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. 2022 Jun 14;9(6):575-580.
doi: 10.1021/acs.estlett.2c00266. Epub 2022 May 26.

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

Alexandria B Boehm  1 , Bridgette Hughes  2 , Marlene K Wolfe  3 , Bradley J White  2 , Dorothea Duong  2 , Vikram Chan-Herur  2
Affiliations

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

Alexandria B Boehm et al. Environ Sci Technol Lett. .

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.

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Conflict of interest statement

The authors declare the following competing financial interest(s): B.H., D.D., V.C.-H., and B.J.W. are employees of Verily Life Sciences.

Figures

Figure 1
Figure 1
Concentrations of N, del143–145, LPPA24S, and S:477–505 at eight POTWs in the study (name indicated in corner). Error bars are 68% confidence intervals that include error from variation among 10 replicate wells and Poisson error (“total error” as reported by the instrument). If error bars cannot be seen, they are smaller than the symbol. Asterisks near the x-axis indicate samples that are nondetects for the associated target as indicated by the color.
Figure 2
Figure 2
Relative concentrations of del143–145 and LPPA24S (their concentrations normalized by the N gene) at eight POTWs in the study (name indicated in corner). Markers are raw ratio values. Lines represent 5-day trimmed moving averages.
Figure 3
Figure 3
Percentage of clinical cases in California classified as indicated BA.1* and BA.2* as a function of specimen collection date; data represent 7-day moving average as acquired from GISAID. Data available through 13 April when downloaded from GISAID on 21 April 2022. Gray area represents the time period for which data were incomplete on 14 April 2022, when wastewater measurements for the last date in our data series (12 or 13 April 2022) were available.
See this image and copyright information in PMC

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