As SARS-CoV-2 was spreading through his home country of China early this year, biomedical engineer Zhugen Yang realized that his expertise in both sensory technology and wastewater monitoring could be the perfect combination for helping to track COVID-19 outbreaks. Yang had previously created field-ready diagnostic assays for pathogens in bodily fluids (cow and human). He had also helped develop sensors for monitoring wastewater—initially for cocaine and methamphetamine, and then for sequences of human mitochondrial DNA, which can serve as biomarkers for various cancers. Now at Cranfield University in the UK, Yang decided he would develop an easy-to-use, low-cost test to check for the presence of SARS-CoV-2 at wastewater treatment plants.
In recent months, wastewater epidemiology—specifically, the idea of looking to sewage to detect and quantify infections in local populations—has become a popular approach for tracking the pandemic. Several studies suggest that SARS-CoV-2, while rarely released in urine, is shed in the stool of about one-third to one-half of infected individuals, particularly during the first few days of infection, says Mariana Matus, CEO and cofounder of Biobot, a Boston-based company focused on wastewater epidemiology that has begun testing samples weekly from hundreds of wastewater treatment plants across the US for SARS-CoV-2 RNA. Several countries are now organizing widespread screening programs for traces of SARS-CoV-2 RNA.
We don’t see them necessarily as a replacement of the laboratory work.—Mariana Matus, Biobot
Existing methods involve sending samples to labs, where trained researchers perform the gold-standard technique, the resource- and time-intensive method of quantitative PCR (qPCR), to detect the virus’s genetic material. Yang set his sights on something simpler. His approach, described in an opinion in Environmental Science & Technology in March, should be able to yield a sample within an hour without any power or advanced facilities, he says.
The assay Yang envisions, an adaptation of one he and colleagues developed a couple of years ago for identifying sexually transmitted bovine pathogens in cow semen, will involve several steps. First, a user would run a wastewater sample through a filter to remove large particles, before pipetting or dropping the water onto a membrane that retains anything bigger than 50 nanometers across—including SARS-CoV-2, which has a diameter of at least that.
The user then adds chemicals to release nucleic acids harbored within viruses and organisms on the membrane and transfers the resulting solution to a folding, paper-based device that absorbs those nucleic acids thanks to embedded glass fibers, which generate an electrostatic pull. Finally, the user rinses the genetic material from the paper into a small plastic chamber and adds reagents to amplify SARS-CoV-2’s RNA. If the virus is present, amplification of those sequences triggers a reaction that causes a color change visible on the outside of the plastic chamber.
Such a test would give workers at wastewater treatment plants the ability to perform the tests onsite, and so avoids the need for cold storage and shipment of the samples, as well as the inherent delays in such a process. Yang’s not the only one interested in such an approach. Matus says her company is working with several partners to see if sensors for SARS-CoV-2 that were first developed for clinical COVID-19 testing could work for monitoring sewage for signs of the virus.
“Given the huge demand for analyzing wastewater, we’re beginning to explore how the technology can be used in that context,” says Matus. For the traditional qPCR testing Biobot is currently using, the turnaround time is typically about three days, she says. “The opportunity that I see with rapid testing, paper-based strips or other [technologies], is . . . almost like a prescreening of the wastewater samples. We don’t see them necessarily as a replacement of the laboratory work, but used in combination, it can provide a more holistic service for a treatment plan, because now [wastewater treatment plants] will be in control of testing, ideally every day.”
Pilar Domingo-Calap, a virologist at the University of Valencia in Spain, raises concerns about the sensitivity of an onsite testing protocol, particularly one that lacks a robust filtration step to remove bacteria and other biological material from the wastewater sample before analysis of the genetic material it contains. She says she wonders if such a test would be able to pick up trace amounts of viral RNA amongst the loads of other biological material in wastewater. For her and her colleagues, who are currently analyzing wastewater samples from more than 20 Spanish towns, sensitivity of the test will be critical. Right now, she notes, because only a small fraction of Spain’s population has been infected with SARS-CoV-2, “you need a big city with lots of people to really know what is happening” based on samples of sewage.
Matus doesn’t share Domingo-Calap’s concerns about the lack of filtration, however. “Detection can still happen in the absence of filtration,” she says, but adds that “it will be interesting to understand how to boost detection in that very raw sample. . . . That’s our main concern with the technology: sensitivity.”
Matus notes that the inclusion of an amplification test in Yang’s proposed protocol could help address the problem. Typically, she says, paper-based tests do not amplify genetic material, but rather have antibodies that bind to a particular target. “If [Yang’s assay] could overcome sensitivity issues that are observed with antibody-based rapid tests, then this would be a game changer,” Matus says.
Yang is still in the early stages of developing the wastewater test, however. His university was shut down from mid-March until early June, during which time he focused on making the necessary preparations to hit the ground running when he and his team did get back into the lab. This included the in silico development of the primers that amplify SARS-CoV-2 RNA, purchasing necessary reagents, and lining up collaborators and funding.
He is now working with a local water company that will send samples to him to test in the lab and eventually will allow him to test the assay onsite. Yang says he hopes to have optimized the test enough to begin validation experiments on wastewater samples within a couple of months, and to send his kits for testing at the wastewater company three to four months after that. “The progress is a bit slow,” he admits, but “we are now in a very positive way ready to start this experiment.”
This story is part of a series by The Scientist on how researchers around the world are pitching in to aid the effort against COVID-19.
Click through to find out about more projects that research teams in other countries are working on.