COVID-19 variants can be found in wastewater, scientists say


PCR and rapid testing aren’t the only places where evidence of SARS-CoV-2 is showing up. The virus that causes COVID-19 is also showing up in a city’s wastewater, which has become a powerful tool during the pandemic to give scientists an early glimpse of where infections peak. Wastewater analysis often warns health officials several days before hospitals and other healthcare facilities notice an increase in symptoms and positive tests.

Now scientists have devised an even more precise way to analyze wastewater that can identify specific variants of SARS-CoV-2 in addition to the presence or absence of the virus. That could help public health experts prepare for a greater burden of COVID-19 cases and ultimately better advise communities on risks, as well as off-the-shelf tests and new treatment responses, if needed, to deal with different versions of the virus. to offer.

In a paper published in Nature on July 7, Rob Knight, director of the Center for Microbiome Innovation at the University of California, San Diego, and his team, along with scientists at Scripps Research, developed a system to determine the genetic signatures of variants and determine the relative proportion of those variant strains in the wastewater samples they tested. Identifying variants has been challenging with wastewater samples, which contain not only SARS-CoV-2, but also numerous other bacteria, viruses and pathogens. Viral concentrations are also highly diluted, as the wastewater at collection points (such as municipal waste treatment plants) comprises the wastewater of millions of people in a given area.

To improve their chances of accurately identifying SARS-CoV-2 variants, the scientists focused on nearly 20,000 samples collected daily on the UC San Diego campus from 131 sites with 360 buildings. They genetically sequenced a subset of the SARS-CoV-2 virus they found in the positive samples and compared these sequences to those of positive COVID-19 tests from campus clinics. They also compared these sequences with those collected at test sites in San Diego and with wastewater samples from San Diego County.

Thanks to those analyses, the researchers were able to use just a few spoonfuls of wastewater to determine when COVID-19 infections among the 10,000 students living on campus and the 25,000 people who spent time in the school showed an upward trend — up to 14 days before they hit the campus. the campus were tested. † Knowing where the positive samples had been collected, the team was also able to locate right into the building where the infections were spreading. Such advance warning from wastewater monitoring is helpful in containing outbreaks in an environment such as a college campus, as school officials have been able to expand testing and isolation policies to limit the spread of the virus.

With their new system for detecting variants, the researchers also found that they could pick up a wider variety of SARS-CoV-2 strains in the wastewater than sequencing positive PCR tests from the campus clinics, giving a more accurate picture of the diversity of tribes circulating in a community such as a university campus. Their tool essentially created a genetic barcode of mutations unique to specific variants, which then allowed the scientists to determine what proportion of the virus in a wastewater sample contained specific barcodes for the different variants. They collected samples from November 2020 to September 2021 and were able to detect and determine the proportions of the main variants circulating at the time, including Alpha, Delta and Epsilon.

To track Omicron, which began spreading in the US in late 2021, the team also collected data through February 2022 and documented the rapid replacement of Delta with Omicron in their samples. Working with samples from the Point Loma wastewater treatment plant, near the UC San Diego campus, they were also able to detect Omicron on Nov. 27; the first clinical identification of Omicron from on-campus testing came only 10 days later, on Dec. 8.

The power of wastewater monitoring has not been lost to public health officials. The U.S. Centers for Disease Control and Prevention launched a national wastewater monitoring program in 2020, which tracks virus loads in wastewater across the country and provides that data to the public. In addition to alerting health officials to spikes in cases and the emergence of new variants faster than testing can, wastewater also has the advantage of being an unbiased measure of virus levels in a given community, as waste is universal. Testing can reflect bias based on the populations being tested or accessing health systems when people feel symptoms. Testing also misses some infections because some people who are infected but develop no symptoms usually don’t get tested.

“Wastewater is an information-rich resource for estimating the prevalence of specific viral lineages, providing a community-wide snapshot of not only overall infection dynamics, but also the rise and fall of specific variants of concern,” the authors write, describing their findings. “As SARS-CoV-2 continues to develop, the risk of new variants of concern remains high…[and] Developing technologies that are cost-effective, reduce bias, and provide leading rather than lagging indicators of infection is essential to removing ‘blind spots’ in our understanding of local virus dynamics.”

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