> we can hope there’s a less infectious strain out there
But how? We are able to surveil only a tiny fraction of genomes, relative to strains circulating. How would a "less infectious strain" ever emerge to the extent we'd have a high probability of sampling it? Darwin argues against this version of the idea.
Nevertheless, the OP is also wrong that it's faster to produce a live attenuated vaccine by finding one in the wild than it is to use tried-and-true viral vectors that are easy to reengineer, have previously received regulatory approval, and indeed are already in active trials (e.g. Oxford's adenoviral trial). It's also easier to trial heat-killed virus -- and indeed, that too is being trialed.
We can actually sample quite a large percentage of the strains out there if we actually try. COG-UK has already sampled 10,000 out of the few 100,000s in the UK without really trying.
Can you please stop saying I am arguing for things I am not arguing for? More time spent reading and less posting would improve your argument.
Yes, there are about 13k genomes deposited in the databses right now, but they are from all over the world -- not just the UK.
But yes, given infinite capacity it would be excellent to sequence from every single patient. It would be a dream, but sadly we're barely able to get enough cotton swabs and RNA isolation kits right now to run a basic qPCR for 10% of the population, let alone get all those viral genome sequences. It would be fascinating to have that many, of course.
You do realise that there are over a million positive samples sitting in freezers in the USA alone. You do know that a single modern DNA sequencing instruments can sequence more than 500,000 viral genomes in one 48 hour run?
It’s my understanding that viruses have a complex fitness function. If you think about it, the ideal virus spreads like crazy but doesn’t make anyone sick. If you make someone sick, you reduce the time they spend in the world so you spread less. Killing the host is definitely a no-no from the viral perspective, now you spread dramatically less. So viruses actually tend to evolve toward less intense disease. It’s why novel viruses kill so much more than viruses that have been around in the human population for a long time.
Forced evolution to lower infectivity is also a common way to make vaccines, so I’m quite certain one of the 100 or so vaccine efforts is trying this.
However, it’s not clear that the deletions in the OP are attenuating. If we end up with attenuated virus, it will likely come from a directed evolution experiment, not just getting lucky with a natural strain. Even such a natural strain would likely need to go through a fair bit of directed evolution to attenuated it to the point of harmlessness.
We don’t know if the deletions already seen in the current genome data set are attenuated or not as nobody has checked. I am suggesting that we check.
The bigger point I was making is that there are many deletion mutants out there. We should be looking for more and checking if they are attenuated or not. We might be very unlucky and find there are none, but that seems rather defeatist given we haven’t even tried.
I don’t know. It is a novel idea as it wasn’t possible more than 10 years ago to search. My personal experience is new ideas struggle to get any support until they are shown to be correct and then everyone says it was always obvious.
But how? We are able to surveil only a tiny fraction of genomes, relative to strains circulating. How would a "less infectious strain" ever emerge to the extent we'd have a high probability of sampling it? Darwin argues against this version of the idea.
Nevertheless, the OP is also wrong that it's faster to produce a live attenuated vaccine by finding one in the wild than it is to use tried-and-true viral vectors that are easy to reengineer, have previously received regulatory approval, and indeed are already in active trials (e.g. Oxford's adenoviral trial). It's also easier to trial heat-killed virus -- and indeed, that too is being trialed.