Researchers in California have cleaned up a ton of data from toilet litter. For the first time, scientists were able to detect a specific variant of SARS-CoV-2 in sewage before it showed up in testing clinics.
The wastewater data tracked “waves of different viruses,” said Rob Knight, a microbiologist at the University of California, San Diego (UCSD) and co-author of the study, which was published in nature July 7th. Knight said the technology could eventually be used to track emerging variants and speed up the public health response. “When the next pressure comes, we’ll be ready.”
Research groups around the world have used Sewage monitoring SARS-CoV-2 was tracked, but these methods usually only detect the presence and quantity of the virus. It is then used to estimate the amount of transmission in the community. But efforts to determine which variants are circulating and how prevalent they are have been plagued by low-quality data.
To overcome this problem, the California team developed a method that uses nanobeads to increase the amount of viral RNA that can be sequenced from wastewater samples. Whereas previous technologies allowed scientists to sequence no more than 40 percent of the viral RNA in a sample, the nanobead approach allowed researchers to sequence nearly 95 percent of the viral RNA. The California team also developed a tool called Freyja to identify the variants present in each sample and their relative abundance.
To test their method, the scientists spent nearly a year collecting samples from a wastewater treatment plant in San Diego, which treats wastewater from about 2.3 million people. Data collection began in February 2021. They also collected wastewater from maintenance holes and sewers at more than 130 locations on the UCSD campus over a 10-month period.
Researchers detected alpha and delta variants of the coronavirus in wastewater for up to two weeks before swabbing and testing people in clinics. They also detected Omicron about ten days before the first person in San Diego tested positive, and tracked the surge of Omicron BA.1 variants in the population.
On the UC San Diego campus, researchers consistently detected Alpha, Delta, and a lesser-known variant, Epsilon, found mostly in the United States. This was surprising because within a few weeks the variants all but disappeared from clinical surveillance, said co-author Joshua Levy, an applied mathematician at the Scripps Research Institute in La Jolla, California.
But it’s unclear whether the technology could be used to track the fast-spreading Omicron BA.4 and BA.5 variantsThey are difficult to distinguish from each other, said Ana Maria de Roda Husman, an infectious disease researcher at the Netherlands National Institute for Public Health and the Environment in Biltofen.
Given that it takes nearly two weeks to collect post-processing results, the prospect of a variant-specific early warning system may be a while away, said Phong Thai, an environmental scientist at the University of Queensland in Brisbane, Australia. a sample. “If you want a tool to be really useful for public health, it has to return results within a few days,” Thai said.
But Knight said the team has managed to reduce the time it takes to sequence a sample from weeks to days, which is a “game changer.”
This article is reproduced with permission, first published July 8, 2022.