Genome Dominance And Co-Infection
In my previous post, on Omicron’s actual status in the typology of breakthrough infections, I alluded near the end to a fact that strikes me as requiring much more of an explanation than is usually given. The fact in question is that in the SARS-CoV-2 epidemic, every time a new, rapidly-reproducing variant has burst on the scene, within a few months it has driven all its rival variants clean out of the community-spread genome.
Take a look at The Covariants.org Per-Country page, and let your mouse scroll over the United Kingdom chart—the UK has been consistently sequencing more specimens more assiduously, completely, and regularly and since far earlier than any other nation, as you can see from the number of sequences (the “num seq” pop-up figure), so it’s the best case study. You can see that until 12 October 2020 there was a variant winningly named “EU1” cruising to dominance over its competitors. But on 14 September something new had happened: 3 specimens had turned up with a new variant, named “Alpha”. By 8 March, Alpha has secured 98% of the circulating genome (34648/35670 specimens) and appeared on its way to crushing EU1 (173/35670 specimens), but again, something new had just happened: 6 specimens of a new variant, “Delta” had just shown up. You already know how this story goes: Delta swept the board. By Mid-August, Alpha sightings were as common as Elvis sightings (21/75887), and EU1 sightings were like unicorn sightings (2/75887). In the 1 November data—just prior to Omicron’s appearance—out of 96120 specimens only 9 were not Delta or some cousin of Delta. At that level, to explain the non-Delta signal, we’re really looking at accidents rather than spread: things that interfere with good mixing, such as small, isolated communities perhaps, or travel from distant areas. Natural alternatives to Delta had clearly been driven out of the larger circulating SARS-CoV-2 genome by the time Omicron showed up.