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

Abstract

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.

Keywords: SARS-CoV-2; Sequencing; Sewage; Variants; Wastewater.

Graphical abstract

Fig. 1

Wastewater sampling locations across Israel. (A) Sampling locations across Israel. (B) Table of cities/settlements in the catchment areas of the WWTP and percentage of sampled population. *Estimated number of population in the catchment areas is calculated by flow rate for average wastewater per person. **The percentage of the catchment population from overall population in Israel; calculated using estimated catchment population divided by Israel population size (9,210,000). Total percentage of coverage of Israel population is about 50%.

Fig. 2

Mutations associated with SARS-CoV-2 VOCs identified in wastewater samples across time and regions. SARS-CoV-2 sequenced from wastewater samples in 9 different regions from August 2020–February 2021 (n = 58). Each row represents a mutation associated with a VOC: B.1.1.7 (UK), B.1.351 (South Africa), P.1 (Brazil/Manaus), B.1.429 (USA/California), B.1.525 (unknown origin), B.1.526 (USA/New York), and A.23.1 (Uganda). Scale denotes log2 frequency in the population, calculated as the % of mutated nucleotides from the total nucleotides mapped to the position.