It may stink a little more than other ways to control COVID-19, but analyzing wastewater is a cheaper, faster, and more accurate way for public health officials and researchers to detect the increase in cases. Infected people throw pieces and pieces of the SARS-CoV-2 virus into toilets and toilets; more copies of the virus found in wastewater means more people are sick. But until now, most wastewater analysis methods grouped all SARS-CoV-2 viruses as one.
Now, scientists at Scripps Research and the University of California, San Diego, in collaboration with the San Diego COVID Epidemiology and Health Research Alliance (SEARCH), have changed that. The team has reported that with just two teaspoons of dirty wastewater, they can accurately determine the genetic mix of SARS-CoV-2 variants present in a population and identify new variants of concern up to 14 days before clinical trials. traditional. In San Diego wastewater, the group detected the Omicron variant 11 days before it was first reported clinically.
Its algorithm, called “Freyja”, to identify variants of SARS-CoV-2 in wastewater, described today in Nature, has been quickly adapted by many public health laboratories and is a great help for the surveillance efforts they have. with the aim of detecting new variants of SARS-CoV-2.
“In many places, standard clinical surveillance of new variants of concern is not only slow, but has an extremely prohibitive cost,” says Kristian Andersen, PhD, Professor of Immunology and Microbiology at Scripps Research and lead author of the new work. . “But with this new tool, you can take a wastewater sample and basically outline the whole city.”
The project required close collaboration between hospitals, state and local governments, sequencing facilities, and academic scientists, including Andersen Laboratory researchers and UC San Diego microbiologist Rob Knight, PhD. Knight Laboratory deployed 131 automatic wastewater samplers to collect wastewater from 343 UCSD campus buildings and 17 public schools in 4 San Diego school districts, and acquired samples from large wastewater treatment facilities. county wastewater. For 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 are now being widely used by public health laboratories across the country and the world. The Andersen laboratory then took on the challenge of quantifying viral variants from the sequencing data.
“It’s a challenge to catch all these little bits of virus floating in wastewater and find out which ones are of different variants and what their relative abundance is,” says Scripps Research postdoctoral professor Joshua Levy, PhD, co-first author of the new article. role with Smruthi Karthikeyan of UC San Diego.
Many SARS-CoV-2 variants, including Omicron and Delta, differ in a small number of mutations. But because these changes can affect the way the virus spreads or infects people, public health officials need to keep a close eye on them. They have usually done this by sequencing patients ’virus genomes, which is a slow and costly process and has become less effective at capturing the extent and diversity of COVID-19 variants, as many people resort to testing at house.
Levy developed a library of “barcodes” that identify SARS-CoV-2 variants from short fragments of their RNA that are unique to each variant. He then coded a new computational tool that filters the mass of genetic information into wastewater to find these barcodes. It made the new Freyja program easy to use and free.
“If you’re in a lab that can already sequence a wastewater sample, you can go there; you just have to run that code and in 20 more seconds, you’re done,” he says.
When researchers applied Freyja to their wastewater samples and compared the results with clinical data collected in San Diego by SEARCH, they found that the tool detected worrying variants, such as Alpha, Delta and Omicron, in the waters. residuals up to 14 days before. was reported clinically. The Mu variant (B.1.621) was detected in UC San Diego wastewater on July 27, 2021-; four weeks before his first clinical detection on campus. And, using more recent data not included in the original study period, the team also reported that the Omicron variant could be detected at the Point Loma wastewater treatment plant, with an abundance of just over one percent of all SARS-CoV-2 viruses. in a contributing population of more than two million people-; on November 27, 2021, 11 days before its clinical detection in the city.
“Wastewater contains a massive amount of very valuable information about our health, including these viral genomes that can allow us to follow the course of a pandemic or epidemic,” Karthikeyan says.
“It took a lot of collaboration between public health and academic actors to establish this system in San Diego, and now that we’ve proven its effectiveness, we hope it inspires other localities to use these tools,” Knight adds. “We are also very excited to expand them to pathogens beyond SARS-CoV-2.”
Researchers say they continue to improve the set of tools they use to analyze viruses in wastewater, but that the current set of methods is already a leap forward from previous approaches. The same strategies could be used not only to monitor variants of SARS-CoV-2 but other human pathogens.
“When you rely on clinical sampling, not only do you introduce a lot of socioeconomic and geographic bias into who contributes to genomic surveillance data, but you also have the problem that asymptomatic people don’t get tested and those who only use domestic tests don’t contribute to the dataset, ”Levy says. “But with wastewater, we don’t have those blind spots.”
In addition to Levy, Karthikeyan, Andersen, and Knight, the study’s authors, “Wastewater Sequencing Detects Early and Cryptic Transmission of the SARS-CoV-2 Variant,” include Christine Aceves, Catelyn Anderson, Karthik Gangavarapu , Emory Hufbauer, Ezra Kurzban, Justin Lee. , Nathaniel Matteson, Edyth Parker, Sarah Perkins, Karthik Ramesh, Robles-Sikisaka Refuge, Madison Schwab, Emily Spencer, Shirlee Wohl, Laura Nicholson and Mark Zeller of Scripps Research, as well as collaborators at UC San Diego, Rady Children’s Institute for Genomic Medicine, Scripps Health, Sharp Healthcare, Helix, the San Diego County Human Services and Health Agency, the California Department of Public Health, and the Centers for Disease Control and Prevention.
Source:
Scripps Research Institute