With limited surveillance of Covid-19 variant, it’s déjà vu all over again

As health officials in the United States announced a second and possibly a third person infected with a new, more transmissible strain of the SARS-CoV-2 virus, infectious diseases experts are feeling a sense of déjà vu all over again.

A little less than a year ago, the early response to the coronavirus crisis was stifled by an inability to scale up testing to detect the virus and curb its spread. Now, once again, it’s unclear how prevalent the new strain, which first surfaced in the U.K., might be in the U.S. Already a possible and a probable case have been detected in Colorado and one case has been reported in California. But it’s likely the variant’s spread hasn’t stopped there.

“It feels a lot like that time between Jan. 19 or so when we had that first case in the Seattle area and six weeks later, when all of a sudden, it looks like we’ve got community transmission in California and Seattle and who knows where else,” said Michael Worobey, a professor of evolutionary biology at the University of Arizona. “It does have that feeling.”

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Trevor Bedford, a computational biologist at Fred Hutchinson Cancer Research Institute, told STAT he doesn’t believe the new variant, which is called B.1.1.7, is widespread yet. There are 250 genetic sequences of SARS-2 viruses from December cases in the U.S. that have been logged into an international virus sharing database known as GISAID; there isn’t a B.1.1.7 among them, Bedford said. But he believes it may just be a matter of time.

“How I imagined this working is … very similar to back to January, February,” he said. “There are seeding events that have occurred throughout the country. Some have taken, some haven’t.… And you could imagine it should be more likely to be in places like New York and Boston with good travel connections to London, but it could have just by happenstance get picked up a bit elsewhere.”

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Worobey agreed the new variant is probably already spreading in a number of parts of the country, traveling under the radar because the U.S. is not doing enough sequencing of SARS-2 viruses.

“We’re a little behind the eight ball in terms of our genomic sequencing, both in terms of absolute numbers and the sort of delay between sampling and getting the sequences out there, compared to the U.K.,” Worobey said. He warned that if the U.S. doesn’t find the cases and slow spread it will likely see the same kind of rapid dissemination of the variant that the U.K. has seen.

The new variant sports an unusual number of mutations, including some that appear to change the virus’ behavior. It seems to be significantly more transmissible, increasing the rate at which infected people infect others.

There’s no evidence to date that the variant triggers more severe disease. But hospitals are straining to handle Covid patients as it is; more infections could lead to a higher death rate, because of diminished quality of care.

“The case fatality rate increases if health care systems get overwhelmed,” said Nahid Bhadelia, medical director of the special pathogens unit at Boston Medical Center. “That’s just how it works.”

There are efforts afoot to try to figure out how widely the new variant is spreading — one of them led by Worobey’s laboratory. His team is trying to develop an assay that could be used to test for variant viruses in wastewater from community sewage systems. If the test works, he said, the lab will ship testing materials to other laboratories, test samples in their own lab, or share the recipe for making the primers and probes to get the test into wide use.

“I do think that wastewater is going to be the best way in the very near term to get a better handle rather than waiting for the odd lab like Colorado that comes across one of these in an individual patient sample,” Worobey said.

The Centers for Disease Control and Prevention is also stepping up efforts to increase the sequencing of SARS-2 viruses, officials said Wednesday.

Gregory Armstrong, who is leading the CDC team monitoring virus variants, said the national SARS-CoV-2 strain surveillance system, which was started in November, is scaling up to be able to handle 750 samples submitted by states for sequencing and study every week. The CDC is also working with national reference laboratories in the country, providing funding for sequencing on several times that many viruses. The hope is to get to about 3,500 a week, Armstrong noted.

He said experts at the CDC and elsewhere do not believe the mutations contained in B.1.1.7 will significantly undermine the protection generated by Covid vaccines in use or in production. “It may cause a small impact. But keep in mind it’s likely that the amount of immunity that is induced either by natural infection or vaccination is great enough that a slightly decreased [antibody] titer may not have any noticeable effect at all,” Armstrong said.

But Bedford said…