A while back, in the spring, some travelers arriving in Angola from Tanzania tested positive for what was, AT THE TIME, the most divergent variant ever sequenced...to date. It was wildly and unexpectedly divergent, like Omicron. It was only found because some people traveled FROM Tanzania to Angola. It never went anywhere though and was forgotten. In Tanzania, their President denied the virus existed. They never tested people, never sequenced the virus, and basically ignored it. Zero cases, great success, right? That President is dead now, from covid. But anyway, that variant back in March/April from Tanzania, was a descendant of a different branch of the original covid, dating back to China. A whole different evolutionary tree basically from what created Alpha, Beta, Gamma, Lambda, Mu, Delta, and everything we've been monitoring basically. It may very well be that the original B.1 variant is NOT the ancestor of Omicron....it may not be properly named. In this prior rare African variant (that went nowhere, or did it?), convergent evolution had given it SOME of the B.1 mutations, even though it descended from a prior branch of the virus it evolved to have those same B.1 mutations but otherwise came from a different ancestor lineage. Let me find the article...
The versatility of SARS-CoV-2 to evolve new variants that increase transmissibility, virulence, and immune evasion is a new troubling feature of the Covid-19 pandemic. The recent discovery of a novel variant emerging from Tanzania adds a new chapter to this disturbing story.
This may explain how Omicron developed so many unique and unknown mutations, and possibly why Africa has been spared much of the worst of the virus. They have a different virus there, possibly less deadly, and it's evolving on its own there. Over time, their tree is also favoring many of the same mutations that have been seen in the rest of the world, but more slowly and adding them to a very different ancestor virus base. The thinking is this is still a B.1 variant, hence B.1.1.529, BUT, if you follow the evolution of the rest of the virus, which we haven't/can't because of a lack of surveillance, it could very well be the B.1 mutations making Omicron labeled as a B.1 family variant, are actually examples of convergent evolution where a whole other branch evolved the same mutations.
Would be interesting to see a comparison of Omicron to whatever they found in Angola in the spring. So basically this is a whole new virus, even more divergent than Delta, and may have a very different ancestor way back from everything else circulating. It could end up being the world's most contagious head cold, or something worse, won't know until enough people get it. And this is why everyone is freaking out, because this was something that came out of left field from an area of zero surveillance, where the virus has evolved over time VERY different mutations from a very different ancestor.
The Moderna CEO probably knows this, as do many scientists. But to date our vaccines have "worked" against the tree/lineage that has impacted the rest of the world, that we know about. But this came from a whole other tree, and is picking up on the common mutations that have made covid perpetuate, BUT it's a different ancestral virus branch overall, meaning it's back to square 1 with the vaccines. Let's hope it's a less severe disease. So the vaccine doesn't work, no problem if it's just a bad cold. Or horrible if it's as bad as what we have been following. Have to wait and see.
Here's a chart showing spike mutations in Africa over time, in a tree format.