As public health officials around the world monitor the new Omicron variant, it is now more important than ever to continue investing in wastewater-based epidemiology. Our current PCR assay indiscriminately detects all known variants of COVID-19, including Omicron. Additionally, this week, we began using our viral genomic sequencing R&D platform to examine whether we can begin detecting the presence of Omicron in wastewater as the first line of defense.
The Delta Wave as Precedent
During the Delta variant wave in the United States, our partner communities witnessed increases in virus concentration in their wastewater data. Although the data did not differentiate between the Alpha or Delta variants, it provided communities an immediate indication that cases were climbing. Reported clinical cases also rose, and a fuller picture eventually appeared of the Delta variant’s high transmissibility.
You can view this trend on Biobot’s Nationwide Wastewater Monitoring dashboard:
Viral genomic sequencing to track variants
Over this past summer, Biobot partnered with the U.S. HHS and CDC to collect qPCR and viral genomic sequencing data from over 300 wastewater treatment facilities across the U.S. Over 2,500 samples representing all 50 states were sequenced through the duration of this program (mid-June to mid-August 2021) and uploaded to the NCBI SRA repository to support R&D efforts on variant detection. Our team built a bioinformatics pipeline to call variants from the sequencing data, and preliminary results demonstrate that wastewater tracks the rise of the Delta variant, and the fall of the Alpha variant. With the emergence of Omicron, sequencing data has the potential to help us understand how the new variant is spreading.
Wastewater Monitoring in South Africa and Next Steps
Now, in South Africa, wastewater virus concentration results are trending upwards. There is still much to learn about the Omicron variant. However, this increased concentration in wastewater likely indicates increased population-level transmission, as it did with the Delta variant.
Therefore, it remains critical to closely monitor wastewater data within the United States to track potential increased transmission rates due to Omicron. If your community is interested in collecting and/or sequencing wastewater samples, please contact email@example.com for more information.
Written by Biobot Analytics