New tool to detect Covid variants in wastewater developed

Scientists in the US have developed new tools that can identify SARS-CoV-2 variants of concern in wastewater up to 14 days before traditional clinical testing.

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

Bits and pieces of the SARS-CoV-2 virus are flushed down toilets and washed down sinks by infected individuals. More copies of the virus found in sewage mean more people are sick.

However, until now, most wastewater analysis methods lumped all SARS-CoV-2 viruses together as one.

The scientists at Scripps Research Institute and the University of California, San Diego (UCSD), US, show that with just two teaspoons of raw sewage, they can accurately determine the genetic mixture of SARS-CoV-2 variants present within a population.

In San Diego wastewater, the researchers in collaboration with the San Diego Epidemiology and Research for COVID Health (SEARCH) alliance detected the Omicron variant 11 days before it was first reported clinically.

The algorithm, ''Freyja,'' for identifying SARS-CoV-2 variants in wastewater, described in the journal Nature, has quickly been adopted by many public health labs.

''In a lot of places, standard clinical surveillance for new variants of concern is not only slow but extremely cost-prohibitive,'' said Kristian Andersen, a professor at Scripps Research, and a senior author of the new work.

''But with this new tool, you can take one wastewater sample and profile the whole city,'' Anderson said.

The project required a tight collaboration between hospitals, state and local governments, sequencing facilities, and academic scientists, including researchers in the Andersen lab and UC San Diego microbiologist Rob Knight.

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

Over nearly a year, the group analyzed more than 20,000 wastewater samples.

In the process, they developed improved methods for concentrating viral RNA in wastewater, which is now being widely used by public health labs across the country and the world.

''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 with Smruthi Karthikeyan of UC San Diego.

Levy developed a library of ''barcodes'' that identify SARS-CoV-2 variants based on short snippets of their genetic material, RNA, that are unique to each variant.

Then, he coded a new computational tool that sifts through the mass of genetic information in wastewater to find these barcodes.

''If you are 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,'' he said.

The researchers applied Freyja to their wastewater samples and compared the results to clinical data collected from around San Diego by SEARCH.

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 Mu variant was detected in UC San Diego wastewater on July 27, 2021 -- four weeks before its first clinical detection on campus.