California researchers have extracted a wealth of data from toilet waste. For the first time, scientists were able to detect specific variants of SARS-CoV-2 in wastewater weeks before they appeared in testing clinics.
The wastewater 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.1which was published in Nature July 7. Knight says the technique could eventually be used to track emerging variants and accelerate public health response. “When the next strain comes, we’ll be ready for it.”
Research groups around the world have used sewage monitoring to track SARS-CoV-2, but these approaches typically only detect the presence and amount of the virus. This was then used to estimate the amount of transmission in a community. But efforts to identify circulating variants and their prevalence have been undermined 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 wastewater sample. Previous techniques allowed scientists to sequence no more than 40% of the viral RNA in a sample, whereas the nanobead method allowed researchers to sequence nearly 95%. The Californian team also developed a tool, called Freyja, to identify the variants present in each sample, and their relative abundance.
To test their methods, the scientists spent nearly a year collecting samples from a San Diego sewage treatment plant that treats sewage from about 2.3 million people. Data collection began in February 2021. They also collected wastewater from maintenance holes and sewer lines at over 130 sites on the UCSD campus for 10 months.
Researchers detected Alpha and Delta variants of the coronavirus in sewage up to two weeks before the strains were detected by swabbing and testing people at clinics. They also detected Omicron about ten days before the first person tested positive in San Diego, and traced the rise of the BA.1 variant of Omicron in the population.
On the UCSD campus, researchers consistently detected Alpha, Delta, and another lesser-known variant, Epsilon, which was found primarily in the United States. This was surprising because there were weeks in which these variants nearly disappeared from clinical surveillance, 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 to track the fast-spreading Omicron BA.4 and BA.5 variants, which have been difficult to tell apart from each other, says infectious disease researcher Ana Maria de Roda Husman. at the Dutch National Institute for Public Health and the Environment in Bilthoven.And t
he prospect of an early warning system for specific variants could still be a long way off, says Phong Thai, an environmental scientist at the University of Queensland in Brisbane, Australia, given that it takes nearly two weeks to process results after sample collection. “If you want to create a tool that’s really useful for public health, it has to come back in days,” says Thai.
But Knight says the team was able to shorten the time it takes to sequence samples from weeks to days, which is a game-changer.