Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection

• Published in: Clinical microbiology and infection Vol. 26; no. 9; pp. 1248 - 1253
• Main 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., 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., 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.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.09.2020; European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd
• Subjects: Betacoronavirus - genetics; Betacoronavirus - isolation & purification; Clinical Laboratory Techniques - methods; Coronavirus Infections - diagnosis; Coronavirus Infections - epidemiology; COVID-19; COVID-19 Testing; Diagnostic Tests, Routine; Diagnostics; Group testing; Humans; Infectious diseases; Original; Pandemics; Pneumonia, Viral - diagnosis; Pneumonia, Viral - epidemiology; Reproducibility of Results; Reverse Transcriptase Polymerase Chain Reaction; RNA, Viral - genetics; RT-PCR; SARS-CoV-2; Sensitivity and Specificity; Specimen Handling; COVID-19; Infectious diseases; Diagnostics; Group testing; RT-PCR
• ISSN: 1198-743X; 1469-0691
• DOI: 10.1016/j.cmi.2020.06.009

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. 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. 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. 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.