Regional Replacement of SARS-CoV-2 Variant Omicron BA.1 with BA.2 as Observed through Wastewater Surveillance

Abstract

Greater knowledge of circulating SARS-CoV-2 variants can inform pandemic response, vaccine development, disease epidemiology, and use of monoclonal antibody treatments. We developed custom assays targeting characteristic mutations in SARS-CoV-2 variants Omicron BA.1 and BA.2 and confirmed their sensitivity and specificity in silico and in vitro . We then applied these assays to daily wastewater solid samples from eight publicly owned treatment works in the greater Bay Area of California, United States, over four months to obtain a spatially and temporally intensive data set. We documented regional replacement of BA.1 with BA.2 in agreement with, and ahead of, clinical sequencing data. This study highlights the utility of wastewater surveillance for real-time tracking of SARS-CoV-2 sublineage circulation. The results suggest that concerted efforts to design RT-PCR assays that target variant and variant sublineage characteristic mutations for wide-scale wastewater monitoring implementation will be informative for pandemic response.

Prevalence of Positive Rapid Antigen Tests After 7-Day Isolation Following SARS-CoV-2 Infection in College Athletes During Omicron Variant Predominance

“…Wastewater samples were used to infer the circulating variant rather than clinical samples because a large number of students in the cohort never underwent polymerase chain reaction testing, limiting the availability of samples for sequencing. However, wastewater data are specific to the university population and are likely to represent the variants in circulation well . The eFigure in the Supplement illustrates the overlap between case incidence and wastewater virus levels.…”

“…Herein we report the results of these test-out antigen tests. Campus wastewater data were used for circulating SARS-CoV-2 variant identification, using previously published methods (eMethods in the Supplement) . This study followed the reporting guideline for case series.…”

“…However, wastewater data are specific to the university population and are likely to represent the variants in circulation well. 12,18,19 The eFigure in the Supplement illustrates the overlap between case incidence and wastewater virus levels. Wastewater data were used as a surrogate for variant typing, but the efficacy of this approach with subsequent strains will need to be revisited.…”

Identifying trends in SARS-CoV-2 RNA in wastewater to infer changing COVID-19 incidence: Effect of sampling frequency

“…Data between November 15, 2020, and March 31, 2021, have been previously published by Wolfe et al [35] and are publicly available through the Stanford Digital Repository (https://doi.org/10.25740/bx987vn9177) [38]. Data between January 1, 2022, and April 12, 2022, have been previously published by Boehm et al [39] and are publicly available through the Stanford Digital Repository (https://doi.org/10.25740/cf848zx9249) [40]. The remaining data (April 1, 2021–December 31, 2021, and April 13, 2022–September 15, 2022) have not been previously published.…”

“…Moreover, we created separate heatmaps for three major COVID-19 waves that occurred during our analysis period. Here, a wave is defined as a substantial rise and eventual decline in N/PMMoV concentrations caused by one or more SARS-CoV-2 variants as described by Wolfe et al [49] and Boehm et al [39] for this wastewater treatment plant. During the analysis period, the three waves that occurred were caused by the following SARS-CoV-2 variants: Delta, BA.1 Omicron, and BA.2 + BA.4 + BA.5 Omicron.…”