Wastewater analysis tool used for early discovery of Covid-19 variants

Scientists have developed a process that allows them to identify the different varieties of Covid-19 currently circulating in an urban population by analyzing a small amount of wastewater.

Sewage testing is a cheaper, faster, and more accurate way for public health officials and researchers to detect rising cases.

Pieces of Covid-19 are flushed down toilets and sinks washed by infected individuals; more copies of the virus found in sewage means more people are sick. But until now, most wastewater analysis methods have combined all the different variants into one.

Scientists from Scripps Research and the University of California, San Diego (UCSD) have developed a method that allows them to accurately determine the genetic mix of Covid-19 variants present in a population from just two teaspoons raw sewage.

This allows them to identify new variants of concern up to 14 days before traditional clinical testing. In San Diego wastewater, the group detected the Omicron variant 11 days before it was first reported in the clinic.

Their algorithm, named “Freyja,” was quickly adapted by many public health labs and could be a boon to surveillance efforts aimed at detecting new variants.

“In many places, standard clinical surveillance for new variants of concern is not only slow but extremely expensive,” said Kristian Andersen, professor of immunology and microbiology at Scripps Research and lead author of the new work. “But with this new tool, you can take a sewage sample and profile the whole city.”

The lab deployed 131 automatic wastewater samplers to collect wastewater from 343 buildings on the UCSD campus and 17 public schools in four San Diego school districts, and acquired samples from major treatment facilities county wastewater.

For almost a year, the group analyzed more than 20,000 samples. In the process, they developed improved methods for concentrating viral RNA in wastewater that are now widely used by public health laboratories.

“It’s hard to take all these tiny bits of virus floating around in wastewater and figure out which are from different variants and what their relative abundance is,” said Scripps Research postdoctoral fellow Joshua Levy, co-first author of the new article.

Many variants of Covid-19, including Omicron and Delta, differ only in a small number of mutations. But because these changes can impact how the virus spreads or infects people, public health officials need to monitor them carefully. They usually did this by sequencing viral genomes from patients, which is a slow and expensive process.

A “barcode” library has been developed to identify Covid-19 variants based on short snippets of their RNA that are unique to each variant. A new calculator, available free of charge, then sifts through the mass of genetic information in the wastewater to find those barcodes.

“If you’re in a lab that can already sequence a wastewater sample, you’re good to go — you just run this code and in another 20 seconds you’re done,” Levy said.

When the researchers applied Freyja to their wastewater samples and compared the results to clinical data collected around San Diego, they found that the tool detected variants of concern, including Alpha, Delta and Omicron, in the sewage up to 14 days before clinical reporting. .

The researchers say they continue to improve the set of tools they use to analyze viruses in wastewater, but the current suite of methods is already a leap forward from previous approaches. The same strategies could be used not only to track Covid-19 variants, but also for other human pathogens.

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