Still, in the race to understand an evolving enemy, Musser worries scientists are flooding the field with incomplete intelligence and bogging down the whole endeavor. “Without having the entire context behind a viral genome, we’re not going to be able to adequately move the needle,” he says.
He’s not the only one who’s worried about that.
“Right now, while we’re in an emergency, it would be helpful to have a coordinating body that could make sure any variant that’s popping up is being characterized in a standardized and timely way,” says Lane Warmbrod, a senior analyst at the Johns Hopkins Center for Health Security and coauthor of a new report that reads like a policy roadmap for how to stay ahead of variants. In it, she and her colleagues argue that the US needs to establish a risk assessment framework for SARS-CoV-2, like the one the CDC began developing in 2010 to help scientists swiftly and systematically evaluate new influenza variants for pandemic potential.
For SARS-CoV-2, the first priority, says Warmbrod, should be to look for any enhancements in transmissibility. Does a new variant spread faster or more easily? Next would be trying to understand if it kills more frequently, eludes immune system responses, or resists antiviral treatments. A central coordinating agency could not only set standards for what kinds of experiments should be run to answer those kinds of questions, but it could also manage resources and delegate the study of each variant to different labs so that nothing slips through the cracks. “Nothing like that is happening now,” she says.
But it could be—very soon.
Topol and Andersen of Scripps have been working with the Rockefeller Foundation in New York to organize a national network of public, academic, and industry labs tasked with coordinating genomic surveillance and research into how new variants spread, evade drugs and immune cells, and make people sick. On February 16, the Rockefeller Foundation convened a virtual meeting of potential participants, including academic researchers and representatives from the Association of Public Health Laboratories, Illumina, LabCorp, the National Institutes of Health, and the CDC.
The idea, says Topol, is to link up a handful of regional sequencing centers that are already deeply involved in decoding coronavirus genomes with the research labs best-equipped to run those kinds of experiments. In essence, it will create what Topol calls an “immunologic phenotyping corps.” He says he expects plans for the consortium to go public in a matter of days.
A spokesperson for the Rockefeller Foundation declined to provide specifics, but did confirm that an announcement about the foundation’s work toward improving the US’s genomic surveillance systems will be made on Monday. In October, Rockefeller pledged a billion dollars over three years to address the Covid-19 crisis and its aftermath, including investing in pandemic preparedness.
Topol is hoping that at some point in the near future, the CDC and NIH will both get on board. With $200 million in dedicated genomic surveillance funds from the Biden administration, the CDC could be a powerful partner. (A spokesperson from the CDC declined to comment.) “I’m optimistic that with that funding we’re going to see better genomic surveillance. But we can’t just run with that. We have to get these immunotyping assays in high gear,” says Topol. “Otherwise we’re just going to have a lot of interesting sequences and not know what to do with them.”
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