318 karma · joined February 14, 2016
The ghost admixture story(s) will turn out to be much more localized, I imagine.
https://www.cell.com/cell/fulltext/S0092-8674(20)30059-3 https://www.pnas.org/doi/full/10.1073/pnas.1313787111
IMO his is the best random project channel on youtube
Original paper: https://www.pnas.org/doi/10.1073/pnas.2209766119
This is "incomplete lineage sorting". There's no need to invoke anything more exotic than standard vertical inheritance, but the existence of genetic diversity within populations after they split/speciate (i.e. it's not a single Adam & Eve that give rise to a new species) produces counter-intuitive patterns of relatedness like this.
v2, now with a Y chromosome
https://www.ncbi.nlm.nih.gov/grc
The complete Y chromosome from HG002 was added with v2 (after the paper was written). Probably a patched form of GRCh38 will be made using T2T sequence, but IMO it makes more sense to use T2T-CHM13 as a reference with its single origin instead of a weird chimera, at least until pan-genome graph methods mature.
Even if Ct values are unchanged between vaccinated and unvaccinated cases, this is conditioned on being infected in the first place, and isn't the whole story. Duration of infectiousness matters.
Yes, boosters are necessary to reduce infection with Omicron, the antibodies from the original vaccine are just too big of a mismatch. That's not news. I'm glad to hear you're not taking those negative efficacy estimates at face value - it's almost certainly the result of missing confounders present at the start of their omicron wave. Unvaccinated individuals are probably less likely to live in urban areas, travel internationally, or even seek a covid test, for example.
The other important factor is that because your immune system is primed to recognize SARS-CoV-2 after vaccination, even if you do get infected, it responds and clears the infection more quickly than it would otherwise. That could mean you're never infectious, or infectious for fewer days, reducing transmission. Pre-omicron, breakthrough infections were infectious for 5.5 days on average, compared to 7.5 days for infections in unvaccinated people (https://www.nejm.org/doi/full/10.1056/NEJMc2102507). Yes, all this to maintain some semblance of healthcare for society, and to fill up fewer reefer trucks with body bags.