New virus variant found in Colorado while UK struggles to limit it

This week, the UK released more data on the newly evolved strain of SARS-CoV-2, providing further evidence that it spreads more readily than previously circulating strains of the virus. Despite efforts to keep it limited to the UK, most public health experts expected it was already too late—a fear confirmed by the discovery of cases in Colorado. There is some good news, however, as the UK’s data indicates the new strain doesn’t appear to be more dangerous to people once they become infected.

In another bit of good news, health authorities in the UK approved the use of another vaccine, this one from a collaboration between Oxford University and the pharmaceutical company AstraZeneca. While the vaccine doesn’t appear to be as effective as the two others already in wide use, the addition of another supplier ensures that the UK should now have enough vaccine for its entire population early next year.

New, but decidedly not improved

Because the coronavirus accumulates mutations over time, there are now many distinct strains of SARS-CoV-2 circulating. The one that’s now causing concern first drew the attention of medical authorities in the UK because it drove a wave of new infections at a time where targeted lockdown policies were reducing the levels of other strains. By the middle of December, the strain had a name (B.1.1.7), was circulating widely within the UK, and had already been spotted elsewhere in Europe. But nearly everything else about the strain was an open question, including whether it was actually more infectious, or had simply ended up circulating within groups that were more likely to pass it on to others.

In a new report, Public Health England attempts to answer some of these questions, while adding confusion by calling the strain by a completely different name (its report uses VOC 202012/01, for “variant of concern”). We’ll continue to refer to it as B.1.1.7.

While the UK originally identified it by sequencing viral genomes, B.1.1.7 has a deletion that removes part of one of the three viral RNA sequences recognized by a commercial test being used in the UK. That has allowed health authorities to track it in every region where the test is in widespread use (about 30-35% of the tests used can recognize it). There are other strains, however, that also lack this sequence, so the numbers generated in this report should be viewed as an upper bound on B.1.1.7’s spread.

Given that caveat, the rise to prevalence demonstrated by B.1.1.7 is astonishing. As recently as mid-October, it represented only about three percent of the viruses sampled in the UK. By mid-November, that number had gone up to 88 percent, and it was at 98 percent a month later. There were no apparent significant differences in who it was infecting—all ages, genders, and ethnicities showed similar proportions of the new strain compared to total infections.

The UK’s national health system allowed researchers to track the outcomes of those infected with B.1.1.7. The researchers at Public Health England identified 2,700 of them, and matched their demographics to a group of 1,770 infected by other SARS-CoV-2 strains. There were no significant differences in terms of the percent who ended up hospitalized or died due to their infections. So, it seems possible that the only difference between B.1.1.7 and other strains is an elevated infectivity.

It’s everywhere

The UK’s contact tracing capabilities paid off when it came to estimating what’s called the attack rate, or the percentage of those exposed to a viral host who actually end up contracting the virus. In the UK, all other strains of the virus had an attack rate of just under 10 percent. B.1.1.7’s attack rate was over 15 percent. That’s definitely consistent with the idea that this strain is able to spread among humans more readily than the ones that have been circulating previously.

While a number of countries restricted travel with the UK in response to earlier reports about B.1.1.7, most health authorities indicated that such moves were too late—it was so common and widely distributed within the UK that it had clearly had opportunities to spread further before restrictions were put in place. It was no surprise when the virus was found in a number of other countries as well.

The viral surveillance system in the US isn’t as thorough as that in the UK, so the variant was expected to already be circulating here, as well. That was confirmed yesterday, with the discovery of a case in Colorado, followed by the announcement of another suspected case there today. These two cases worked in the same facility, and the person who definitely has B.1.1.7 has no history of recent travel outside the US. Combined, this suggests that B.1.1.7 is already circulating within communities within the US, meaning it will be very difficult to contain it.

If the higher attack rate of the virus occurs here, as well, it could significantly raise the challenge of caring for everyone infected. Given a number of areas in the US are already out of hospital capacity, that would make the new year even more grim than it was already destined to be.

Another vaccine

For the UK, more help could be on the way, as the country’s Medicines and Healthcare products Regulatory Agency has granted approval to another vaccine, this one from a collaboration between Oxford University and pharmaceutical giant AstraZeneca. The vaccine is based on a harmless chimpanzee virus from a family of viruses that cause cold-like symptoms in humans. It has been engineered to produce the coronavirus spike protein in any cells it infects. Producing the virus is incredibly simple, making it cheaper, and it can be stored in standard freezers, making it easier to distribute.

The downside is that it doesn’t appear to be as effective as the RNA-based vaccines made by Moderna and Pfizer/BioNTech. Full-dose trials indicated it was only 62 percent effective, compared to over 90 percent for the RNA-based vaccines. A subgroup that used a different protocol had seen 90 percent protection, but there were questions as to whether that group was representative. Still, the UK has made it the centerpiece of its vaccination policy, and has ordered 50 million doses—enough to cover most of its population—and expects to have them as early as March.

(There may be a bit of nationalism at play, with Matt Hancock, the UK Secretary of State for Health and Social Care, referring to Oxford’s role by calling this a “British success story.” In contrast, Andrew Pollard of Oxford, who ran the clinical trials, called it “an endorsement of the huge effort from a devoted international team of researchers and our dedicated trial participants.”)

According to the New York Times, the UK will also be taking an unusual approach to delivering the vaccinations. Like others, the Oxford/AstraZenica vaccine requires two doses. But, instead of delivering those to people on a schedule, the UK will be focusing on getting as many people as realistically possible their first dose, hoping for some partial protection, before ensuring that anyone receive their second.

Even if the vaccine is only partly effective, it can help drop the viral reproduction rate to the point where additional controls, such as mask use and social distancing, lower the viral reproduction number sufficiently to cause the pandemic to fade out. The UK’s experience in this regard will be critical, as the price and ease of transport make it likely that the Oxford/AstraZenica vaccine will see widespread use in developing countries.