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Variants of COVID found in sewage weeks before being detected in tests

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Researchers from California washed a lot of data from toilet waste. For the first time, scientists were able to detect certain variants of SARS-CoV-2 in sewage weeks before they appeared in clinics for testing.

The sewage data tracked “wave after wave of different viruses,” says Rob Knight, a microbiologist at the University of California, San Diego (UCSD) and co-author of the study, which was published in Nature July 7. Knight says the method could eventually be used to track new variants and speed public health responses. “When the next strain comes along, we’ll be ready for it.”

Research groups around the world have used sewer surveillance to track SARS-CoV-2, but these approaches usually detect only the presence and quantity of the virus. This was then used to estimate the rate of transmission in the community. But efforts to determine which variants were circulating and how common they were were hampered by poor quality data.

To overcome this, the California team developed a method that uses nanobeads to increase the amount of viral RNA that can be sequenced from a sample of sewage. Previous methods allowed scientists to sequence no more than 40% of the viral RNA in a sample, while the nanobead method allowed researchers to sequence almost 95%. The California team also developed a tool called Freyja to identify the variants present in each sample and their relative abundance.

Samples of waste water

To test their methods, the scientists spent nearly a year collecting samples from San Diego’s sewage treatment plants, which treat the wastewater of approximately 2.3 million people. Data collection began in February 2021. Over the course of 10 months, they also collected wastewater from utility vents and sewer pipes at more than 130 sites on the UCSD campus.

Researchers detected alpha and delta variants of the coronavirus in sewage two weeks before the strains were detected by swabbing and testing people in clinics. They also discovered Omicron about ten days before the first person tested positive for it in San Diego, and tracked the surge of the Omicron BA.1 variant in the population.

On the UCSD campus, researchers have consistently discovered Alpha, Delta, and a lesser-known variant, Epsilon, which was found mostly in the United States. This was surprising because there were weeks during which these variants almost disappeared from clinical observation, says co-author Joshua Levy, an applied mathematician at the Scripps Research Institute in La Jolla, California.

But it’s not yet clear whether the technique will work for tracking the fast-spreading Omicron Options BA.4 and BA.5which were difficult to distinguish from each other, says Ana Maria de Roda Husman, an infectious disease researcher at the Netherlands National Institute for Public Health and the Environment in Bilthoven.

And the prospect of an early warning system for certain variants may still be a long way off, says Fong Tai, an environmental scientist at the University of Queensland in Brisbane, Australia, given that it takes about two weeks to process the results after collection. sample. “If you want to make a tool really useful for healthcare, it has to return a result within a few days,” Ty says.

But Knight says the team has managed to reduce the time it takes to sequence samples from weeks to days, which is a “game changer”.

This article is reproduced with permission and was first published July 8, 2022

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