Researchers are hunting through waste water for heavily mutated SARS-CoV-2 variants that could be the next Omicron.
Clockwise from front-left: Scientists Shelby O’Connor, Max Bobholz, David O’Connor, Mitchell Ramuta, William Vuyk and Olivia Harwood at the University of Wisconsin–Madison have been tracking a heavily mutated variant of SARS-CoV-2 in waste water. Credit: Jeff Miller/UW-Madison
The dogs turned out to be another red herring in the team’s months-long quest to trace the variant’s origin. “It’s such smart detective work. It’s phenomenal,” adds Bill Hanage, an epidemiologist at Harvard T.H. Chan School of Public Health in Boston, Massachusetts. “We still don’t really know where variants come from.”
Waste-water sequencing for SARS-CoV-2 can be exquisitely sensitive. But when Omicron cases flooded the watersheds that Johnson was studying in late 2021, they drowned out the cryptic lineages that his team was hunting. To overcome this, Johnson developed a sequencing approach to identify rare, non-Omicron lineages that might have been infecting just a single person. “You’re really looking for a needle in the haystack,” he says.
Source: Dave O’Connor and Marc Johnson https://openresearch.labkey.com/_webdav/Coven/human-source-cryptic-SARS-CoV-2-lineages/%40files/SPHERES-wastewater/index.html Since its discovery, the lineage had gained extra mutations and its genetic diversity had grown — hallmarks of a virus evolving in a single person’s body without spreading. Experiments showed that the variant was even better than the Omicron lineage BA.1 at thwarting antibodies triggered by vaccination and previous infection.
Environmental biogeochemist Martin Shafer with the Wisconsin municipal engineers who collected wastewater samples to track the cryptic lineage.Johnson, O’Connor and their team haven’t given up their search. They continue to detect the variant, and at quantities that Johnson has never seen before in wastewater.
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