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

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

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

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

Their algorithm, named 'Freyja', has quickly been adapted by many public health labs, and could be a boon to surveillance efforts that aim to detect new variants. 

“In a lot of places, standard clinical surveillance for new variants of concern is not only slow but extremely cost-prohibitive,” said Kristian Andersen, professor of immunology and microbiology at Scripps Research and a senior author of the new work. “But with this new tool, you can take one wastewater sample and basically profile the whole city.” 

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

Over the course of nearly a year, the group analysed more than 20,000 samples. In the process, they developed improved methods for concentrating viral RNA in wastewater that are now being widely used by public health labs.

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

Many Covid-19 variants, including Omicron and Delta, differ by just a small number of mutations. But since these changes can impact how the virus spreads or infects people, public health officials must carefully track them. They have typically done this by sequencing virus genomes from patients, which is a slow and costly process.

A library of 'barcodes' was developed that identify Covid-19 variants based on short snippets of their RNA that are unique to each variant. A new computational tool, which has been made freely available, then sifts through the mass of genetic information in wastewater to find these 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 from around San Diego, they discovered that the tool detected variants of concern, including Alpha, Delta and Omicron, in wastewater up to 14 days before it was reported clinically.

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