First, it was 96% identical. But that was in 2013. Presume it's being passed bat to bat every few days for 6 years, then at some point made the jump to another species, most likely in a wet market. It's really not unreasonable to imagine a 4% drift in that time.
Second, we don't identify every virus or every strain of every virus. Just because we found one that was 96% similar doesn't mean that all the other bats carry an identical virus. It's quite likely we found a distant cousin of the umpteenth-grand-parent of covid-19, and sequenced it.
Can you explain how that evolutionary path led to the virus becoming better adapted to humans than it is to bats, and can you explain how all the samples we have ever found, from the very beginning of this outbreak, are uniquely adapted to humans?
It's not an unreasonable question. But my own guess? Selection bias applies.
Viruses grow by the millions, billions, and mutations occur frequently. This virus's ancestor might have hopped around civets for months. Then, a few random mutations on one got lucky and made it really good at infecting humans. That's when it made the leap. We don't see the billions of attempts and mutations that sucked at infecting humans. We see the one that did.
Now, my own bias is that my honours thesis was on evolutionary algorithms and I spent a lot of time being amazed at how well random mutations can lead to optimal answers.
You’ve asked the same question in 3 spots. You’re asking the question backwards and not reading the other comments here (for example, the particular response you responded to) There are some very good reasonable answers for why and how this could have happened, unless you’re a biologist and are going to tell us how it happened (which the paper you cited doesn’t) you’re beating on a painful drum
First, it was 96% identical. But that was in 2013. Presume it's being passed bat to bat every few days for 6 years, then at some point made the jump to another species, most likely in a wet market. It's really not unreasonable to imagine a 4% drift in that time.
Second, we don't identify every virus or every strain of every virus. Just because we found one that was 96% similar doesn't mean that all the other bats carry an identical virus. It's quite likely we found a distant cousin of the umpteenth-grand-parent of covid-19, and sequenced it.