U.S. arrival of highly contagious variant draws CDC scrutiny

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Federal Health officials are ramping up their surveillance of the highly transmissible covid-19 variant first identified in India as experts warn that under-vaccinated areas in the U.S. could become hot spots for the mutation.

While U.S. cases attributed to the B.1.617 variant currently sit below 1%, the growth rate remains unclear due to the small sample size. Meanwhile, one science group said the strain could be as much as 50% more transmissible than B.1.1.7, the variant that emerged from the U.K. That mutation was first seen in the U.S. in late December, and is now dominant nationally.

A just-released U.K. study found the Pfizer-BioNTech vaccine was “highly effective” against a form of the B.1.617 variant two weeks after the second dose, affirming preliminary data from Phase 3 clinical trials. Still, the mutation has arrived in the U.S. at a time when anti-pandemic measures are loosening and around 60% of the population isn’t yet fully vaccinated.

“From everything I can tell the vaccines are highly effective against this variant,” said Samuel Scarpino, a co-founder of Global.health, an organization that tracks Covid cases and variants internationally. “But there are some states in the U.S. with quite low vaccination coverage putting them at risk for potential outbreaks.”

The B.1.617 variant that has devastated India was first detected in the U.S. between late February and late March of this year. On May 4, the U.S. Centers for Disease Control and Prevention designated B.1.617 as a variant of interest. It is now studying whether to escalate its standing to a variant of concern, said Jade Fulce, a CDC spokesperson.

Currently, the CDC has classified eight variants of interest, three of which are forms of the B.1.617 strain, according to the CDC website. The agency says these variants are “predicted to affect” transmission, diagnostics, therapeutics, or immune escape, but still have limited prevalence or expansion in the U.S. or in other countries.

The latest models by the Institute for Health Metrics and Evaluation, or IHME, show that despite abrupt drops in mask use due to the new CDC guidance, daily covid deaths will drop nationwide by the end of July thanks to rising vaccination rates. The IHME, though, expects covid cases to creep up in late August.

Infection rates could increase even faster, the group said, with the spread of new escape variants, particularly B.1.617 and the P.1 mutation first detected in Brazil.

There are five variants of concern listed by the CDC. This category covers those that show “evidence of impact” on diagnostics, treatments or vaccines along with increased transmissibility and/or disease severity.

Local health agencies are urged to report these cases to the CDC, who will also report them to the World Health Organization. The designation will also spur efforts to control the variant’s spread and, potentially, development of new diagnostics or the modification of vaccines or treatments.

So far, according to the CDC’s Fulce, there is “insufficient data to evaluate with a high degree of confidence whether these lineages are variants of concern.”

Agency efforts to determine variant classification include reviews of the latest case percentages, as well as laboratory, epidemiological and clinical research data, according to Jasmine Reed, another CDC spokesperson. The CDC also is in touch with global partners, including the WHO, to share data and coordinate genomic surveillance and characterization of variants, Reed said.

The recently-released U.K. study by Public Health England found both the Pfizer vaccine, authorized for use in the U.S. on an emergency basis, and the AstraZeneca shot, which isn’t yet available in the U.S., to be “highly effective” against the B.1.617.2 form of the variant first detected in India.

The study was conducted from April 5 to May 16. Pfizer-BioNTech shot was 88% effective against the B.1.617.2 variant two weeks after the second dose. Two doses of the AstraZeneca vaccine were 60% effective.

“We expect the vaccines to be even more effective at preventing hospitalization and death,” said Mary Ramsay, head of immunization at Public Health England. “So it is vital to get both doses to gain maximum protection against all existing and emerging variants.”

Still, some health experts are questioning if the CDC is doing enough as experts warn that with states opening up, and anti-pandemic measures loosening, under-vaccinated pockets of the U.S. could be at risk of B.1.617 outbreaks.

U.S. vaccine rollout efforts vary state by state. New Mexico, Maine and New Jersey have administered enough doses to cover more than half of their population. Other regions, however, are lagging. Idaho, Wyoming and Louisiana have administered enough doses for just under 35% of their population, while Mississippi and Alabama have administered enough for only 30%.

“I think the CDC should be doing more in terms of communicating the risks of this variant, and that should translate into states taking precautions more seriously than we’re currently doing,” Global.health’s Scarpino said.

Scientists pay most attention to mutations in the gene that encodes the SARS-CoV-2 spike protein, which plays a key role in viral entry into cells. Targeted by vaccines, this protein influences immunity and vaccine efficacy. B.1.617 is among several variants that carry multiple mutations affecting the spike protein.

The WHO earlier this month declared B.1.617 a variant of global concern based on early evidence suggesting it is highly contagious and carries at least some propensity to evade antibodies, including bamlanivimab, a monoclonal antibody therapy developed by AbCellera Biologics and Eli Lilly & Co. The mutation was detected in 44 countries as of mid-May amid a dramatic spike in cases.

It is “highly likely that this variant is more transmissible than B.1.1.7,” the variant first detected in the U.K., and possibly as much as 50% more transmissible, the U.K.’s Scientific Advisory Group for Emergencies said on May 13.

President Joe Biden has banned most travel from India, though the order doesn’t apply to U.S. citizens or permanent residents. Countries including Singapore, the U.K. and Tanzania have also curbed travel to and from India over B.1.617 fears.

The U.S. has been increasing its surveillance efforts in order to get a better understanding of the covid variants that exist in the U.S. They are collaborating with state and local public health laboratories to increase the number of specimens that are sequenced. The CDC has also increased sequencing capacity through contracts with commercial diagnostic laboratories.

Despite these efforts the U.S. still lags behind more than 20 other countries in terms of having a clear idea of how many variant cases there are, according to the latest ranking by GISAID, an international group that promotes the rapid sharing of data from the coronavirus that causes covid-19.

The U.K. is sampling around 50% to 60% of all positive covid-19 samples, said Moritz Kraemer an epidemiologist at the University of Oxford, which provides crucial detail of the distribution of the B.1.617 variant. Rigorous sequencing allowed authorities to identify 2,323 cases of the mutation on Monday.

In Bolton and Blackburn, towns in northwestern England, cases of the India variant doubled in just a week. Most people with the India variant in areas around Bolton had not been vaccinated.

Almost 40% of Americans have been fully vaccinated, and roughly half of the U.S. population have received at least one shot. But as more people are interacting and socializing there are more possibilities for transmission, Kraemer said during a phone interview.

For now, the B.1.1.7 mutation first detected in the U.K. remains dominant in the U.S., said William Lee, vice president of science at Helix, a company that tracks variants. “The vaccines are highly effective,” he said. “So as long as we maintain our surveillance activities and continue to vaccinate the population, we should be able to stay ahead of this and other new variants.”