Some experts suggest Omicron variant may have evolved in an animal host
You can look at the phylogenetic tree here:<p><a href="https:&#x2F;&#x2F;nextstrain.org&#x2F;ncov&#x2F;gisaid&#x2F;global" rel="nofollow">https:&#x2F;&#x2F;nextstrain.org&#x2F;ncov&#x2F;gisaid&#x2F;global</a><p>with Delta being the large green and blue parts at the top, and Omicron being a few red dots a little up from the bottom. If you trace back, you&#x27;ll see that its nearest relative is wildtype from the spring of 2020. That&#x27;s pretty weird, and there are really only three ways I can think of that it could happen:<p>1. human manipulation in a lab using early wildtype samples. This seems unlikely, because what would be the point and how did they let it escape?<p>2. chronic infection in a single immunosuppressed patient. We&#x27;ve seen this before (see, for example, this: <a href="https:&#x2F;&#x2F;www.nejm.org&#x2F;doi&#x2F;full&#x2F;10.1056&#x2F;NEJMc2031364" rel="nofollow">https:&#x2F;&#x2F;www.nejm.org&#x2F;doi&#x2F;full&#x2F;10.1056&#x2F;NEJMc2031364</a> ) and southern africa has a lot of immunosuppressed people thanks to HIV. Additionally, there are some genetic markers that suggest evolution in a human.<p>3. spillover of wildtype in spring 2020 to some animal, evolution in that population for about 17 months, then spillback last month into humans.<p>I&#x27;m with the article, in that I favor 3 even though there&#x27;s some evidence for 2 just because i can&#x27;t quite understand how the omicron patient might have gone all that time without infecting anybody else with a proto-omicron version of the virus (which would then spread and be picked up on that chart). It&#x27;s possible, I guess, that omicron got increased transmissability in a mutation in the recent past, and it could have lived in the patient with bad transmissability for a long time previous. And since delta is so amazingly transmissable, any proto-omicron could have infected a couple of people and then died out undetected. But still.