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Wastewater provides early detection of Covid-19 surges

Wastewater sequencing can provide dramatic new insights into levels and variants of SARS-CoV-2 in various communities, which can help scientist detect in advance Covid-19 surges, as well as the emergence of new coronavirus variants. This is the conclusion of a new study led by the University of California, San Diego and Scripps Research.

According to the experts, this method is a scalable, cheaper, and faster way for communities and regions to detect the coronavirus and take appropriate actions to curb its transmission.

“The coronavirus will continue to spread and evolve, which makes it imperative for public health that we detect new variants early enough to mitigate consequences,” said study co-senior author Rob Knight, a professor of Pediatrics, Bioengineering, and Computer Science at UC San Diego.

“Before wastewater sequencing, the only way to do this was through clinical testing, which is not feasible at large scale, especially in areas with limited resources, public participation, or the capacity to do sufficient testing and sequencing. We’ve shown that wastewater sequencing can successfully track regional infection dynamics with fewer limitations and biases than clinical testing to the benefit of almost any community.” 

In the summer of 2020, Professor Knight and his colleagues began robotic sampling of wastewater on the UC San Diego campus, as part of the Return to Learn effort – an initiative aiming to bring student safely back on campus. This program has been a success, and managed to keep levels of coronavirus transmission on campus lower than in the surrounding communities. 

In March 2021, wastewater surveillance went regional, with several samples collected each week from San Diego county’s main wastewater treatment plant at Point Loma. Later that year, working with county, state, and federal public health agencies, the scientists started to issue warnings when viral loads in regional wastewater exceeded certain levels, which usually signaled a corresponding spike in Covid-19 cases one or two weeks later.

“The idea is to put everybody on alert that a surge is coming, and act accordingly: Get vaccinated if you’re not vaccinated. Get boosted. Wear a mask. Think twice about attending large indoor gatherings,” said Professor Knight. “It’s a chance to avoid a surge that translates into more patients in hospitals and morgues.”

Moreover, study co-lead author Joshua Levy, a postdoctoral fellow at Scripps Research, developed a new library of “barcodes” to identify coronavirus variants based on short snippets of viral RNA that are unique to each variant, and created a new computational tool that could sift through the genetic information in wastewater to find these barcodes.

These methods turned out to be extremely useful for detecting new Covid-19 spikes in advance and clarifying which variants are the most dominant in specific regions. In the future, they could be employed to help public health authorities cope with a range of different pathogens, and better respond to possible outbreaks.

“We know that other pathogens, ranging from influenza to monkeypox, can be detected in wastewater. Working with county, state and national public health organizations to expand this system beyond SARS-CoV-2 will revolutionize our ability to respond not just to this pandemic, but to future ones,” Professor Knight concluded.

The study is published in the journal Nature.

By Andrei Ionescu, Staff Writer  

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