Wastewater testing could give us quicker warnings of new COVID-19 variants

Embargoed until: Publicly released: 2022-07-08 01:00

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Testing wastewater for different COVID-19 variants could pick up their spread quicker than sequencing COVID-19 swabs, according to international researchers. The team developed a way to better separate different variants of the virus in wastewater testing to track the prevalence of different variants and tested it within a US college community. They say using their wastewater sequencing technique they were able to detect the Epsilon, Alpha and Delta variants within the community at the time, and detect Omicron 10 days before it was first detected using the mainstream method. The researchers say this could be a cost-effective way to track variants moving through the whole community, not just those getting tested.

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From: Springer Nature

Infectious disease: Wastewater SARS-CoV-2 monitoring reveals early variant transmission

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Wastewater-based surveillance of SARS-CoV-2 genomic material can detect changes in the prevalence of known emerging variants of concern up to two weeks earlier than clinical sequencing, reports a study published in Nature. The study describes the development and implementation of a scalable wastewater sampling process that detects multiple variants at high resolution.

Previous studies have shown that measuring the concentration of SARS-CoV-2 RNA in wastewater can successfully track regional infection dynamics. Tracking virus genomic sequences in wastewater may improve estimates of prevalence and detect emerging variants at the community level. However, the potential of this monitoring method has been limited by low-quality sequence data and challenges in separating out different lineages from mixed samples. These issues are overcome with improved wastewater virus sampling and sequencing, together with a computational tool for inferring multiple lineages, implemented by Rob Knight and colleagues.

A wastewater genomic surveillance experiment was set up at the University of California San Diego (UCSD) campus from November 2020 to September 2021, a period that saw surges in the Epsilon, Alpha and Delta variants of concern. Daily samples were collected from 131 wastewater samplers covering 360 campus buildings, and the data were compared with clinical genomic data (from nasal swabs) in the local community. The wastewater genomic data detected the three major emerging variants of concern at the time earlier and more consistently than clinical samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Further sampling of wastewater across San Diego from September 2021 to February 2022 detected the presence of the Omicron variant more than 10 days before the first clinical detection in the city.

The findings add to evidence that sampling SARS-CoV-2 genomic material in wastewater has the potential to capture community viral spread as a more cost-effective alternative to clinical testing and with less-biased abundance estimates.

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conference: Nature

Research:Paper

Organisation/s: University of California San Diego, USA

Funder: This work has been funded by CDC BAA contracts 75D30121P10258 (Helix) and 75D30120C09795 (G.W.Y., R.K., L.C.L., and K.G.A.), NIH NIAID 3U19AI135995-03S2 (K.G.A.), U19AI135995 (K.G.A.), U01AI151812 (K.G.A.), NIH NCATS UL1TR002550 (K.G.A.), the Conrad Prebys Foundation (K.G.A.), NIH 5T32AI007244-38 (J.I.L.), NIH Pioneer Grant 1DP1AT010885 (R.K), NSF RAPID 2029069 (R.K.), San Diego County Health and Human Services Agency (R.F.M), NIH S10OD026929 (K.J.). The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention and California Department of Public Health or the California Health and Human Services Agency. Use of trade names is for identification only and does not imply endorsement by the Centers for Disease Control and Prevention.

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