Tracking COVID-19 in the Environment Using Genetic Methods

Leveraging genetic methods to analyze environmental samples for SARS-CoV-2 and other novel analytes

June 9, 2021
Genetic methods for detecting microbes in environmental samples, such as water, surfaces, and air filters, are important tools for public health decision-making. Currently, genetic methods are being used to measure SARS-CoV-2, the coronavirus that causes COVID-19, in wastewater. Unfortunately, for genetic targets and other novel analytes, there are often no officially recognized standard methods or protocols that have been vetted by regulatory agencies or accreditation organizations. Without a standard method, it can be challenging to select a laboratory to analyze samples, interpret results, or compare results across laboratories.

But while there may be no standard method or laboratory accreditation for a given analytical technique, that technique can still generate valuable and defensible data. One of the strengths of monitoring using genetic methods is the ability to identify very specific targets. In many cases, developing a nationally recognized standard operating procedure (SOP) is infeasible; there are simply too many potential targets of interest, and targets may emerge quickly. For many microbial targets, it is impractical for laboratories to be accredited or evaluated method by method; instead, they must be evaluated based on their general procedures and quality assurance processes.

SARS-CoV-2 provides a timely example. There is currently no official standard method for enumerating SARS-CoV-2 in wastewater, but this information can be valuable for making quick, early decisions to protect public health. Some degree of standardization is possible because the U.S. Centers for Disease Control and Prevention (CDC) has issued guidance for monitoring. The guidance recommends using one of a short list of published primer and probe sets that target regions of specific genes, as well as procedures for sample preparation, RNA extraction, and laboratory controls. Environmental laboratories can be evaluated for their adherence to protocol, such as following in-house or external SOPs, implementing good laboratory practices (GLPs), and establishing plans for data storage and reporting. While being approved or certified for a specific genetic target has many benefits, laboratories that follow well-established SOPs and GLPs may have the ability to pivot quickly or expand capabilities without going through the rigors of accreditation for each new target that emerges, such as identifying SARS-CoV-2 variants of interest.

Users of environmental genetic data need to understand what is being measured and the limitations of the data generated. Without a consensus or standard method, a laboratory test method may use in-house SOPs that may be inconsistent with SOPs from other laboratories. Ultimately it may be difficult to compare results between laboratories, but highly useful to use results from a single laboratory—such as samples collected over time—to support overall decision-making.

How Exponent Can Help

Exponent ecological scientists and environmental engineers are experienced in the chemical, biological, and toxicological evaluation of water, air, and surface samples. We can help design scientifically defensible sampling and analysis plans; audit and select laboratories; evaluate their in-house methods and procedures; develop protocols that may allow data collected by multiple laboratories to be compared; and analyze newly and previously collected data.