The article sets out specifically to caution about the misuse of jargon, so I think that probably is the important point that it seeks to communicate. I think

The article sets out specifically to caution about the misuse of jargon, so I think that probably is the important point that it seeks to communicate. I think that it goes off track and gets bogged down a bit in the details of SARS-CoV-2. There are two critical weaknesses in what has been written, taken as technical communication rather than blowing off steam. Firstly, it does not do a good job of providing the reader with an alternate word that expresses the relationship for which 'strain' is being misused (in the author's opinion). I believe that he himself would describe identical genome sequences as being the same virus 'isolate', but he doesn't explain that well, and the practical etymology of the term — the notion that the same virus isolate could be isolated in two different instances — makes adoption difficult. If this is indeed how 'isolate' would be routinely used (I am not even sure, as he doesn't establish this clearly) then it would be an instance of something that we might call 'deep jargon' or 'cryptic jargon', when normal words have specific meanings in a professional context that require a mental compartmentalization. Secondly, it does not establish why it is important for a less-informed reader to draw the distinction between a _____ of the virus and a new strain of the virus. We can imagine that there are differences in importance between a mere genetic difference, a genetic difference with functional biological consequences, and a genetic difference with epidemiological consequences. It is probably our expectations for the last of these, based on prior experience, which makes the distinction important; a very critical difference would be if the immune response to one strain was ineffectual against the other. However, this is muddled in an attempt to instead explain why it is difficult to distinguish the founder effect from biological selection.