We may have only weeks to act before a variant coronavirus dominates the US

The US may face a rapidly closing window to bring a suspected extra-contagious variant of covid-19 under control.

If the variant strain, first spotted in the United Kingdom, is as infectious as some suspect, it could dominate US case numbers by March, send covid-19 deaths to unprecedented levels, and collide with the rollout of vaccines, research suggests.

British scientists fear that the new strain, which they say is 50% to 74% more transmissible (meaning the average case generates even more follow-on infections), has put wings on the feet of the pandemic in the UK, where covid-19 case numbers have risen swiftly.

More than 40 other countries have now also spotted the variant, including the US, where it was first reported on December 29 in Colorado. According to the US Centers for Disease Control and Prevention (CDC), as of January 11 there were 72 confirmed variant cases in 10 states. California has 32 cases, Florida has 22, and Georgia, Indiana, and Pennsylvania each have one.

That's a drop in the bucket given that the US is confirming over 200,000 cases of covid per day, and the rate of infection per million people has tripled since November-even without considering the variant.

Yet the variant is likely more widespread than it appears. Many cases found so far don't have a clear link to UK travel, meaning that it's already spreading, unseen, in local communities and could pick up speed quickly.

If the variant becomes common [in] the US," Tom Frieden, former director of the CDC, said on Twitter, it's close to a worst-case scenario." He says political turmoil, overtaxed hospitals, and an unrelenting new form of the virus could create a perfect storm."

I've never seen an epi curve like this. The B.1.1.7 variant is spreading like wildfire in the UK and Ireland. If it spreads here, it will make an already-bad situation even worse. pic.twitter.com/VZB5BPm5om

- Dr. Tom Frieden (@DrTomFrieden) January 11, 2021

That appearance of the variant has already led the US to require British visitors to test negative before flying. Some scientific leaders say the US should now consider a coordinated national lockdown period. I think we have to aggressively consider the upsides, and the downsides, of another lockdown to crush the curve," says Ali Nouri, president of the Federation of American Scientists (FAS). We are hitting record numbers of cases and deaths, and on top of it we are dealing with a situation where we may be confronted with a highly transmissible variant. It's going to exacerbate a situation that is already stretching hospitals to the breaking point in some areas. It's a really bad situation."

Easier to spread

The variant virus, known as B117, was discovered by UK scientists in December and carries mutations that many researchers believe allow it to spread between people more easily. There is still scientific uncertainty as to whether the variant is truly more transmissible or whether it's been fueled mostly by superspreading events including holiday gatherings in Europe. However, if more countries, including the US, see the same pattern as the UK, the case for easier spread will look indisputable.

Such data is coming into view already. Researchers at the Serum Institute in Denmark, for example, said on Saturday, January 9, that the variant has been doubling as a percentage of cases every week in that country. It now accounts for 0.9% of cases there, and Danish researchers predict it could become the dominant form by February.

Preliminary data from Denmark also indicate that the growth rate for this variant is 70% higher than for other variants," the institute said.

The variant virus is detected via genome sequencing: diagnostic test swabs are subjected to a detailed analysis that reads out the complete genetic sequence of the virus, revealing what mutations it has.

At Helix in San Mateo, California, a large lab funded by the US to run diagnostic tests for covid-19, researchers also began looking for the variant in December and have identified most of the cases reported to the CDC. Nationally, the company estimates, 0.3% of cases are the B117 strain.

Although that percentage remains small, if the doubling trend from Europe holds, the variant could account for most cases in the US by mid-March. However, groups involved in modeling the pandemic said they are still unable to project the spread of the new variant in the US, or how it will affect the burden of cases.

With not a lot more than anecdotal evidence of cases of the new variant being detected and no systematic testing for the new variant in the US, it would be exceedingly hard to do any modeling of the current and potential future spread," says Theo Vos, a professor of health metrics sciences at the University of Washington. He says higher transmissibility would lead to the expectation that it can eventually become the dominant strain, but when and where is highly uncertain for the moment."

Lack of surveillance

Even as new variants threaten to emerge, the US still lacks the ability to adequately monitor changes to the virus, according to James Lu, cofounder and president of the Helix lab. He says the US as a whole has been sequencing about 300 to 400 virus samples a day but needs to sequence around 7,000 each day (or 5% of all tests) to get an accurate picture of what variations of the virus are spreading.

The UK strain isn't the only one worrying researchers. Additional variants with overlapping constellations of genetic changes have been seen in South Africa and Brazil, leading scientists to conclude that the germ is adapting and raising concerns over what the changes signify.

By comparison with other advanced countries, the US sequences a much smaller proportion of cases. According to the Washington Post, the country is sequencing one in every 300, compared with about 60% in Australia, 12% in Denmark, and 7.5% in the United Kingdom.

We're off by more than an order of magnitude from a proper level of surveillance," says Lu. The goal is to catch it before it before it becomes common."

The Helix lab, funded by the US over the summer to increase testing, currently carries out about 45,000 daily covid-19 tests for hospitals and others. Since December, it has been reanalyzing many of those samples to look for B117, work it carries out with a partner company, Illumina.

We need more data to see the trends, but as we scale up the sequencing, if we start to see it as a larger and larger fraction, then it is likely more transmissible," Lu says. He says the CDC has been coordinating with labs to look for the variant, but we think a cohesive federal response is going to be necessary to get surveillance in place."

Race with vaccine

The possibility of a new surge in a novel form of covid-19 has some researchers comparing 2021 to last spring-that is, we are facing a short window to clamp down on the variant before it, too, spirals out of control.

In an editorial in Stat News, published January 9, MIT professor Kevin Esvelt and Harvard epidemiologist Marc Lipsitch wrote that this time around we are better prepared for this new enemy" and argued that the US should aim its countermeasures at suppressing the new strain.

For instance, as the new variant is found, US contact tracers should drop everything" and focus on isolating contacts of those cases, the two argue. They also say vaccines should be rushed to affected areas to surround variant outbreaks, a concept sometimes known as ring vaccination.

While the UK variant doesn't seem to cause more severe disease, a faster-spreading virus will lead to more death simply by causing many more cases, according to Adam Kucharski, of the London School of Hygiene and Tropical Medicine, who has shown how a 50% more transmissible strain would end up killing many more people than one that is 50% more lethal but spreads no quicker.

The emergence of the variant may also mean there is less time to vaccinate people before they catch the disease. According to Bloomberg, which analyzes CDC data, about 10 million vaccine doses have been given out in the US since the vaccination campaign began shortly before Christmas.

The incoming Biden administration has said it will push for a vaccine blitz that would see at least 100 million" shots given during the president's first 100 days in office, or between late January and the beginning of May.

Nouri, the president of the FAS, says the US vaccination rate remains woefully slow," and he notes it is still unproven whether vaccination stops people from spreading the virus or just from falling ill. He says that means familiar measures, like masks and physical distancing, remain essential, especially as long as the weather remains cold and people spend their time indoors.

In addition, Nouri thinks the US may need to consider going further, with measures such as coordinated restrictions on indoor gatherings. I think the conversation is going to shift if and when this variant gets a greater hold. It could be a game-changer," he says. We can't afford to do the same thing when our enemy is adapting, changing tactics, and becoming more transmissible. We have to have those conversations immediately, because our enemy is getting better and we are not."

-with reporting by Lindsay Muscato