You've forgotten the most likely explanation, which is that this entire thing was an artifact of the method being used (Sequencing, Pcr).

Here’s what I’ve learned over the years about sequencing and genomes:

1. No viral genome has ever been sequenced directly from a purified sample containing only the target virus. Patient samples always contain a mix of human, bacterial, and other genetic material, and total RNA is extracted from all of it together.

2. No viral genome has ever been read in one continuous physical read from start to end - not even with long-read sequencing, although technical feasible, and not even with Sanger sequencing (considered the gold standard). Every published genome is stitched together from overlapping fragments.

3. Published viral genomes are computational assemblies, not direct readouts. Software algorithms take millions of short fragments (~150 bases) of mixed origin and attempt to stitch them into a candidate sequence. The output is a statistical best guess - the algorithms cannot guarantee it corresponds to any single real biological entity.

4. The first published version of the SARS-CoV-2 genome actually contained confirmed human DNA (matching the "human genome" model) at the start and end - confirmed by Edward Holmes, a co-author - in writing. It was quietly removed in later versions.

5. There is no independent verification loop. Every subsequent study that "confirms" a viral genome uses primers and alignment references derived from the original computationally assembled sequence. If the original is wrong, every downstream confirmation inherits that error.

6. Both the US CDC and Germany's RKI have formally confirmed that they do not isolate viral genetic material from other genetic material before sequencing, and neither possesses a dataset where the complete genome was independently reconstructed from scratch.

7. The bottom line: what they call a "viral genome" is a computer model built from fragments of unknown origin, not a molecule that was physically observed or read end-to-end.

You can find all details & receipts on my substack. Cheers!