COVID Variants

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This pandemic is a tragic but informative example of the evolutionary process of natural selection at work.  Viruses are tiny, comparatively simple parasitic lifeforms which lack the ability to reproduce on their own, surviving and reproducing only by hijacking the reproductive mechanisms of more advanced living cells. They repurpose those mechanisms to create a sufficiently large number of copies of themselves to rupture their host cells, thereby killing those cells and perpetuating their species by freeing themselves to attack yet more cells.

Viral genes lack the “quality assurance” mechanisms which more advanced organisms use to ensure accurate copying of the information contained in their respective genomes.  While that is a seemingly inefficient process, the occasional mutation turns out to be beneficial by making it easier to evade host immune systems.  Viruses which incorporate those to-them-beneficial mutations successfully infect more hosts than those lacking those advantages. By being more transmissible, they quickly become the dominant strain, crowding out both their progenitors and other competing strains, at least until the emergence to the next, even-more-transmissible strain.

Over nearly the nearly-four-year span of this pandemic to date, close to 2,000 different COVID-19 (SARS-CoV-2) strains have been identified.  The original 2020 “Wuhan” strain was outcompeted by the Alpha variant within the first year (2020). The pace picked up in 2021 with the Alpha, Beta, Gamma and Delta variants each displacing their predecessors.  By early 2022, Omicron had fully replaced all of those earlier variants, thanks to a record 50 mutations, some 30 of them in the spike protein, which researchers found conveyed on the order of 100 times more transmissibility than Delta.

But rather than ending there, the process of natural selection accelerated as Omicron itself divided into subvariants BA.1, BA.2, and all the way up to BA.5 which retained dominance through most of 2022. Those variants were in turn outcompeted in 2023 by the emergent XBB Omicron subvariant.  Emergence refers to those rare occurances when two or more viruses from different strains infect the same cell at the same time, resulting in a random reshuffling of genes somewhat akin to sexual reproduction. By October, XBB had already differentiated into nearly 800 identified strains.  With so many new variants appearing so rapidly, the pattern of one strain achieving dominance for multiple months has been replaced by a dizzying array of multiple variants rising and falling within a matter of weeks. In recent months, the EG.5 family grew to account for more than half of new North American infections, having further diffentiated into some 50 distinct strains. Now, however, they are being shunted aside by the even-more-immunity-evading JN.1 strain, which is derived from the BA.2 family rather than XBB.  

The only constant is that those strains whose “market shares” are rapidly increasing at their competitors’ expense are almost by definition more transmissible that those which they are replacing.  With most humans having already been infection at least once and an increasing portion having suffered multiple infections, that represent billions of bodies within each of which there are between one and a hundred billion new viruses assembled at the peak of each infection, COVID’s current mutation rate should come as no surprise.   

That could easily have spelled disaster but for one or more of Omicron’s non-spike mutations having reduced the virus’s resistance to interferons, which are key to the human innate immune system’s ability to protect our deep lungs from infection.  Fortuitously that vulnerability, which is unrelated to the virus’s transmissibility, was retained in all subsequent strains, including XBB.  The nightmare scenario would be a more transmissible variant which happened to gain Delta’s interferon resistance.  Politicians who fatuously claim that the pandemic is over and conveniently forget all the costly lessons take it as an article of faith that future strains will never have Delta’s virulence.  Nature remains one unfortunate mutation away from proving them wrong.

The US biweekly CDC data on circulating COVID variants track the “market shares” of the dizzying array of new strains appearing, proliferating and then disappearing as they are outcompeted by their more transmissible successors. For the COVID virus, outcompeting means being better at evading our existing immunity which, by six months after our last booster or infection, has significantly declined. EG.5, an Omicron->XBB->BA.19.2 subvariant currently tops the list with a 24% share, but has already started to decline. Two of its progenies, HV.1 and HK.3 are the fastest-growing, their incidence having respectively soared by nearly 5 and 10 times over the past weeks. Together, the EG.5 family accounts for almost half of new US cases.

The Canadian chart on circulating COVID variants includes the dozen strains with the currently-highest “market share”. Together, they account for some 75% of new infections from a dizzying array of literally dozens of variants within the utterly-dominant XBB family. Almost half are descendants of EG.5, which was first identified in July but has since split into a dozen or more subvariants. While all XBB strains have the ability to bypass immunity gained from any combination of vaccinations and prior infection, that immunity continues to provides decent protection against severe symptoms and death for those with healthy immune systems. That said, each new COVID strain manages to outcompete its recent predecessors and does so by being better at evading our existing immunity which, by six months after our last booster or infection, has significantly declined. That dynamic increases the likelihood of future waves.