key: cord-0911967-oieq51vc authors: Alcoba-Florez, J.; Gil-Campesino, H.; Garcia-Martinez de Artola, D.; Diez-Gil, O.; Valenzuela-Fernandez, A.; Gonzalez-Montelongo, R.; Ciuffreda, L.; Flores, C. title: Increasing SARS-CoV-2 RT-qPCR testing capacity by sample pooling date: 2020-10-27 journal: nan DOI: 10.1101/2020.10.24.20218685 sha: 7ec1979d72e52415e58d75bbbf0b5461987f8fdd doc_id: 911967 cord_uid: oieq51vc Objectives: Limited testing capacity has characterized the ongoing COVID-19 pandemic in Spain, hampering a timely control of outbreaks and the possibilities to reduce the escalation of community transmissions. Here we investigated the potential of using pooling of samples followed by one-step retrotranscription and quantitative PCR (RT-qPCR) to increase SARS-CoV-2 testing capacity. Methods: We first evaluated different sample pooling (1:5, 1:10 and 1:15) prior to RNA extractions followed by standard RT-qPCR for SARS-CoV-2/COVID-19 diagnosis. The pool size achieving reproducible results in independent tests was then used for assessing nasopharyngeal samples in a tertiary hospital during August 2020. Results: We found that pool size of five samples achieved the highest sensitivity compared to pool sizes of 10 and 15, showing a mean ({+/-} SD) Ct shift of 3.5 {+/-} 2.2 between the pooled test and positive samples in the pool. We then used a pool size of five to test a total of 895 pools (4,475 prospective samples) using two different RT-qPCR kits available at that time. The Real Accurate Quadruplex corona-plus PCR Kit (PathoFinder) reported the lowest mean Ct ({+/-} SD) shift (2.2 {+/-} 2.4) among the pool and the individual samples. The strategy allows detecting individual samples in the positive pools with Cts in the range of 16.7-39.4. Conclusions: We found that pools of five samples combined with RT-qPCR solutions helped to increase SARS-CoV-2 testing capacity with minimal loss of sensitivity compared to that resulting from testing the samples independently. The SARS-CoV-2 pandemic causing COVID-19 continue imposing a heavy burden on healthcare systems worldwide because of a shortage of consumables and the demand for scaling up efficient screening approaches. To limit the escalation of cases and amplification of infections, increasing the capacities and developing alternatives to the one-step reverse transcription and real-time quantitative PCR (RT-qPCR) for regular testing of SARS-CoV-2 is key (Mina et al. 2020) . We have assessed a direct heating method of nasopharyngeal (swab) samples to bypass the RNA extraction step for increasing the testing capacity (Alcoba-Florez et al. 2020a,b) . In areas with low COVID-19 prevalence, such as the Canary Islands until June 2020 (Pollán et al. 2020) , testing of samples in pools is another approach that can efficiently increase SARS-CoV-2 testing capacity. Simulation studies support the value of testing on sample pools and the speed of reporting, while the impact of the sensitivity of tests is comparable smaller (Larremore et al. 2020) . Supporting this, a pooled test of SARS-CoV-2 of four samples has received Emergency Use Authorization from the USA Food and Drug Administration (FDA COVID-19 Update 2020). Here we aimed to evaluate the RT-qPCR testing on pooled swab samples with the goal to demonstrate its feasibility as an option to increase SARS-CoV-2 testing capacity in the region. The study was conducted in two stages at the University Hospital Nuestra Señora de Candelaria (Santa Cruz de Tenerife, Spain) during August 2020. Nasopharyngeal swab samples were collected in 2 mL of viral transmission medium (VTM) (Biomérieux). . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 27, 2020. In a pilot stage, we used the Real Accurate Quadruplex corona-plus PCR Kit for testing 15 pools made by combining 5, 10, or 15 retrospective samples, each containing equal volumes of a SARS-CoV-2/COVID-19 positive sample and the respective amounts of negative samples to complete the pool size. In a validation stage, we used the two RT-qPCR kits available on swab samples from prospective subjects using the pooling size achieving optimal results. Then, individual samples from each positive pool were subjected to RNA extraction followed by RT-qPCR using the abovementioned methods to validate the results. Differences between the pooled Ct and the positive sample Ct in the pool (Ct shift) for the two different RT-qPCR kits were assessed by Mann-Whitney U-test using the R v4.0.3 software. When more than a positive sample was present in the pool, the mean Ct of the positive samples was used in the calculation. Sensitivity and the 95% Confidence Interval (CI) was assessed with MedCalc (MedCalc Software Ltd.). . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 27, 2020. ; https://doi.org/10. 1101 /2020 In a pilot study, detection of SARS-CoV-2 was achieved with pool size of five ( In this study, we describe the feasibility of RT-qPCR in pools of five swab samples with a minimal loss of sensitivity compared to the assessment of samples independently. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 27, 2020. ; https://doi.org/10.1101 https://doi.org/10. /2020 expected (Cherif et al. 2020) . Our data suggest that our sample pooling strategy is able to detect COVID-19 positive cases with Ct values £39.4. Pooling with compressive sampling designs, which involves repetitive tests (Shental et al. 2020) , and the use of alternative testing approximations (Peto et al. 2020 ) may help to further lessen the impact of the dilution factor on pooling and continue increasing health capacity building. JAF and CF designed the study. JAF, HGC, DGM, and ODG participated in data acquisition. JAF, LC, and CF performed the analyses and data interpretation. LC, AVF, RGM and CF wrote the draft of the manuscript. All authors contributed in the critical revision and final approval of the manuscript. We deeply acknowledge the University Hospital Nuestra Señora de Candelaria board of directors and the executive team for their strong support and assistance in accessing diverse resources used in the study. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. and "Apuestas científicas del ITER para colaborar en la lucha contra la COVID- is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 27, 2020. ; https://doi.org/10.1101 https://doi.org/10. /2020 The University Hospital Nuestra Señora de Candelaria (Santa Cruz de Tenerife, Spain) review board approved the study (ethics approval number: CHUNSC_2020_24). is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 27, 2020. ; https://doi.org/10.1101/2020.10.24.20218685 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted October 27, 2020. ; https://doi.org/10. 1101 /2020 Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection Simulation of pool testing to identify patients with coronavirus disease 2019 under conditions of limited test availability Update: FDA Issues First Emergency Authorization for Sample Pooling in Diagnostic Testing Pooled testing for surveillance of SARS-CoV-2 in asymptomatic individuals Test sensitivity is secondary to frequency and turnaround time for COVID-8 Rethinking Covid-19 Test Sensitivity -A Strategy for Containment Diagnosis of SARS-CoV-2 infection with LamPORE, a highthroughput platform combining loop-mediated isothermal amplification and nanopore sequencing Prevalence of SARS-CoV-2 in Spain (ENE-COVID): a nationwide, population-based seroepidemiological study Efficient high throughput SARS-CoV-2 testing to detect asymptomatic carriers