Lab Technician Carter Tavaglione loads at Janus G3 automated workstation with coronavirus test samples at Advagenix, a molecular diagnostics laboratory, on August 05, 2020 in Rockville, Maryland. Photo by Chip Somodevilla/Getty Images.
Public health officials are racing to vaccinate Americans against COVID-19 faster than new, more transmissible variants of the coronavirus can proliferate.
Limited visibility into how many of which variant is circulating in Ohio is clouding visibility into who’s winning the race.
The Ohio Department of Health sends either its first 17 coronavirus samples collected in a week, or 25 samples collected in a two-week period, directly into a CDC-contracted lab for genomic sequencing, according to a spokeswoman. From there, ODH’s in-house lab sequences about 100 samples per week.
Combined, it’s about 1% of the more than 11,000 average weekly infections in the state.
“One of the problems in the U.S. and other places is we haven’t had as good of genomic surveillance to tell us what the dynamics really are,” said Yonatan Grad, a professor of immunology and infectious disease at Harvard University’s T.H. Chan School of Public Health.
Genomic sequencing is the process by which scientists analyze virus’ genomes — their genetic maps — to see how they’re changing. Variations are normal in any virus, and some of those can make them deadlier, or more transmissible, or resistant to vaccines, or sometimes bear no difference at all.
In Ohio, officials have identified 91 people infected with the coronavirus strain known as B.1.17, first identified in the United Kingdom, which is believed to be more highly transmissible than the original coronavirus in circulation for the last year.
Similarly, officials know of one Ohioan infected with the P.1 variant, believed to have originated in Brazil, which may be able to reinfect people who have already recovered from COVID-19 caused by other novel coronavirus strains.
Among the reasons genomic sequencing is so sparse in Ohio: It requires expensive machines, highly skilled operators, and a lot of time. Plus, it’s tricky to scale up quickly and costs a lot more than standard diagnostic tests.
Grad said many public health departments are hoping to be able to sequence about 5% of all coronavirus samples, given the financial constraints.
Dr. Daniel Jones runs the James Molecular Lab at Ohio State Wexner Medical Center. He said between Jan. 19 and March 2, his lab has sequenced about 400 samples from the Columbus area, along with another 300 samples for the CDC.
He said the DNA sequencing is labor intensive and expensive. It takes about a week to sequence and fully analyze a batch of samples, plus a lot of accumulated knowhow on the coronavirus’ genome. He estimated it’s about five times more expensive to conduct genomic sequencing on a sample as it is to run a standard PCR (diagnostic) test.
Kelly Wroblewski, director of infectious disease for the Association of Public Health Laboratories, advised that states, regardless of their population, should be testing about 300 samples per month.
That might not show how prevalent a variant is in a population, but it’s enough to know whether a given variant is in circulation. On a national level, there’s a more compelling interest to understand the prevalence of the variants; for states, it’s less necessary given the basic precautions are the same, she said.
She said the limited visibility makes the public health messaging harder. More tangible outcomes like hospitalizations and deaths, she said, move people more than genetic mutations and assumptions of their prevalence.
“I agree with the fact that the urgency has faded and that the messaging could be better,” she said. “I think people get scared when they see hospitalizations increase, or deaths increase. Do people get scared when they see variants increase?”
During a statewide tour of vaccination sites, ODH Medical Director Dr. Bruce Vanderhoff told the Columbus Dispatch late last month it can “absolutely” be assumed the B.1.17 variant is in all 88 counties (there were 19 confirmed cases of the variant at the time).
Dr. Christine Schmotzer, chief of pathology for University Hospitals, said the network started sequencing coronavirus samples about six weeks ago and has analyzed more than 100 samples in that time.
“What we want to keep an eye on is any virus changes that would lead to the vaccine being less effective or these therapies less effective,” she said.
UH started sequencing in part due to a growing understanding of variants of concern in the U.S, Schmotzer said. There was also a tradeoff: When hospitals were more focused on securing scarce protective gear like masks or caring for patients during the winter surge, there was less time and resources to focus on sequencing.
On a national level, the CDC’s National SARS-CoV-2 Strain Surveillance system can process about 750 samples per week. The agency also has contracts with commercial diagnostic labs that can sequence about 6,000 samples per week, along with contracts with seven universities.
The U.S. in December ranked 43rd in terms of the rate by which countries sequence coronavirus samples, according to the GISAID Initiative, a global database of coronavirus genomes, as reported by the Washington Post. The Lancet, a medical journal, noted that even poorer countries like Gambia, Equatorial Guinea, and Sierra Leone have a higher rate of sequencing than the U.S.
It’s not entirely clear how much genomic sequencing is occurring statewide. ODH, for weeks, declined to state how many tests it is conducting or how much else is occurring statewide.
Quest Diagnostics, a large private lab network, is currently sequencing 2,000 samples per week nationally for the CDC, according to a spokeswoman. She declined to provide geographic information on the sampling. LabCorp, another lab network, is contracting with the CDC nationally as well.
Several large hospital networks involved with diagnostic testing like the Cleveland Clinic or OhioHealth did not respond to inquiries.
Some labs are not conducting any sequencing on the coronavirus, including the University of Cincinnati’s Genomics, Epigenomics and Sequencing Core, according to its director, Xiang Zhang.
Battelle Memorial Institute — a science and technology company that conducts COVID-19 testing and deployed N95 mask sterilization technology early in the pandemic — is not conducting any, though spokesman T.R. Massey said the company might begin to do so in the future.
Ohio University’s genomics facility isn’t sequencing coronavirus samples either, according to a spokesman.
A spokesman with Case Western Reserve University declined to answer when asked whether the institution is conducting any sequencing.
Wroblewski said with overall transmission at a comparative lull, the U.S. is in a great position to vaccinate as many people as possible and stave off any surge before a variant becomes dominant.
“We should be concerned there are variants circulating, especially because we’re so close to the finish line,” she said.
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