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From Source.

I emailed the CDC to ask them how they are verifying what variant is dominant. This was their answer. Thoughts?

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Since the treatment plans for the various strains are roughly the same, there is no diagnostic reason for WGS on individual patient results. It would be a waste of doctors' time. But there is a likelihood that test samples are being sent to some central (state) lab for research. WGS could be used on a selection of the samples to analyze the overall spread of variants, the "surveillance purposes".