CAP TODAY Pathology/Laboratory Medicine/Laboratory Management
One approach to this is to sequence the virus on hospitalized patients, which is what the public health response has been, with the support of laboratories to provide samples to sequence. “And there are now a number of new tests available to labs,” one of which is the Thermo Fisher custom TaqMan assay, which allows allelic discrimination of some of the variants. Another is the Roche Cobas SARS-CoV-2 Variant Set 1 that looks for targets N501Y, E484K, and del69–70, which can be run on the 6800 and 8800 systems. (There’s no positive control, he notes, but he said Twist Bioscience has good controls for variants.) “The idea with tests like this is that a lab can screen. We can screen in high numbers fairly easily, identify those variants, and transfer those variants on to public health.”
SmartGene’s modules for SARS-CoV-2 are another example, Dr. Hansen said, “and we are strong partners with SmartGene in our lab as well.” This is France’s solution for decentralized sequencing and national surveillance, he said, and it supports Sanger and next-generation sequencing. “This is software you can buy that will allow whole genome assembly and lineages. They have a great functionality report to upload to the databases, and this is something you can do in your lab if your lab is familiar with next-generation sequencing or Sanger methods.”
Seegene has three assays: Master, Variants I, and Variants II. In 48 hours of variant testing using a Seegene assay at Hennepin, Dr. Hansen said, 83.1 percent of all positives were a variant of some type: 65 percent were B.1.1.7, and six percent were a combination of the Brazilian, Japanese, and South African variants.
What will be done with variant data?
“There’s no question that they’re going to filter into booster strategy,” he said. “We also know that interacting with our plasma cells will be an answer, to stimulate the immune system to produce specific antibodies.” Another strategy would be a third shot of a current vaccine that would increase the antibody affinity for what it is hoped can be established.
But there’s the always-present question of who pays. “Variant testing at this point is not covered, to my knowledge, in CMS pathways,” Dr. Hansen said. He reminds public health authorities, he said, that there is $1.7 billion under the American Rescue Plan, and public health offices need to understand the value of partnering with local hospitals. “It’s one of the lessons learned from the outbreak. Public health did not do a good enough job of engaging testing on the ground with local hospitals, and we need to learn from that. So is there an opportunity for public health to help laboratories help screen some of these samples to move them on to public health agencies?”
If there is no clinical impact in terms of treatment or management, he asks, why do it? One of the lessons learned in the outbreak is the tremendous need for preparation, he said.
“The CDC office was opened in 1946 exactly for what just happened with COVID-19, and we fumbled it. So you can look at these assays and say, ‘How useful are these assays? There’s a new variant coming every week. As soon as I validate, it’s going to be out of current pace.’
“The value of the commercial variant assays,” he said, “lies in showing us how these assays can be produced and made available to labs across the country, hopefully on a much smaller scale than what we experienced initially.”
Variant assays offer a “road map,” Dr. Hansen said, of how to develop and apply the assays so that if and when a variant arises that has an impact on clinical care beyond transmission rates, labs can be prepared.
“A number of diagnostic colleagues have now shown us these assays are possible, and this is the message we can take from variant assays today.”
Sherrie Rice is editor of CAP TODAY.