“But probably still and arduous task to run through 1000s of samples.”
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I’m sure you’re right. It’s a near certainty that they don’t sequence 100% of cases. The percentage breakdowns between variants is probably simply based on the sequence results of whichever subset of cases they happened to sequence. That’s likely “close enough for government work”.
Surely not all the cases are sampled and tested. We get information in percentage e.g. “40% of new cases are Delta” and “10% of cases in the Southeast are Colombian variant” etc but how many samples run?
They should be able to break down the variants by their sequences. It’s really just 4 different parts of amino acids strung together over a billion times. So any variation from the original sequence becomes a new variant. Though, this is fully expected in nature. As anything replicates (viruses, human cells etc) they sometimes mutate and/or degrade. Billions of cells replicating billions of times it sometimes doesn’t come out the same.