Are the vaccines already (partially) obsolete?

A few weeks ago I compared the emergence of the British variant of coronavirus to the twist at the end of a “Twilight Zone” episode. The entire planet spent 2020 waiting for a cure to the plague, and then it arrived to global jubilation just before New Year’s — only to be followed immediately by ominous news that a new strain of the virus had begun to circulate widely.

The TZ analogy didn’t really work in that case because scientists believe that the current vaccines *will* provide solid immunity from the UK variant. Maybe not 95 percent, as it does against the most common version of coronavirus, but still enough to end the pandemic if we vaccinate enough people.

Now here we are with news of another new variant, this time from South Africa, and the twist ending suddenly feels more real. Imagine a Sisyphean nightmare over the next few years in which we’re constantly rolling the vaccine boulder up a hill, only for a resistant new strain to appear and spread just before we reach the top.

Maybe we’ll end up with a Scott Atlas “natural herd immunity” strategy whether we want to or not. That couldn’t possibly cost more than … one or two million deaths.

Simon Clarke, an associate professor in cellular microbiology at the University of Reading, said that while both variants [UK and South Africa] had some new features in common, the one found in South Africa “has a number additional mutations … which are concerning”.

He said these included more extensive alterations to a key part of the virus known as the spike protein – which the virus uses to infect human cells – and “may make the virus less susceptible to the immune response triggered by the vaccines”.

Lawrence Young, a virologist and professor of molecular oncology at Warwick University, also noted that the South African variant has “multiple spike mutations”.

“The accumulation of more spike mutations in the South African variant are more of a concern and could lead to some escape from immune protection,” he said.

The vaccines train the body’s immune system to recognize and then neutralize the virus’s spike protein — more specifically, the particular spike protein found on the most common strain of coronavirus. If that spike protein mutates, the body will recognize it a little less. If it mutates a lot, as it has with the South African strain, less still. The good news is that Moderna and Pfizer can tweak their vaccines so that they’ll train the body to recognize the new, mutated spike protein instead. They’re already testing the extant vaccines against the new strains, in fact, and would only need a few weeks to make those tweaks if necessary.

The bad news is that’s the easy part. The hard part, which took eight months this year, is testing those modified vaccines on people for safety and efficacy. Either that testing process will need to be truncated somehow — challenge trials, maybe? — or we’ll need to make do with whatever partial immunity the current vaccines provide against the new strains until the new vaccines are ready. That means a longer pandemic and a higher death toll than we’re all expecting.

And because the virus will continue to mutate, especially in response to partial immunity among a growing part of the population, there’s no guarantee that yet another new strain resistant to the *new* vaccines won’t arrive just as those vaccines are rolling out. Sisyphean.

A little more from Politico on the South African strain:

The first (as yet unpublished) paper documenting the South African variant found it spread rapidly and, within weeks, was the dominant variant in several regions in the country. The researchers suggest the variant may be associated with increased transmissibility.

Eminent South African infectious diseases epidemiologist Salim Abdool Karim, co-chair of the country’s advisory committee on COVID-19, wrote in a briefing on December 18 that the higher viral load in swabs of the new variant may translate into higher transmissibility — and that this variant is transmitting more quickly. This could mean that South Africa’s second wave is larger than the first, he noted.

What’s not yet known is whether the variant makes for more severe disease. In fact, the World Health Organization (WHO) said on December 31 that there’s “no clear evidence of the new variant being associated with more severe disease or worse outcomes.” However, as the WHO notes, more cases could mean more hospitalizations and ultimately more deaths.

If you’re finding comfort in the fact that this strain may be no more deadly than common COVID is, rethink. Higher transmissibility can make for a much bigger body count than higher lethality depending upon how much higher each is. Here’s the case trendline in South Africa recently. Not looking great:

Daily deaths this week are higher than they’ve ever been except for a single day in July. Here’s a revealing map of the continent from Google too. The bigger the circle, the more cases there are:

South Africa’s outbreak is singular. Nigeria has more than three times the population but less than 10 percent the number of cases (12,561 over two weeks versus 182,638 for SA). The disparity in deaths is even more arresting, with Nigeria recording 91 versus South Africa’s 5,104. Maybe some of that is due to reporting differences: In a number of African countries, COVID deaths aren’t reported reliably. But bear in mind in trying to gauge the scale of South Africa’s outbreak that it’s summer down there right now. You wouldn’t expect a country to be suffering its worst stage of a viral pandemic during summer — unless something else was happening to drive those numbers, like a dangerous new strain.

Exit question: Do we have a travel ban against South Africa right now? This page at the CDC doesn’t list it among the countries from which travelers are prohibited from entering the U.S., but that page hasn’t been updated since September. This page by the U.S. embassy in South Africa says that Americans are free to travel there, which means at a minimum that U.S. citizens are able to go pick up the South African strain and deliver it back here upon returning home to wreak havoc. I realize that the president no longer cares even a little bit about containing COVID, preferring instead to obsess about election conspiracy theories, but this seems like a fine time for a border hawk to lay down a ban on foreign travel. If Biden wants to lift it 15 days from now, that’s on him.

David Strom 4:41 PM on September 26, 2022