We have advocated sequencing a reasonable percent of known infected individuals for the corona virus infection. We have also advocated that such sequenced results should be made available on an open sourced data based so that anyone can have access and provide analysis. The virus is about 30,000 nucleotides long, not that large and the spike is some 3,000 nucleotides.
Using NGS one could expect that sequencing is a readily done process. Science notes:
But to date, fewer than 100 coronavirus samples have made it to his sequencers at the McDonnell Genome Institute, and the United States remains nearly blind to several coronavirus strains that have recently upended the course of the pandemic. “We have it all worked out but there's not a lot of takers,” Milbrandt says of his center's sequencing abilities. “We are getting more inquiries from the press than from people who need the information. … Some of us have pipelines available—they are just not being utilized.” The Centers for Disease Control and Prevention (CDC) plans to rapidly change that by coordinating a national surveillance system for coronavirus variants. Scientists and public health experts welcome the plan. “The hardware is set up, the people are trained, the infrastructure is in place,” says genome scientist Chris Mason of Weill Cornell Medicine. “It's just a big question: Who's gonna pay for it?”
What is amazing is that we can sequence a human genome of 3 billion nucleotides for a few hundred dollars and one millionth that seems to be an insurmountable process.
In my opinion this is another of a long line of gross failures of the CDC. I would suggest sequencing at least one percent of all infected and doing so on a near real time basis. That way one hope we can both see the new mutant/variant and more importantly modify vaccines accordingly.
It is truly amazing that no matter the Administration we have these incessant missteps and outright bumblings.
Posts
