Combining community wastewater genomic surveillance with state clinical surveillance: A framework for SARS-CoV-2 public health practice
Authors: Smith Ted , Holm Rochelle H. , Yeager Ray , Moore Joseph B. , Rouchka Eric C. , Sokoloski Kevin J. , Talley Daymond , Arora Vaneet , Moyer Sarah , Bhatnagar Aruni 
Published: December 2021

Study objective

To garner a framework for combining community wastewater surveillance with state clinical surveillance that influence confirmation of SARS-CoV-2 variants within the community, and recommend how the flow of such research evidence could be expanded and employed for public health response.

Design, setting, and participants

This work involved analyzing wastewater samples collected weekly from 17 geographically resolved locations in Louisville/Jefferson County, Kentucky from February 10 to November 29, 2021. Genomic surveillance and RT-qPCR platforms were used as screening to identify SARS-CoV-2 in wastewater, and state clinical surveillance was used for confirmation.

Main results

The results demonstrate increased epidemiological value of combining community wastewater genomic surveillance and RT-qPCR with conventional case auditing methods. The spatial scale and temporal frequency of wastewater sampling provides promising sensitivity and specificity to be useful to gain public health screening insights about community emergence, seeding, and spread.

Conclusions

Better national surveillance systems are needed for future pathogens and variants, and wastewater-based genomic surveillance represents opportune coupling. This paper presents current evidence that complementary wastewater and clinical testing is enhanced cost-effectively when linked; making a strong case for a joint public health framework. The findings suggest significant potential for rapid progress to be made in extending this work to consider pathogens of interest as a whole within wastewater, which could be examined in either a targeted fashion as we currently do with SARS-CoV-2 or in terms of a global monitoring of all pathogens found, and developing evidence based public health practice to best support community health.

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What is already known on this subject?

The primary approach for the genomic surveillance of SARS-CoV-2 relies on the sequencing of clinical COVID-19 samples. Variants of SARS-CoV-2 can also be tracked in community wastewater.

What this study adds?

We propose that, for comprehensive community surveillance, the first line of community pathogen screening should involve geographically-resolved wastewater samples collected at a regular frequency and employ both Next Generation Sequencing (NGS) and RT-qPCR. These results could then be compared with state clinical surveillance. This framework is a more comprehensive and cost-effective approach for surveillance in practice to catch community emergence, seeding, and spread.

Policy implications

Our results present a framework that could support the implementation of better surveillance policies directed to solve future community pathogen and variant detection. We anticipate this work can help public health officials implement rational community sampling schemes and develop sensible coordination with other clinical surveillance. The utility of this for COVID-19 extends to many other infectious disease models and other public health hazards such as toxic exposures.