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This New COVID Variant Ran Rampant While We Weren’t Looking

·6 min read
Xinhua News Agency/Getty
Xinhua News Agency/Getty

There’s a new variant of the novel coronavirus spreading fast from its apparent birthplace in Uganda.

The A.23.1 variant—“lineage” is the scientific term—shares some characteristics with other major variants, including Delta, the one that’s most prevalent in the United States. But its origins differ: Evolutionarily speaking, A.23.1 is a part of a “family” of viral variants—the “A” lineages. Delta, the highly infectious lineage that’s dominant in the United States right now, is a “B” lineage.

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Compared to the oldest forms of the SARS-CoV-2 pathogen, A.23.1 features changes to the spike protein, the part of the virus that allows it to “grab” on to and infect our cells. Those changes could make A.23.1 more infectious than older lineages.

This Is Where the New ‘Mu’ COVID Variant Started—and Raged

But don’t panic. Well, don’t panic any more than you already are. The leading COVID-19 vaccines, including the three the U.S. Food and Drug Administration has authorized for distribution in the United States, work just fine against all the lineages that came before A.23.1. There’s no reason to believe they won’t also work against A.23.1 itself.

What’s most worrying about A.23.1 is that it first appeared in a part of the world where there’s precious little testing or genetic surveillance. It should come as no surprise that those largely unmonitored regions are also under-vaccinated. And it’s there, in these surveillance and vaccine gaps, that much more dangerous new lineages might eventually evolve.

Early in the pandemic, the initial A and B lineages were both present in Uganda, a landlocked, low-income country of 44 million in East Africa. Then A began to take over, according to a new paper in Nature by lead authors Daniel Lule Bugembe and My V.T. Phan, both with the Uganda Virus Research Institute. By the summer of 2020, A lineages accounted for half of the viral samples gathered in Uganda.

A.23, the immediate parent of A.23.1, first appeared in a pair of mass outbreaks at Ugandan prisons in August 2020. A month later, A.23 was the dominant lineage across Uganda, and the first few cases of the further-evolved A.23.1 had appeared.

A.23.1 took over fast. In December and January, virologists sampled 113 Ugandans with COVID. 102 had A.23.1. From its “base” in Uganda, A.23.1 traveled fast. It spread into neighboring Kenya and Rwanda, most likely in the respiratory systems of infected truck drivers. Early this year, it accompanied air travelers to the United Kingdom and the United States. A.23.1 is now found in 27 countries.

A.23.1 owes its success to various mutations to its spike protein. Two particular mutations, which scientists call the “E484K and N501Y amino acid changes,” are especially foreboding. “These two amino acid changes are shown to substantially compromise vaccine efficacy and antibody treatments,” Bugembe, Phan and their Nature authors warned.

Several other major lineages, which long ago split off the oldest forms of SARS-CoV-2, also have these E484K and N501Y mutations. In other words, A.23.1 evolved separately, but in the same way, as other lineages.

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That’s not as weird as it might sound, Niema Moshiri, a geneticist at the University of California, San Diego, told The Daily Beast. “From a general evolutionary perspective, convergent evolution—multiple lineages independently encountering the same mutations purely from random chance—is not surprising to me.”

A virus can mutate in only so many ways, Moshiri explained. There have been so many COVID lineages and sub-lineages for so long, each mutating twice a week, that many of them are bound to “find” the same mutations.

Authorities should keep an eye on A.23.1, and scientists should continue studying it for signs it’s making vaccines less effective, Bugembe and Phan’s team advised. “Our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable.”

But there’s no reason to freak out quite yet. A.23.1 is dominant in Uganda, but it’s worth noting that Uganda has suffered relatively lightly from COVID: just 122,000 cases and fewer than 3,200 deaths. The country’s death rate from COVID, seven per 100,000 residents, is a fraction of the U.S. death rate of 200 per 100,000 residents.

Moreover, seeing as A.23.1 features some of the same mutations that characterize Delta and other major lineages, it probably also has the same limitations as the other lineages. Despite its “stickier” spike protein, Delta barely made a dent in the effectiveness of the leading vaccines.

April data from New York pharma Pfizer, maker of the most popular vaccine in the United States, indicated the company’s jab was 95-percent effective against all lineages.

Meanwhile a study published in The New England Journal of Medicine in August found that, against Delta specifically, the Pfizer vaccine is just short of 94-percent effective. In other words, the vaccines still work, even against newer and nastier lineages.

That could change, of course. Every day without global immunity is an opportunity for SARS-CoV-2 to evolve. It’s possible some future lineage will mutate in some way that allows it to dodge the current vaccines.

That’s a compelling argument for the world’s most vaccine-rich countries to send their surpluses of jabs to under-vaccinated countries.

The United States, for one, is sitting on a stockpile of at least 80 million doses, but administers fewer than a million doses a day while continuing to accept fresh vaccine shipments from the manufacturers. Around 55 percent of Americans are fully vaccinated. That figure grows by around .1 percent daily.

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Uganda, by contrast, has virtually no access to vaccines. Since jabs first became available late last year, the country has administered just 1.5 million doses, enough to fully vaccinate less than one percent of the population.

Moreover, Uganda routinely tests very few people. There’s a reason that A.23 was first detected at prison outbreaks. Prisons have controlled populations and 24-hour government surveillance. They’re fairly easy to monitor for viral outbreaks.

Monitoring the general public is much harder, especially in a low-income country with an underdeveloped health system. “Additional testing and sequencing are urgently needed in Africa,” Rob Knight, the head of a genetic-computation lab at the University of California, San Diego, told The Daily Beast.

As high-income countries steadily vaccinate their way toward some degree of population-level “herd immunity,” lower-income countries with much lower vaccination rates could become refuges for the surviving coronavirus lineages—and breeding grounds for new lineages.

If in coming months and years some lineage develops the ability to evade the vaccines, it might be because it had access to an unprotected population in a mostly unmonitored, unvaccinated country. A country like Uganda.

Read more at The Daily Beast.

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