The United States is largely flying blind on the extent to which variants of the coronavirus are spreading.
The U.S. lacks the needed genomic sequencing to track variants, a weakness that only recently has the Centers for Disease Control and Prevention begun to address.
The seven-day average of new COVID-19 cases in the U.S. is 69,632. That’s up sharply from March 22, when it was 54,052, the lowest it had been since last fall.
According to CDC Director Rochelle Walensky, the current surge is being driven by the U.K. variant of the coronavirus, also known as B.1.1.7.
“Based on our most recent estimates from CDC surveillance, the B.1.1.7 variant is now the most common lineage circulating in the United States,” Walensky said last Wednesday.
Some public health professionals say that adequate genomic sequencing would have warned the U.S. that B.1.1.7 was spreading much earlier.
“There is evidence that some of these variants are more transmissible, so if you know you have a variant that is starting to spread in the community, then you can start to put out public health advisories that give people advice on how to protect themselves from getting one of these strains,” said Dr. Lee Harrison, professor of epidemiology and medicine at the University of Pittsburgh.
MICHIGAN AND NEW JERSEY COVID-19 SURGES DRIVEN BY UK VARIANT
Genomic sequencing is a test that enables researchers to know if a particular case of COVID-19 is caused by the original strain or a variant like B.1.1.7. If a large enough sample of cases, about 5%, is genomically sequenced, it can inform public health officials whether a variant strain is spreading.
The United Kingdom has been ahead of the rest of the world on genomic sequencing, at times testing up to 10% of samples. This enabled the U.K. to identify B.1.1.7 first and to alert authorities that it was spreading by December. In January, U.K. Prime Minister Boris Johnson ordered a lockdown in response.
At present, the U.S. has sequenced just over 1% of its confirmed cases of COVID-19, a far cry from Britain. Over one-third of the sequencing in the U.S. has occurred since the beginning of March. However, more sequencing earlier was needed to have had a decent chance at mitigating the surge.
“All the public health experts were waving the flag that this was a possibility back in February, but they didn’t have the data to point to it,” said Meg Wyatt, a senior director of diagnostics for Premier, a healthcare analytics company. “The genomic sequencing would have given them the data they could’ve pointed to.”
Vaughn Cooper, a professor of microbiology and molecular genetics at the University of Pittsburgh School of Medicine, said that greater genomic sequencing a few weeks earlier could have made a difference with a virus that grows exponentially.
“We would have noticed when B.1.1.7 had taken hold in a region earlier,” said Cooper. “Arguably, that might have prompted a bit more of a public response.”
The CDC is ramping up its efforts at genomic sequencing, having received $1.75 billion for it in the recently passed COVID-19 relief bill. And some states, such as New York, Michigan, and Washington, have also been expanding sequencing capacity.
But in many other states, there is limited data on the extent to which B.1.1.7 is circulating. For example, cases are increasing in South Carolina, but the state only sequences on average about 70 COVID-19 samples a week, according to the South Carolina Department of Health and Environmental Control.
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Thus far, South Carolina has only sequenced about 0.6% of its cases. It is far from alone. At present, half the states in the U.S. have sequenced less than 1% of their cases.
