false-negatives were observed for swab pooling. In additional 18,922 patients screened with swab pooling (1,344 pools), mean Cq differences between individual and pool samples ranged from 0.1 (Cr.I. -0.98 to 1.17) to 2.09 (Cr.I. 1.24 to 2.94). Overall, 19,535 asymptomatic patients were screened using 4,400 RT-qPCR assays. This corresponds to an increase of 4.4 times in laboratory capacity and a reduction of 77% in required tests. Therefore, swab pooling represents a major alternative for reliable and large-scale screening of SARS-CoV-2 in low prevalence populations.
Article activity feed
-
SciScore for 10.1101/2020.09.03.20187732: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This study was approved by the Hospital Israelita Albert Einstein Ethics Committee (number 36371220.6.0000.0071).
Consent: The patient informed consent was waived off by the ethics committee as the research was performed on de-identified, anonymised samples.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. 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 …SciScore for 10.1101/2020.09.03.20187732: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This study was approved by the Hospital Israelita Albert Einstein Ethics Committee (number 36371220.6.0000.0071).
Consent: The patient informed consent was waived off by the ethics committee as the research was performed on de-identified, anonymised samples.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. 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:Nonetheless, there is always a limitation towards samples with Cq’s higher than 35, in which case mean differences as small as 1 Cq could still result in false-negative tests regardless of the pooling strategy. Operationally, the major difference between swab pooling and traditional methods regards sample collection: while in swab pooling we combine multiple swabs in the same tube at the time of sample collection, traditional strategies pool equal volumes from individually collected samples. Beyond dilution, the latter methodology adds complexity to laboratory operations and may lead to increased workload to already saturated laboratory facilities. Traditional pooling requires significant sample manipulation with a risk of contamination and even sample exchange during the laborious pooling process. On the other hand, collecting two swabs from the same patient can be operationally trivial. While one swab goes into the pooling tube, the other one will only be processed by the laboratory if the pool tests positive. A critical step, this sample collection process can still represent an important limitation of swab pooling as it can cause variation between pooled and individual swabs. In this study, we detected 12 pools with positive results but no positive associated individual test. Of these, 8 pools were associated with two specific collection events (4 pools collected each day). Thus, it is likely that such inconsistencies are attributable to the sample collection process. Sti...
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.
-
-
