While what you say is certainly possible, it's not (IMHO) very likely. It doesn't matter that countries closed borders and restricted travel, or that not all countries were sequencing with the same rigour. That doesn't affect the eventual outcome as we randomly sample patients in the rest of the world.
If a country were hypothetically completely isolated and not sequencing, then we could have a new unknown variant develop. But from a given previously known origin genome, it would be mutating within that population over time at a fairly predictable rate, which would lead to a family of variants rooted at that known origin. We would see a spectrum of variants in a cluster branching from the origin. However, it clusters far from its origin, and this does raise a red flag.
It's possible that as we collect more data, we will "fill in the gaps" and get a better picture of how it evolved to the point it is at today. If there is a hypothetical country where this evolved naturally, those variants will still exist within the local population, and we will gradually sample a range of them in other countries over time as they too travel abroad where they can be detected.
If however it is not natural, then those intermediates will not exist, or will only exist as frozen down passages in a lab freezer. Maybe we'll identify the lab in time, if that's the case. They should be able to match it if they sequenced it.
Whichever hypothesis is correct, the data can't lie. We will know one way or the other fairly definitively in time.
If a country were hypothetically completely isolated and not sequencing, then we could have a new unknown variant develop. But from a given previously known origin genome, it would be mutating within that population over time at a fairly predictable rate, which would lead to a family of variants rooted at that known origin. We would see a spectrum of variants in a cluster branching from the origin. However, it clusters far from its origin, and this does raise a red flag.
It's possible that as we collect more data, we will "fill in the gaps" and get a better picture of how it evolved to the point it is at today. If there is a hypothetical country where this evolved naturally, those variants will still exist within the local population, and we will gradually sample a range of them in other countries over time as they too travel abroad where they can be detected.
If however it is not natural, then those intermediates will not exist, or will only exist as frozen down passages in a lab freezer. Maybe we'll identify the lab in time, if that's the case. They should be able to match it if they sequenced it.
Whichever hypothesis is correct, the data can't lie. We will know one way or the other fairly definitively in time.