Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection. (September 2020)

• Record Type: Journal Article
• Authors: Ben-Ami, R.; Klochendler, A.; Seidel, M.; Sido, T.; Gurel-Gurevich, O.; Yassour, M.; Meshorer, E.; Benedek, G.; Fogel, I.; Oiknine-Djian, E.; Gertler, A.; Rotstein, Z.; Lavi, B.; Dor, Y.; Wolf, D.G.; Salton, M.; Drier, Y.; Klochendler, A.; Eden, A.; Klar, A.; Geldman, A.; Arbel, A.; Peretz, A.; Shalom, B.; Ochana, B.L.; Avrahami-Tzfati, D.; Neiman, D.; Steinberg, D.; Ben Zvi, D.; Shpigel, E.; Atlan, G.; Klein, H.; Chekroun, H.; Shani, H.; Hazan, I.; Ansari, I.; Magenheim, I.; Moss, J.; Magenheim, J.; Peretz, L.; Feigin, L.; Saraby, M.; Sherman, M.; Bentata, M.; Avital, M.; Kott, M.; Peyser, M.; Weitz, M.; Shacham, M.; Grunewald, M.; Sasson, N.; Wallis, N.; Azazmeh, N.; Tzarum, N.; Fridlich, O.; Sher, R.; Condiotti, R.; Refaeli, R.; Ben Ami, R.; Zaken-Gallili, R.; Helman, R.; Ofek, S.; Tzaban, S.; Piyanzin, S.; Anzi, S.; Dagan, S.; Lilenthal, S.; Sido, T.; Licht, T.; Friehmann, T.; Kaufman, Y.; Pery, A.; Saada, A.; Dekel, A.; Yeffet, A.; Shaag, A.; Michael-Gayego, A.; Shay, E.; Arbib, E.; Onallah, H.; Ben-Meir, K.; Levinzon, L.; Cohen-Daniel, L.; Natan, L.; Hamdan, M.; Rivkin, M.; Shwieki, M.; Vorontsov, O.; Barsuk, R.; Abramovitch, R.; Gutorov, R.; Sirhan, S.; Abdeen, S.; Yachnin, Y.; Daitch, Y.;
• Is Part Of: Clinical microbiology and infection. Volume 26:Number 9(2020)
• Page Start: 1248
• Page End: 1253
• Publication Date: 2020-09
• Subjects: COVID-19 -- Diagnostics -- Group testing -- Infectious diseases -- RT-PCR; Medical microbiology -- Periodicals; Diagnostic microbiology -- Periodicals; Communicable diseases -- Periodicals; Infection -- Periodicals; 616.01
• DOI: 10.1016/j.cmi.2020.06.009
• Languages: English
• ISSNs: 1198-743X

Abstract

Abstract: Introduction: Testing for active SARS-CoV-2 infection is a fundamental tool in the public health measures taken to control the COVID-19 pandemic. Because of the overwhelming use of SARS-CoV-2 reverse transcription (RT)-PCR tests worldwide, the availability of test kits has become a major bottleneck and the need to increase testing throughput is rising. We aim to overcome these challenges by pooling samples together, and performing RNA extraction and RT-PCR in pools. Methods: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. We tested 184 samples both individually and in pools to estimate the effects of pooling. We further implemented Dorfman pooling with a pool size of eight samples in large-scale clinical tests. Results: We demonstrated pooling strategies that increase testing throughput while maintaining high sensitivity. A comparison of 184 samples tested individually and in pools of eight samples showed that test results were not significantly affected. Implementing the eight-sample Dorfman pooling to test 26 576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. Discussion: Pooling approaches for SARS-CoV-2 testing allow a drastic increase in throughput while maintaining clinical sensitivity. We report the successful large-scale pooled screening of asymptomatic populations.