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National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel
Authors:Itay Bar-Or  Victoria Indenbaum  Merav Weil  Michal Elul  Nofar Levi  Irina Aguvaev  Zvi Cohen  Virginia Levy  Roberto Azar  Batya Mannasse  Rachel Shirazi  Efrat Bucris  Orna Mor  Alin Sela Brown  Danit Sofer  Neta S. Zuckerman  Ella Mendelson  Oran Erster
Affiliation:1.Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.);2.Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 69978, Israel
Abstract:
In this report, we describe a national-scale monitoring of the SARS-CoV-2 (SC-2) variant dynamics in Israel, using multiple-time sampling of 13 wastewater treatment plants. We used a combination of inclusive and selective quantitative PCR assays that specifically identify variants A19/A20 or B.1.1.7 and tested each sample for the presence and relative viral RNA load of each variant. We show that between December 2020 and March 2021, a complete shift in the SC-2 variant circulation was observed, where the B.1.1.7 replaced the A19 in all examined test points. We further show that the normalized viral load (NVL) values and the average new cases per week reached a peak in January 2021 and then decreased gradually in almost all test points, in parallel with the progression of the national vaccination campaign, during February–March 2021. This study demonstrates the importance of monitoring SC-2 variant by using a combination of inclusive and selective PCR tests on a national scale through wastewater sampling, which is far more amendable for high-throughput monitoring compared with sequencing. This approach may be useful for real-time dynamics surveillance of current and future variants, such as the Omicron (BA.1, BA.2) and other variants.
Keywords:SARS-CoV-2   variant B.1.1.7 (Alpha)   RT-qPCR   wastewater surveillance   differential PCR
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