Wastewater for public health: timely, sensitive, and reliable SARS-CoV-2 omicron variant monitoring in California

Abstract

The SARS-CoV-2 Omicron (BA.1/BA.1.1) variant was declared a variant of concern (VOC) on November 26, 2021 and rapidly became the dominant lineage globally. Monitoring for VOCs is a public health priority, but standard case-based surveillance requires a robust, local whole genome sequencing (WGS) network and results may take weeks. Wastewater monitoring of VOCs is appealing as a potentially sensitive and timely approach to VOC monitoring that could provide complementary information to case-based WGS and a more complete picture of VOC circulation. However, wastewater VOC monitoring through PCR assays and WGS each have unique advantages and disadvantages that are not well characterized. The California Department of Public Health collaborated with academic partners to conduct wastewater VOC monitoring during the emergence of Omicron BA.1./BA.1.1 in late 2021. Wastewater monitoring was conducted via RT-PCR assays targeting specific mutations and via wastewater sequencing. Wastewater data was analyzed within the context of case-based WGS data to track the emergence of Omicron in California. In most locations across California, wastewater PCR provided early identification of the emergence and subsequent dominance of Omicron BA.1./BA.1.1. These results were then corroborated and confirmed as case-based WGS results became available. These data helped guide real-time public health response during the Omicron surge. Wastewater monitoring of VOC's provides a timely, accurate, and sensitive methodology for VOC monitoring. Successful implementation of wastewater VOC monitoring requires wastewater surveillance infrastructure as well as ongoing investment and research to support the development and deployment of assays and sequencing methodologies for emerging variants.