How are you calculating those odds? And then once you have calculated them, what are you using to determine your threshold for "low" odds? The odds that a bunch of atoms ended up turning into you and me and the rest of humanity are extremely low or extremely high depending on what your criteria for "low" odds are.
Given the number of bats in the world, the number of human hosts, and probably most importantly, the number of individual virions within each infected host (and therefore the number of replication cycles) is...astronomically high. There are somewhere between 1 and 100 BILLION virions of COVID in each infected person. Now imagine a few thousand bats infected...we are already talking about maybe 1 QUADRILLION different virions (1,000 trillion). It only takes one virion to incorporate some very handy and fitness-increasing HIV-1 RNA into its genome and it is off to the races.
I truly have no idea what the answer is, but as someone well versed in economics, econometrics,and statistics, to me the relevant odds are not about independent coin tosses etc. I would like to know P(A|B) where:
A: sequence of 30 nucleotides appears in a virus identified in nature
B: sequence appears in a patent application that predates discovery in nature
Seems to me that would involve a whole bunch of arithmetic, but that ought to be calculable using this database.
the mutation rate simply is not as high as you imagine it to be. If it were, then we would (likely) see more wobbling around the wobble pairs in the cleavage site coding region.
I never mentioned mutation rate so your gotcha is not as crafty as you might think. Also a mutation in the sense you seem to be implying (random base pair changes due to lack of proof reading) is not really what I am talking about. I am talking about HIV-1 genome being incorporated into SARS-CoV-2 by the host cell or either virus during replication. That is not that crazy when you have quadrillion of replication cycles and a selective pressure to mutate and incorporate new RNA.
we're talking about the odds of the founder event. My guess is odds are about 1 in 3^{5-6} (3-ish wobble options, five to six wobble sites, haven't looked at the sequence to confirm this. Probably someone can do a better analysis based on codon usage in humans. I suggest doing it as an exercise in understanding molecular biology.
alright, do you want a specific answer? My guess is it's somewhere around one in 3^{5-6}-ish, for the singular founder event that establishes and fixes that sequence as the canonical sequence for the furin cleavage site of COVID-19.
Given the number of bats in the world, the number of human hosts, and probably most importantly, the number of individual virions within each infected host (and therefore the number of replication cycles) is...astronomically high. There are somewhere between 1 and 100 BILLION virions of COVID in each infected person. Now imagine a few thousand bats infected...we are already talking about maybe 1 QUADRILLION different virions (1,000 trillion). It only takes one virion to incorporate some very handy and fitness-increasing HIV-1 RNA into its genome and it is off to the races.