Tracking SARS-CoV-2 variants in wastewater

July 26, 2022

In short

  • A system that combined advanced sample preparation with powerful computational analysis was able to identify individual variants of SARS-CoV-2 in wastewater.
  • Using wastewater to track the emergence of new variants of concern could be faster and cheaper than clinical testing.

When infected with SARS-CoV-2, the virus that causes COVID-19, people flush the virus down the drain every time they wash their hands or go to the toilet. This can happen whether or not someone has symptoms of the disease.

Scientists tracked levels of SARS-CoV-2 in sewage to estimate whether infections are increasing or decreasing in communities. Using sewage to track viral transmission has many potential advantages over clinical testing, which is expensive and requires people to get tested.

To date, it has been difficult to obtain information on specific variants of SARS-CoV-2 from wastewater. RNA, the genetic material of the virus, is easily damaged. It is also relatively rare in water samples. This made it difficult to collect enough high-quality SARS-CoV-2 RNA from wastewater to identify variants rather than just detect the virus in general.

In a new study, a team of researchers from the University of California, San Diego (UCSD) and the Scripps Research Institute aimed to overcome these limitations. They designed a type of nanobead that efficiently binds to viral RNA in wastewater, allowing more of it to be captured intact for sequencing.

The team also developed a computer analysis tool to recognize small, distinct pieces of these sequences. It could quickly tag different viral variants in collected samples and estimate their abundance.

The researchers tested the new monitoring system between November 2020 and September 2021. They examined wastewater collected daily around the UCSD campus. They also looked at daily samples from the primary sewage treatment plant serving greater San Diego County. The results of the study, funded in part by the NIH, were published on July 7, 2022 in Nature.

Trends in wastewater samples mirrored those in clinical testing over the study period. But the sewage sampling system detected Alpha, Delta and other early variants about two weeks before they started showing up in clinical test samples. The system reported the presence of the original Omicron variant in San Diego more than a week before it was detected by clinical sampling in the community. This early detection occurred despite the fact that researchers had less than 3% of wastewater samples in the form of clinical swabs.

Sewage sampling continued to detect variants in the community weeks after they no longer showed up regularly in clinical tests. It also detected rare variants that were not often found in the clinic.

“The coronavirus will continue to spread and evolve, making it imperative for public health to detect new variants early enough to mitigate the consequences,” says UCSD’s Dr. Rob Knight, one of the lead authors of the study.

“In many places, standard clinical surveillance for new variants of concern is not only slow but extremely expensive,” adds Dr. Kristian Andersen of Scripps, who also helped lead the work. “But with this new tool, you can take a sewage sample and profile the whole city.”

—by Sharon Reynolds

Related links

References: Wastewater sequencing reveals early transmission of the cryptic variant of SARS-CoV-2. Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C , Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA , Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Ba rr ett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W , Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Nature. July 7, 2022. doi: 10.1038/s41586-022-05049-6. Online ahead of print. PMID: 35798029.

Funding: NIH National Institute of Allergy and Infectious Diseases (NIAID), National Center for Advancing Translational Sciences (NCATS), National Center for Complementary and Integrative Health (NCCIH), and Office of the Director (OD); US Centers for Disease Control and Prevention; Conrad Prebys Foundation; National Science Foundation; San Diego County Health and Human Services Agency.

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