COVID-19 Variants Can Be Found in Wastewater, Scientists Say

PCR and rapid tests aren’t the only places where evidence of SARS-CoV-2 shows up. The virus that causes COVID-19 also turns up in a city’s wastewater, which has become a powerful tool during the pandemic to give scientists early glimpses into where infections are peaking. Health officials are often notified by wastewater analysis of an upsurge in infection days before other facilities notice increases in symptoms or positive tests.

Scientists have now developed a more accurate way to test wastewater for SARS-CoV-2 variants. They can also identify the presence and absence of the virus. This could allow public health professionals to prepare for increased COVID-19 case loads and better inform communities about the risk. They can also provide ready testing, new treatment options, and other information if necessary, in order to face different variants of the virus.

A paper was published in NatureRob Knight (director of the Center for Microbiome Innovation, University of California San Diego) and his team developed, with Scripps Research scientists, a method for identifying variant genetic signatures and determining their relative percentage in wastewater samples. It has proved difficult to identify variants in wastewater samples that contain SARS-CoV-2, as well as other pathogens, bacteria and viruses. Because the waste from thousands of people is collected at the collection site (like municipal wastewater treatment facilities), the virus concentrations can be very low.

Scientists focused their attention on almost 20,000 samples taken daily at UC San Diego from 131 different locations. These samples covered 360 buildings to increase the likelihood of correctly identifying SARS/CoV-2 variants. The scientists genetically sequenced the SARS-CoV-2 viruses found in positive samples. They compared their sequences with those obtained from COVID-19 positive tests at campus clinics. The sequences were also compared with those from San Diego County wastewater sampling sites and the ones collected at testing sites.

Those analyses allowed the researchers to determine, with just a few spoonfuls of wastewater, when COVID-19 infections among the 10,000 students living on campus and the 25,000 people spending time at the school trended upward—up to 14 days before testing on campus documented them. They knew exactly where they had collected the samples and could pinpoint where there was infection. This advance notice from wastewater surveillance can be helpful in controlling outbreaks on a campus like a university. School officials were able increase testing and to establish isolation policies in order to reduce spread.

Researchers also discovered that the new method for finding variants allowed them to detect more SARS strains in wastewater than they were able to sequence positive PCR test results at campus clinics. Thus, it is possible to get a much better idea of the strains that are circulating on a campus. The tool created a unique genetic barcode that identified specific mutations. This allowed scientists to determine the percentage of virus present in wastewater samples. From November 2020 through September 2021, they collected samples and were able detect and quantify the main variants that circulated at the time.

Omicron began to spread across the U.S. around the end of 2021. To monitor the outbreak, Omicron collected data up through February 2022. This allowed the team to document the swift replacement by Omicron of Delta 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 November 27; the first clinical identification of Omicron from tests on the school’s campus didn’t come until 10 days later, on December 8.

The power of wastewater surveillance hasn’t been lost on public health officials. In 2020, the U.S. Centers for Disease Control and Prevention established a National Wastewater Surveillance Program. This program monitors virus levels in waterways throughout the nation and makes that information available to the general public. Not only does it alert health officials to cases spikes and the rapid emergence of new variants, but wastewater has the added advantage of providing an objective measure of viruses in a community since it is universal. It is possible for testing to reflect biases that are based on who gets tested, or who has access to the health system when symptoms occur. Testing also misses some infections, since some people who are infected but don’t develop symptoms usually don’t get tested.

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

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