Discussion
Our results show that the HV69–70 and Del156–157/R158G mutation assays as used for wastewater settled solids were sensitive and specific. By using these PCR mutation assays, we found strong correlation between wastewater estimates and case isolate sequencing–derived estimates of circulating Alpha and Delta in 2 large metropolitan communities in California, USA. Mutations were detected in wastewater samples collected 1–3 weeks earlier than when Alpha and Delta variant estimates generated by case-isolate sequencing were available and reliable. Targeted mutation assays applied to SARS-CoV-2 RNA extracted from wastewater solids can be a rapid, efficient, and reliable way to monitor VOCs introduced to and circulating in a community. Monitoring for VOCs using wastewater may provide earlier complementary surveillance data than from case isolate sequencing data, if mutation assays are or can be developed for new and existing VOCs and put into use in a timely manner.
Use of PCRs targeting characteristic mutations thought to be particular to a SARS-CoV-2 variant may concurrently detect other SARS-CoV-2 strains that carry the same mutations. Targeting a single mutation in wastewater, as was done in our study for Alpha, carries an increased potential risk for mischaracterization. For example, on September 8, 2021, according to GISAID (https://www.gisaid.org
