One of the signs to determine if we are facing a new wave of Covid-19 has been the identification of the SAR-CoV-2 coronavirus in wastewater. The more virus in people, the more copies of the virus are found in sewage, which means more people get sick. But until now, most wastewater testing methods grouped all SARS-CoV-2 viruses together as one.
In a study published in the journal “Nature” they present a method that hardly uses two teaspoons of raw sewage to pinpoint the genetic mix of SARS-CoV-2 variants present in a population and identify new variants of concern up to 14 days before traditional clinical testing. In San Diego sewage, the group detected the Omicron variant 11 days before it was first reported clinically.
Their algorithm, called “Freyja,” for identifying SARS-CoV-2 variants in wastewater has been rapidly adapted by many public health laboratories and is a boon to surveillance efforts aimed at detecting new SARS-CoV-2 variants. CoV-2.
The group detected the Omicron variant 11 days before it was first reported clinically.
“In many places, standard clinical surveillance for new variants of is not only time-consuming but extremely expensive,” says Kristian Andersen, lead author of the new paper. “But with this new tool, from a wastewater sample you can profile the entire city.”
The project required close collaboration between hospitals, state and local governments, sequencing facilities and scientists.
Over the course of nearly a year, the group analyzed more than 20,000 water samples residuals.
During this process, researchers developed improved systems for concentrating viral RNA in wastewater, which are now being used by public health laboratories across the US and the world.
In the second phase, Andersen’s lab took on the challenge of quantifying viral variants from sequencing data.
“It’s challenging to take all these little bits of virus floating around in sewage and figure out which ones are different variants,” says Joshua Levy, co-first author of the study.
Many variants of SARS-CoV-2, including Omicron and Delta, are differentiated by a small number of mutations. But since these changes can affect how the virus spreads or infects people, public health professionals need to track them carefully.
They have typically done this by sequencing virus genomes from patients, which is a slow and expensive process and has become less effective at capturing the range and diversity of Covid-19 variants as many people turn to it. to home testing.
It’s a challenge to take all these little bits of virus floating around in sewage and figure out which ones are different variants.
Levy developed a “barcoding” library that identifies SARS-CoV-2 variants based on short snippets of their RNA, which are unique to each variant. He then coded a new computational tool that analyzes the vast amount of genetic information in wastewater to find these barcodes.
When the researchers applied Freyja to their wastewater samples and compared the results to clinical data collected by another tool, SEARCH, throughout San Diego, they found that theirs detected variants of concern, including Alpha, Delta and Omicronin the wastewater up to 14 days before.
“Wastewater contains a lot of very valuable information about our health, including these viral genomes that can allow us to track the course of a pandemic or epidemic,” the researchers conclude.