If you want to understand SARs-CoV-2, you must first understand Viroids
1) Thank you, but this post is too difficult for amateurs to read, it makes our brains hurt. This should be published in an obscure journal where only a thousand of your peers will have to see it!
2) You note that viroids don't infect mammals, so I suspect your cat is safe. If you could explore the mammalian mechanism of resisting viroids you might find a useful pathway (other than Burbank methods) to protect your grow-ops.
3) Would your lab potentially be able to take samples from 10 vaxxed people and ten unvaxxed and determine the existence of spike transfection into DNA in (human) vivo? The vaxxed should all have Wuhan spike incorporated (somewhere), while the naturally infected (at least 90% of us) may have Wuhan spike, any Greek letter spike, or preferably no incorporation. Lymphocytes from blood donors might be an accessible source, and you could also have your grad student or fellow look at the T-cells to confirm immune status.
Crazy mutations in the photos. Do the mutations appear similar in other species, say tomatoes?