The ascendancy of more transmissible (and possibly also more pathogenic) Delta strains is a consequence of the worldwide vaccination campaign. This is now the most salient and the most important side-effect of our vaccines. They elicit antibodies that select for more aggressive SARS-2 lineages, which escape vaccine-induced immunity by replicating in the lungs of infected people faster and earlier.
All our evidence is that the alpha (Kent) and delta (Indian) lineages emerged at the same time, in September or October 2020. Delta was more aggressive than alpha, but alpha had the upper hand until vaccines killed it off. Probably, Delta is too aggressive in completely unvaccinated populations, causing severe illness before very many of its hosts can do much spreading.
Consider the entirely typical case of my country, Germany. Most first doses here were administered over the course of nine weeks, from early April to early July. In precisely this period, Delta began its rise to absolute dominance. The genetic diversity of SARS-2 has been totally destroyed in Germany and everywhere else too.
What you see happening to Alpha in this chart, is what the vaccines were supposed to do to Corona as a whole. But then it was Corona’s move, and Delta is the hand it played.
Nothing about how the pandemic plays out now can be disentangled from the vaccines. The more aggressive spread of Delta among the unvaccinated is as much a part of this campaign, as its continued spread among the vaccinated. We have totally changed the environment in which SARS-2 circulates, and in response SARS-2 has become more transmissible and more volatile across the board.
Let’s have another look at the Yeh and Contreras preprint I linked in my post on Vaccine Failure and the Way Out. This paper has been kicked about by disingenuous or stupid people pretending it proves that the vaccines stop mutations. It proves no such thing. Mutations happen at a more or less constant rate across all virus genomes, with or without vaccines. What the paper does show, is that the vaccines reduce the overall mutation frequency of SARS-2. That is, the more you vaccinate, the more genetically uniform SARS-2 becomes. What these people do not understand, or pretend not to realise, is that this is basically the opposite of victory. Reducing mutation frequency is the same as exerting positive selection pressure on SARS-2. This is what happens when vaccines select for vaccine-resistant strains.
From the paper:
This graph depicts mutation frequency in Delta strains. As a rule, the more heavily vaccinated a country (x-axis), the less genetic diversity you see in sequenced SARS-2 Delta viruses from that country (y-axis). But look at the the shape of the curve. As you approach 70% vaccinated, the effect levels off. Beyond a certain point the vaccines stop killing off strains, because all the strains that remain are the ones the vaccines can’t kill. This is the subset of Delta strains optimised to circulate in vaccinated populations.
Here’s another chart, which explains the seasonally atypical infection wave that hit the United Kingdom in July:
By the middle of April, almost half the UK population had been vaccinated at least once. Cases bottomed out, and the genetic diversity of Delta SARS-2 strains in the UK (the blue line) plunged accordingly. By the end of May, though, UK infections began to spike again, with one important difference: This time, the genetic diversity of SARS-2 remained low. This is because the new infections were caused by a subset of closely-related Delta strains with vaccine adaptations.
This is why Yeh and Contreras, the authors of this paper, conclude that “More virulent SARS-CoV-2 strains have emerged with enhanced transmissibility and immune evasion properties to cause breakthrough infections” and that “the virus becomes more contagious as it is screened through the vaccinated population.” They also propose using these measures of genetic diversity to predict future infection waves. As with the Marek Effect in chickens, overly aggressive viral strains that take their hosts out of circulation too early face substantial disadvantages, but they become the flavour of the month when you change the equation by introducing widespread partial immunity.
For some months now, I’ve suggested that Corona, like mass and momentum, tends to be conserved. For whatever reason, containment often seems not to suppress infections, but merely to move them around. You close schools and pubs, and Corona starts raging in nursing homes instead. The vaccines have had a similar effect. It is as if Corona has an optimal virulence, where it spreads most efficiently. By vaccinating millions of people, we have prompted it to become more aggressive, in order to reattain the same net population-wide virulence. This would be why the vaccines have had no real effect on the broader course of the pandemic, even though the vaccinated appear to enjoy substantial protection against severe outcomes.
There is no reason to think this effect will stop here. Third and probably even fourth doses will be administered widely in the coming months. Delta-specific vaccines are also in the works. All of these will increase pressure on the virus, very likely in the same direction. These vaccinations will favour more transmissible, more pathogenic strains – strains which are already out there somewhere, circulating at low levels. Strains that right now are disadvantaged because they make even the vaccinated too sick too soon to spread effectively. Our best hope is that most vaccinated people develop mild Corona infections over the coming months, while the vaccines still protect the more vulnerable among them from serious symptoms. Governments everywhere should cease all containment measures. The worst case, would be to keep everyone immunologically naive while continuing to pursue mass vaccination policies that only make the virus more dangerous.