A strategy for new Covid variant: keep calm and carry on vaccinating

At least we’re learning. Remember when the early reaction to the outbreak of a deadly virus in Wuhan was to discourage people from changing their travel plans?
 

South Africa’s government didn’t sit on information about a new worrying variant of SARS-CoV-2, which the World Health Organization has now dubbed omicron. It didn’t downplay it. On the contrary, authorities shared detailed slides so that countries could develop their responses.

Now it’s up to governments and local authorities to adapt to a fast-changing viral picture — one that remains blurry in places.

Genomic sequencing of infections in South Africa found that the variant B.1.1.529 contained many more mutations than the dominant delta variant. More worrying, some of the mutations occur in the area of the spike protein that is targeted by antibodies. That could mean existing vaccines will be less effective, something we should know with more certainty in the coming weeks.

On Friday evening, the WHO dubbed the variant omicron (not “nu,” which seemed to be the Twitter consensus; and, in some conversations, a previous mutation designated “mu”). It’s also been called a “variant of concern,” which signifies it contains genetic changes that are known to affect transmissibility, disease severity or evade vaccines and therapies.

Certainly, omicron’s transmissibility seems extremely high. The WHO was alerted on Nov. 24 and says the variant was identified from a specimen collected on Nov. 9. It is already in evidence in most of South Africa’s provinces, along with Botswana, and cases have been found in Hong Kong, Israel and Belgium. On Saturday, the U.K. government said two cases of omicron have been found in Britain. It’s quite likely it has spread elsewhere, too. 

While South African officials are unhappy with it, travel restrictions are the obvious first response. The U.K. government announced a temporary travel ban on several countries Thursday night. However, when a flight from Gauteng — the South African province that includes Johannesburg — arrived in London Friday, some 300 passengers were released into the wild with only an advisory message to self-isolate and take some tests. (For a government that has done a lot of complaining about lax French border controls, that counts as an own goal.)

Meanwhile, Israel put in new travel restrictions, quarantines and PCR testing at the border. The EU recommended an “emergency brake” on travel from South Africa. These restrictions merely buy a little time to map out the next steps. If scientists confirm that omicron can indeed escape the defenses of current vaccines, then the race is on to develop a better defensive weapon.

Pfizer Inc. says it can deliver a vaccine that would counter the new variant within 100 days of sequencing. That’s fast. Regulators like the U.S. Food and Drug Administration are likely to speed approval processes for vaccines that are just tweaked for new variants. Pfizer estimates it could make 4 billion doses in the first 12 months. Another 8 billion doses of the Moderna Inc. and AstraZeneca Plc vaccines are likely to be available in a similar time frame.

Even so, testing will need to be done on the updated vaccine. Getting it into enough arms will take many months, even with delivery systems primed by the current vaccine roll-out.

Other lines of defense will be important, too. There are questions about whether the new variant may change the effectiveness of monoclonal antibody treatments, proteins that attach to a specific target in the spike protein of the virus and can be a key tool in treating early infection and even as a prophylaxis in those vulnerable to serious illness.

Maybe we’ll get lucky. The authors of a study published in the journal Nature in September found the presence of “abundant” neutralizing antibody targets on the spike protein of the SARS-Co-V-2 virus; it apparently takes a lot of mutations to escape vaccines or natural infection. Then again, omicron has around 50 mutations and more than 30 in the spike protein, far more than the delta variant. Ten of the mutations are in the so-called receptor binding domain (RBD), which is the part of the virus that makes contact with cells first; that’s compared to two with delta.
 

Omicron was a statistical probability long before it actually turned up. With a 24% vaccination rate, it’s hardly a surprise it first appeared in South Africa. The Hong Kong case was in a vaccinated traveler; the Belgian in an unvaccinated one. The longer it takes to vaccinate whole populations, the faster we’ll cycle through the Greek alphabet with new variants; the only way to prevent that is to vaccine more people faster.

Wherever omicron is seeded, it’s likely we’ll need the now familiar range of detection and mitigation measures — mask mandates in public places, more frequent testing and work-from-home guidance. While these measures are already back in place in much of Europe, it would be an unwelcome regression for the U.K., where mask-wearing is progressively rarer.

South Africa’s transparency and the early response suggests we’re at least learning the first lesson of pandemic management: that “wait and see” is a losing strategy.

--With assistance from Sam Fazeli.