CDC foresees spread in U.S. of highly contagious coronavirus variant

The cases have been mostly isolated: One in New York, one in Florida, one in Georgia and two in Colorado. The exception has been California, and specifically San Diego County, where a robust surveillance operation has found 32 cases of the variant. National Institutes of Health Director Francis Collins told The Washington Post on Wednesday: “I would be surprised if that doesn’t grow pretty rapidly.”

There is no evidence that the variant, which has recently been detected in more than 30 countries, carries a greater risk of severe disease or death. But the appearance of coronavirus variants, including another mutation-laden variant that has shown up in South Africa, presents a challenge for every country hoping to crush the pandemic.

A more transmissible virus could drive more patients into hospitals and boost the covid-19 death toll. It also could prolong the march toward herd immunity. That’s the point at which a pathogen circulating through a population will slam into so many people with immunity that any outbreak quickly dies out and doesn’t turn into an epidemic. The percentage of people who need to be immune for a population to achieve herd immunity is higher for more infectious pathogens.

The rise of variants also could limit the efficacy of monoclonal antibody treatments because such therapeutics are very narrowly focused and potentially could be eluded by a single mutation.

The implications for vaccines are fuzzy over the long term because the coronavirus will keep mutating. But the consensus is that the newly authorized vaccines are likely to remain effective against any variants seen so far because they elicit a broad array of neutralizing antibodies and other immune system responses. Moreover, the mRNA (messenger RNA) vaccines from Pfizer/BioNTech and Moderna can be readily tweaked if necessary in response to mutations.

All of this argues for increased surveillance of the virus as it spreads through the population and collides with natural and vaccine-induced immunity. The virus is not static, and although the mutations are random, natural selection will lead to variants that are more capable of infecting and replicating in human beings. A study published last week by scientists at Imperial College London, and not yet peer-reviewed, estimated that the variant first detected in Britain is 50 percent more transmissible than the more common strain of the virus.

“Here at the CDC, we’re definitely taking this seriously, and we’re assuming for now that this variant is more transmissible,” said Greg Armstrong, the leader of the strain surveillance program at the CDC, which is still ramping up. The British variant “is probably not in every state at this point, but I think in a lot of states.”

Experts say this heightens the urgency of vaccinating as many people as possible, and some respected scientists have argued that the protocol for distributing two-dose vaccines should be altered to get more people inoculated, even if that means cutting doses in half or delaying the second dose. The Food and Drug Administration this week said it would stick with the two-shot dose backed by randomized clinical trials.

All viruses mutate, and SARS-C0V-2, the novel coronavirus, doesn’t mutate quickly or in any unusual way. But with tens of millions of people infected around the world, the virus has had abundant opportunity to shape-shift randomly, and natural selection does the rest, potentially giving the virus the ability to evade natural or vaccine-induced immunity.

“We are in a race against time,” said Jennifer Nuzzo, an epidemiologist with the Johns Hopkins Center for Health Security. “We need to increase our speed in which we act so that we don’t allow this virus to spread further and allow this variant to become the dominant one in circulation. The clock is ticking.”

The United States has been slow to develop the kind of genomic sequencing that has enabled Britain to closely monitor mutations in the virus and the spread of different variants. The CDC established a consortium last spring to collect data on genomic sequences and in November created the new program in strain surveillance.

Armstrong said in an interview that in the next two weeks, the agency and its contracted partners hope to more than double the number of genomic sequences posted on public websites.

“We’re not sequencing enough yet, and we need to continue to build what we’re doing,” Armstrong said.

The South African variant hasn’t been detected in the United States, he said. But the British variant may have been here since October, according to preliminary data from private coronavirus tests. That data is not fully conclusive because it is not based on comprehensive genomic sequencing.

Instead, the British variant is missing a portion of the genetic code seen in the common coronavirus. By chance, the commonly used Thermo Fisher PCR test can detect that dropped gene in positive test results. Other variants that are not of concern also have that missing gene, and so it is not possible, without a full genomic sequence, to know if a dropout is actually a signal of the British variant.

But according to Armstrong, the dropout signal increased from .25 percent to .5 percent in a couple of months among the positive results detected by that PCR test. In Britain, the same pattern held — very gradual increases in the prevalence of the variant, followed by a sudden surge in which it became the dominant strain in southern England and led to a new set of lockdowns.

The variant first appeared in genomic sequences obtained by British scientists in late summer or early fall, according to the Imperial College study. But it was formally identified as a “variant of concern” in early December and was announced to the British public and the rest of the world on Dec. 14.

Armstrong said CDC officials immediately assumed it was already present in the United States because of the large volume of travel between the countries. He said the CDC anticipates it will become a rising proportion of all cases: “Assuming the data we’re seeing out of the U.K. is correct — it’s 50 percent more transmissible — over the next couple of months we’re likely to see this increase.”

There is no evidence that this variant is driving the fall/winter surge in the United States. If it were, it would have turned up in more of the genomic sequences analyzed by researchers in recent weeks.

The variant, dubbed B.1.1.7, has 17 mutations, including eight that affect the structure of the spike protein that protrudes from the surface of the virus. Although the precise consequences of each mutation are unknown, the genetic alterations appear to allow the virus to bind more easily with receptor cells in humans, resulting in a higher viral load in those infected with it.

That higher viral load may not mean a more severe illness but plausibly would lead to greater transmission as people shed more virus with every cough or sneeze.

“The data are really concerning. All signs right now are pointing to the fact that this is something we should be worried about,” said Mary Kathryn Grabowski, an infectious-disease epidemiologist at Johns Hopkins Bloomberg School of Public Health.

Even a seemingly modest increase in transmissibility, she said, “can mean huge, huge numbers of cases.”

The spread of the variant could potentially compel public officials to impose new restrictions or delay scheduled reopenings.

“If [the variant] starts to take over because it is more aggressive, the measures that we’ve had in place that aren’t working that great to begin with are going to be less effective in controlling the virus,” Columbia University epidemiologist Jeffrey Shaman said.

The more contagious coronavirus variant may have had a disproportionate impact on people under 20, according to the Imperial College study. This may have had a societal cause — it was observed when schools were open but the rest of the country was under lockdown — rather than a biological one, the study authors said.

The study authors analyzed genomic and epidemiological data collected in Britain from early November into December. By measuring what’s called the reproduction number — the tally of other people infected by an individual with the virus — the scientists concluded that the variant has a “substantial transmission advantage” compared with other strains.

In the United States, schools superintendents and boards of education are monitoring infection rates in their communities involving the new covid-19 strain, said Michael Casserly, the executive director of the Council for the Great City Schools, a nonprofit organization that represents the largest urban school districts in the country.

“The exact opening dates in many of our big-city school districts continue to be fluid as our superintendents and boards monitor infection rates in their communities from this new strain of covid,” he said.

Bob Runcie, the superintendent of Broward County Public Schools in Florida, said school resumed Monday for any student who wanted to attend in person.

“Given the data that we have, and the consultation we’ve had with public health officials and medical experts, our school sites are not places of significant transmission of the coronavirus, and so our schools are relatively safe,” Runcie said.

Valerie Strauss contributed to this report.