National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel.

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.

Detection of SARS-CoV-2 variants by genomic analysis of wastewater samples in Israel.

Investigation of SARS-CoV-2 spread and identification of variants in sewers has been demonstrated to accurately detect prevalence of viral strains and is advantageous to clinical sampling in population catchment size. Herein, we utilized an established nationwide system of wastewater sampling and viral concentration approaches to perform large-scale surveillance of SARS-CoV-2 variants in nine different locations across Israel that were sampled from August 2020 to February 2021 and sequenced (n = 58). Viral sequences obtained from the wastewater samples had high coverages of the genome, and mutation analyses successfully identified the penetration of the B.1.1.7 variant into Israel in December 2020 in the central and north regions, and its spread into additional regions in January and February 2021, corresponding with clinical sampling results. Moreover, the wastewater analysis identified the B.1.1.7 variant in December 2020 in regions in which non-sufficient clinical sampling was available. Other variants of concern examined, including P.1 (Brazil/Manaus), B.1.429 (USA/California), B.1.526 (USA/New York), A.23.1 (Uganda) and B.1.525 (Unknown origin), did not show consistently elevated frequencies. This study exemplifies that surveillance by sewage is a robust approach which allows to monitor the diversity of SARS-CoV-2 strains circulating in the community. Most importantly, this approach can pre-identify the emergence of epidemiologically or clinically relevant mutations/variants, aiding in public health decision making.