The promise of COVID-19 surveillance through wastewater testing

I believe public health and safety organisations, life sciences companies, and researchers need to work together to build a framework that standardises the sampling frequency, testing method, data interpretation, and ways to promote data sharing without oversharing privacy data.

Q: How does wastewater testing work generally and what are some of the advantages in applying it to COVID-19? What kinds of insights does it provide researchers and public health officials?

A: When people are infected with a virus, they shed viral RNA or DNA fragments in their stools, even when they don’t have symptoms; from a public health perspective, this phenomenon has a lot of promise for viral surveillance. The monitoring of viral RNA levels in wastewater can help model pandemic progression, including COVID-19, and also allows researchers to spot trends of infection within a population. An important application lies in its potential as an early warning response system for outbreak detection, especially for future pandemics. One clear benefit of the method, also known as sewer sample surveillance, is that it allows for mass testing at a lower cost than conventional, individualised testing.  

From a lab perspective, it works like this: after a sample is collected and delivered to the lab, it is concentrated, using ultracentrifugation, ultrafiltration, or precipitation. After concentration, the RNA is extracted from the concentrated sample, and it can then be detected in one of two ways: cell culture methods (i.e., applying the concentrated water sample to mammalian cells grown in a lab, and observing for plaques) and molecular methods—target detection of RNA with RT-PCR or RT-ddPCR. 

Q: What areas and organizations are making the most use of wastewater testing? What are some of the challenges in detecting the SARS-CoV-2 genome or fragments in wastewater? 

A: Wastewater surveillance data can help state, tribal, local, and territorial health departments detect, understand, and respond to a pandemic. Public health departments in a number of locations globally have begun making use of wastewater testing, including The Netherlands, Australia, Canada, Spain, and the U.S., among others. Again, what’s promising about wastewater surveillance is that it can provide an early indicator of the presence of, or trends in, cases in a community. But the size of the community may be different depending on the level of public health organisation that’s doing the surveillance. Collection methods vary, from using a container to collect sewer water at a particular time point to using an absorbent material to capture a sampling over a period of several days.

From a lab perspective, there are a number of challenges in testing wastewater. For instance, the organic matter and chemicals added during concentration, in particular precipitation, can inhibit RNA extraction and PCR, which leads to unreliable results. Samples may also contain particles and require cleanup. There is limited data on whether the virus remains infective in untreated wastewater samples (with RT-PCR, it would normally be pasteurised for virus inactivation). Finally, as of now, there is no standardised testing protocol for monitoring viral RNA in wastewater. Researchers have been especially interested in arriving at more automated methods, especially for extraction, while increasing reproducibility and reducing variability.

Q: What has your own research found in terms of promising lab workflows? 

Sample concentration increases the SARS-CoV-2 RNA detection sensitivity, especially for the untreated wastewater samples.

A: As a genomic solutions provider, my team and I have been looking for ways to streamline wastewater surveillance workflows for researchers. We have mainly focused on sample concentration and RNA extraction. Sample concentration increases the SARS-CoV-2 RNA detection sensitivity, especially for the untreated wastewater samples. Recently, we have worked on an ultracentrifugation platform for wastewater sample concentration that takes about two hours to concentrate a 50-mL sample input. It significantly decreases the processing time compared to polyethylene glycol (PEG) precipitation or filtration, which can take up to overnight to complete, so it’s a huge time saver. 

The other area of research for me and my colleagues is the critical RNA extraction step in isolating SARS-CoV-2 viral RNA from the sample. Wastewater is a complex mixture and contains a lot of inhibitors that could negatively affect the sensitivity of the assay. So the RNA extracted from this type of sample needs to be clean and have high purity. In one study, we looked at a new type of extraction kit that’s suitable for experimental samples and compatible with different wastewater concentration methods.¹ It uses bead-based extraction chemistry, meaning that the RNA is immobilized in the magnetic field while the sample gets washed. We were excited to find that it led to high RNA recovery with minimum PCR inhibitors left in the final RNA elutes—compared to other extraction methods, it provided comparable or higher recovery rates. Perhaps best of all, the extraction workflow was compatible with automation (cutting hands-on time by up to half for certain experiments), which is going to be a key requirement in applying wastewater testing more broadly in the future. 

Q: How should wastewater testing be used to prepare for future pandemics? Are there steps that governments, local organizations, and life sciences companies should take now? 

A: Wastewater surveillance offers a cost-effective method to monitor population disease and health status in a way that’s just not possible with individual testing. During the current pandemic, wastewater surveillance helped closed some Covid-19 testing gaps in areas where it was utilised. To leverage the wastewater surveillance effect and be prepared for the future, I believe public health and safety organisations, life sciences companies, and researchers need to work together to build a framework that standardises the sampling frequency, testing method, data interpretation, and ways to promote data sharing without oversharing privacy data. This will allow us to have more sophisticated monitoring systems set up and ready to go and be better equipped to handle future pandemics.   

Author: Dr Han Wei is Market Development Scientist at Beckman Coulter Life Sciences 

Reference:

1. Fitzgerald S, Corbishley A, Andrews T, Mahuzier P-E, Wei H. Infectious disease-based pandemic monitoring using distributed sewer water samples. Poster presented at: AGBT; March 1-3,2021 Virtual.