The coronavirus variant that shut down much of the United Kingdom is spreading rapidly across the United States, outcompeting other mutant strains and doubling its prevalence among confirmed infections every week and a half, according to new research made public Sunday.
The report, posted on the preprint server MedRxiv and not yet peer-reviewed or published in a journal, comes from a collaboration of many scientists and provides the first hard data to support a forecast issued last month by the Centers for Disease Control and Prevention that showed the United Kingdom variant becoming dominant in the U.S. by late March.
The spread of the variant, officially known as B.1.1.7, and the threat of other mutant strains of the virus, have added urgency to the effort to vaccinate as many people as possible as quickly as possible. The variant is more contagious than earlier forms of the coronavirus and may also be more lethal, although that is far less certain.
The mutations do not change the fundamental way the virus spreads, and masks and social distancing will continue to be effective in limiting infections, disease experts point out.
“Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize covid-19 morbidity and mortality,” the authors of the new study write.
Florida stands out in the study as the state with the highest estimated prevalence of the variant. The new report estimated the doubling time of B.1.1.7 prevalence in positive test results at 9.1 days.
Florida leads the nation in reported cases involving B.1.1.7, with has recorded 187 infections involving B.1.1.7 as of Thursday, followed by much-more-populous California with 145 infections, according to the CDC.
The new study only looked at data through the end of January, but the percentage of infections in Florida involving B.1.1.7 may have risen from a little less than 5 percent to approximately 10 percent in just the past week, Kristian Andersen, an immunologist at Scripps Research Institute and a co-author of the new study, said Sunday in an email.
Mary Jo Trepka, an immunologist at Florida International University, said she is not surprised by the spread of the variant in Florida, because the state has not been strict about mask mandates or other restrictions, and it is a hub for international travel. She worries that the variant will reverse recent favorable trends in infection rates.
“We’re in good shape in terms of numbers of cases coming down, the hospitals are doing well. So is that going to reverse because we’re seeing these variants?” she said. “The message is that we have to work harder to prevent transmission of all these cases of covid. If we don’t we’ll potentially see more variants. We need to get everybody vaccinated and we need to do a much better job at preventing transmission.”
The B.1.1.7 variant carries a package of mutations, including many which change the structure of the spike protein on the surface of the virus and enhance its ability to bind to human receptor cells. People infected with the variant have higher viral loads, studies have shown, and they may shed more virus when coughing or sneezing.
Last’s month’s CDC forecast was based on a simple model that extrapolated from trends in the United Kingdom. The new research posted Sunday confirms the forecast trend through the end of January. The researchers scrutinized genomic analyses of the virus samples from 10 states, including from 212 infections involving the variant.
The report concludes that the variant has been 35 to 45 percent more transmissible than other strains of the virus in the United States.
“It is here, it’s got its hooks deep into this country, and it’s on its way to very quickly becoming the dominant lineage,” said Michael Worobey, an evolutionary biologist at the University of Arizona and a co-author of the new paper.
The United States is just emerging from a disastrous winter surge in cases, with new infections and hospitalizations dropping – although the numbers remain higher than they were during the summer surge. The CDC forecast shows that, with a steady rate of a million vaccinations a day, infections will most likely continue to decline even in the presence of the more transmissible variant.
But the decline will be much more gradual than if the variant had not taken hold, according to the CDC’s forecast. And there are other wild cards in play, in the form of additional variants. They include B. 1.351, first seen in South Africa and of elevated concern to the medical community because it contains a mutation (E484K, nicknamed “Eeek”) that limits but does not entirely undermined the efficacy of vaccines.
Even more worrisome is preliminary evidence from a clinical trial in South Africa conducted by Novavax, maker of a successful vaccine, showing that people previously infected by the coronavirus and given a placebo were becoming reinfected with B. 1.351. There was no evidence these follow-on infections were severe or deadly, but authorities view the South Africa variant as well as another that emerged first in Brazil as posing a particularly high risk for reinfections.
The United Kingdom variant does not generally include the worrisome “Eeek” mutation, though it has appeared sporadically. A report published recently in the journal Science, based on laboratory research using different variants of the virus, found that the Pfizer-BioNTech vaccine remained effective against B.1.1.7.
But the virus is continuing to mutate, and with transmission at such high levels – both in the United States and globally – the variants have abundant opportunities to change further as they react to the human immune system and to therapies administered to patients with protracted infections.
“We should vaccinate as fast as we can,” said James Lu, a co-author of the new report and president and co-founder of Helix, a genomics company that provided much of the data used in the research.
The new study does not include any data on the South Africa variant because it has been detected in only a handful of cases in the U.S., while the United Kingdom variant has been seen hundreds of times already. The new study concluded that the United Kingdom variant had multiple introductions to the United States by end of November.
The variant first appeared in genomic surveys in the United Kingdom on Sept. 20, but did not get tagged as a “variant of concern” until early December when its rapid spread stunned scientists and spurred lockdowns in southern England.
When the CDC issued its warning last month about B.1.1.7, it was still present in less than one-half of 1 percent of cases. That jumped to about 3.6 percent at the end of January, the new research found. Those numbers remain small, but the new research highlights the exponential increase in prevalence among positive test results – doubling every 9.8 days nationally.
“What concerns me is the exponential growth in the early stages doesn’t look very fast,” said Andrew Noymer, an epidemiologist at the University of California at Irvine who was not part of the new study. “It kind of putzes along – and then goes boom.”