Before appearing in tests, COVID variants were found in sewage weeks.


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California researchers have discovered a wealth in toilet waste data. Scientists have detected specific variants SARS-CoV-2 in sewage, weeks before they showed up 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, which was published in NatureJuly 7, 2007. Knight said that the technique could one day be used to detect new strains and increase public-health response. “When the next strain comes through, we will be ready for it.”

Worldwide, research groups have used sewage surveillanceSARS-CoV-2 can be tracked, but these methods typically detect only the presence or amount of the virus. This information was used to calculate the community’s transmission. Unfortunately, the quality of data used to determine which variants were in circulation and how widespread they were has been poor.

The team from California devised a nanobead-based method to sequence more viral RNA from wastewater samples. The previous methods could only sequence 40% of the viral DNA in a sample. However, the nanobead technique allowed researchers to sequence almost 95%. Freyja, a tool developed by the California team, allows for identification of variants and their relative abundances.

Samples of sewage

The scientists spent almost a year collecting samples at a San Diego sewage-treatment facility that treats wastewater from approximately 2.3 million people to test their methods. Data collection began in February 2021. Over a period of 10 months, they also collected waste water at 130 locations on campus.

The Alpha and Delta strains of coronavirus were detected in waste water by the researchers up to two week before the strains could be tested in clinics. The researchers also found Omicron ten days earlier than the first San Diego patient tested positive. They then traced the rise in Omicron’s BA.1 variant in the population.

Researchers at UCSD consistently found Alpha, Delta, as well as a lesser-known variant Epsilon. It was most commonly found in the United States. Joshua Levy (an applied mathematician at Scripps Research Institute in La Jolla), California, co-authored this surprising finding.

It isn’t yet clear if the technique will be able to track Omicron, which is fast-moving. BA.4 and BA.5 versionsThese diseases are difficult to identify, according to Ana Maria de Roda Husman (infectious-diseases researcher at the Netherlands National Institute for Public Health and the Environment, Bilthoven).

Phong Thai, an environmental scientist at University of Queensland in Brisbane, Australia says that an early-warning system could still be possible for certain variants. It takes approximately two weeks to process results from collecting samples. “If you want to make a tool really useful for public health, it has to return the result within days,” says Thai.

But Knight says that the team has managed to shorten the time it takes to sequence samples, from weeks down to days, which is a “game changer”.

This article was reproduced with permission. First published on July 8 2022.


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