Wastewater testing is a longstanding method of detecting community pathogen spread. The COVID-19 pandemic and the rise of other, more complex pathogens have increased the use of this testing. Particularly, public health entities have used next-generation sequencing to monitor the spread and evolution of SARS-CoV-2 and monkeypox. When implemented correctly, it is an effective way to detect community spread early in symptomatic and asymptomatic people, without relying on individual diagnostic testing.
Implementing this technology for public health purposes involves many challenges, including:
- Budget constraints of local health organizations
- Expert analysis required to interpret results
- Non-standard sampling practices
- Limited RNA content and a mixture of genetic material in samples
IDT and Psomagen worked with University of Nebraska Medical Center Professor Mike Wiley, Ph.D., to verify an assay for viral wastewater surveillance that would mitigate these issues. They developed a novel amplicon panel with overlapping primers. This design helps with novel variant detection when mutations would otherwise cause primer dropout.
Eight wastewater samples were used to test this new amplicon panel against the performance of two ARTIC primer sets. Total RNA was extracted from each of the wastewater samples to create NGS libraries using the amplicon panels, then sequenced using Illumina NGS technologies.
The xGen SARS-CoV-2 Amplicon Panel ultimately had higher base coverage and less variance across samples. The IDT design successfully confirmed lineage in 88% of samples, compared to 38% for each of the ARTIC primer sets. This solution provides a timely, cost-effective method of wastewater surveillance.
Psomagen is a member of the IDT Align Preferred Provider Program. The company is a CLIA-certified, CAP-accredited multiomics services provider. They have four locations in the United States and several worldwide under their parent company, Macrogen.
Integrated DNA Technologies (IDT) is a genomics company supporting life sciences research. They develop tools and solutions for academic and clinical research, agriculture, medical diagnostics, pharmaceuticals, and synthetic biology.
Mike Wiley, Ph.D. is an assistant professor at the University of Nebraska Medical Center. His research focuses on public health issues, particularly the use of next-generation sequencing technology for the detection of pathogens.