There’s a faster way to detect new COVID variants: testing sewage

BERKELEY, Calif. — The devastating spread of COVID-19’s Delta variant kept America and much of the world still on edge over the summer. There’s been talk that other mutations, including the Lambda and Mu variants, are already on the radars of health officials. So what’s the best way to keep track of the spread of these new COVID variants? According to one recent study, COVID mutations could be detected faster — by testing sewage.

The discovery means that scientists can catch COVID variants without the need to screen people individually. Instead, researchers can find viruses by sampling the wastewater from toilets across large areas, says a team of microbiologists at the University of California at Berkeley.

“SARS CoV-2 virus is excreted by individuals that are infected by COVID-19 and the fecal waste ends up in the wastewater systems. By sampling wastewater, we can get information on infections for a whole population,” explains pofessor Kara Nelson, who led the investigation, in a statement. “Some wastewater systems serve several thousand people. Some serve hundreds of thousands of people. Sampling wastewater is a very efficient way to get information. It is also a less biased source of information, because we can get information from all individuals in the sewershed, whether or not they are being tested in a clinic. We know that there are individuals that have asymptomatic infections that may never get tested.

“When you are sampling the wastewater, you get a more comprehensive and less biased data on your population,” she adds. “It appears that we might be able to get an earlier signal in the wastewater if a new variant shows up compared to only relying on the sequencing of clinical samples. Just knowing that SARS-CoV-2 is present in a population is the first step in providing information to help control the spread of the virus, but knowing which variants are present provides additional but very useful information.”

Dr. Nelson and her team developed a new approach to analyzing the genetic makeup of new COVID mutations. Like a needle in a haystack, researchers have struggled to spot COVID variants among billions of bacteria and other viruses in the sewage. By using new techniques to enrich the virus’ RNA, they can make it easier to find.

Scientists can then “sequence” the virus’ genes, meaning they map out its make-up to see how it is unique. Using a completely new method, created by the UC team, they can look so closely at viruses they can see single nucleotides — the molecules RNA and DNA are made of.

“The way that we need to process the sequence information is complex. One contribution of this paper is the ability to prepare samples for sequencing from wastewater,” says Dr. Nelson. “Instead of directly sequencing everything present, we used an enrichment approach where you first try to enrich the RNA that you are interested in. Then we developed a novel bioinformatic analysis approach, which was sensitive enough to detect a single nucleotide difference. You can’t get any more sensitive than that.”

The findings are published in the journal mBio.

SWNS writer William Janes contributed to this report.