Sample Pooling as an efficient strategy for SARS-COV-2 RT-PCR screening: a multicenter study in Spain

Abstract

<jats:p>Importance: The actual demand on SARS-CoV-2 diagnosis is a current challenge for clinical laboratories. Sample pooling may help to ameliorate workload in clinical laboratories. Objective: to evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of CoVID-19, by using different commercial platforms for nucleic acid extraction and amplification. Design and settings: observational, prospective, multicentre study across 9 Spanish clinical microbiology laboratories including SARS-CoV-2 RNA testing performed in April 2020, during the first three days after acceptance to participate. Participants and Methods: 3519 naso-oro-pharyngeal samples received at the participating laboratories were processed individually and in pools (351 pools) according to the existing methodology in each of the centres. Results: We found that 253 pools (2519 samples) were negative, and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples) we found discordant results when compared to their correspondent individual samples: in 24/29 pools (30 samples), minor discordances were found; for five pools (5 samples), we found major discordances. Sensitivity, specificity, positive and negative predictive values for pooling were 97.93%, 100%, 100% and 99.85% respectively; accuracy was 99.86% and kappa concordant coefficient was 0.988. As a result of the sample dilution effect of pooling, a loss of 2-3 Cts was observed for E, N or RdRP genes. Conclusion: we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. We believe that our results may help clinical laboratories to respond to the actual demand and clinical need on SARS-CoV-2 testing, especially for the screening of low prevalence populations.</jats:p>

Optimally Pooled Viral Testing

“…Finally, another SARS-CoV-2 study reported pooled testing results for 2519 samples performed using a pool size of n = 10 or 11. 3 A total of 1243 tests were required to identify every one of the 241 positive individuals in this population with an average infection rate of p = 241 / 2519 = 0.096 (9.6%). 3 In this case Eq.…”

“…3 A total of 1243 tests were required to identify every one of the 241 positive individuals in this population with an average infection rate of p = 241 / 2519 = 0.096 (9.6%). 3 In this case Eq. 4 predicts that a somewhat larger number of 2519 × T %(0.096, 10) / 100 = 1853 tests should have been required to identify every infected sample.…”

“…In spite of these idealizations, the practical utility of the predictions are quantitatively validated by recent SARS-CoV-2 pooled testing data. [2][3][4][5][6] The results indicate that pooled testing can significantly reduce the number of the SARS-CoV-2 tests required to identify each positive individual, even in populations with infection rates above 10%, although pooled testing is most advantageous in populations with lower infection rates. The field testing validation studies also confirm that the present predictions provide conservative testing efficiency estimates, as non-uniform clustering of infections is predicted to lead to an increase in testing efficiency, above that predicted assuming a uniform infection rate.…”

Modelling pool testing for SARS-CoV-2: addressing heterogeneity in populations

“…This strategy could potentially increase worldwide testing capacity many times over [6], if used correctly, in the right segment of the population and under the specific historical prevalence of positive results [7,8] and test sensitivity [9]. It has also shown promising results as a screening tool in clinical practice [10,11], and it has been implemented on a large scale to test asymptomatic individuals, showing a considerably increased throughput in testing coverage while maintaining test sensitivity [12]. In addition, the WHO has recently established that group testing for SARS-CoV-2 is a feasible strategy that can increase testing capacity and can be applied in low prevalence settings.…”

Improvement of SARS-COV-2 screening using pooled sampling testing in limited RT-qPCR resources

“…In its simplest form, the pooling test works by constituting a set of individual samples, in the case where the pool is COVID-19 negative, all the individuals are identified as negative and if the pool is positive, further tests would be necessary to identify infected individuals in the group ( Dorfman, 1943 ; Olivier Gossner, 2020 ). This approach has been successfully used in the countries with high technological potential to deal with the lack of screening means ( Mutzel et al, 2020 ; Shani-Narkiss et al, 2020 ), as it has been proposed as a massive screening strategy ( De Salazar et al, 2020 ; Bilder and Tebbs, 2012 ).…”