I am way outside my area of expertise and speculating wildly here, but aren't various retroviruses quite common in our environment? Enough so that many COVID-19 infections must have occurred simultaneously with one of many such viruses?
So, logically, COVID-19 viral components likely have coexisted inside our bodies with some quantity of reverse transcriptase, no?
I do know that we find viral DNA in human DNA, likely as a result of past retroviral activity. I wonder if we ever find sequences from non-retroviruses that have hitched a ride so to speak.
Virus genes aren't like lego pieces that just snap together and work. Genetics is a very delicate balance. Retroviral RNA evolved to be packaged up in such a way that it's ready to be transcribed by the reverse transcriptase. Coronaviruses didn't do this.
If this was actually what was happening then we'd expect to either see:
* (if it utilizes a present retroviral reverse transcriptase) only people with active retrovirus infections getting long COVID
* (if a variant picked up the gene from another retrovirus) evidence for reverse transcriptase being copied into a widely circulating variant that for some reason is only activated in some people
We don't see either of these things happening. It would be extremely obvious from the data and genetic samples that that happened. There's also generally very little evidence for viruses picking up features across long genetic distances. If this was common we'd see more of it.
SARS-CoV-2 also generally infects different types of cells than the ones that HIV does, so even if that was a possibility genetically, it's unlikely because they're not active in the same cells.
So, logically, COVID-19 viral components likely have coexisted inside our bodies with some quantity of reverse transcriptase, no?
I do know that we find viral DNA in human DNA, likely as a result of past retroviral activity. I wonder if we ever find sequences from non-retroviruses that have hitched a ride so to speak.