I have a good science background, but not particularly strong for genetic issues, and the origin of the covid virus is mostly a genetics question. A bunch of Americans, including friends of mine, are convinced the virus was engineered. One friend thinks it was created at the University of North Carolina.
I didn't feel capable of evaluating the data, but I tried anyway and learned a fair amount along the way. One of my first attempts was asking Google AI some question (not kept), and it responded that RNA can't be precisely edited, so I thought that settled the issue. However I noticed virologists didn't consider the matter settled, so obviously I shouldn't decide based on one AI response. Back to the investigation I went.
It turns out that RNA isn't a great medium for specific genetic editing. It's not as stable as DNA, so most work is done on DNA and then transcribed to RNA, which is very typical genetic processing. RNA can also be reverse transcribed into DNA, which is less common but some tricky viruses learned how to do this and some tricky virologists copy the tricky viruses. Amazing stuff, right?
So if a virologist wanted to experiment with coronaviruses of the SARS type, he would take one (and several are typed and readily available to scientists in the field), and turn it into DNA and then work on editing the DNA before turning it back into RNA. Then additional tests could be run on the newly created RNA.
This sounds like scary Frankenstein-like hubris, but this happens in nature all the time. Not the DNA part (which is much rarer), but RNA getting smashed up, parts deleted, parts inserted, genes recombined, and general RNA sequences being mashed together in all sorts of ways. In nature, cells/viruses even try to repair smashed up RNA and introduce changes in the attempts. So it's not surprising that virologists try to do this too because they want to try to stay a bit ahead of the viruses when possible.
So it's possible to engineer the covid-19 virus. But is that how it happened? The consensus among most virologists seems to be that it could be done and also it would be hard to tell if it was done. Signs of manipulation can be wiped out readily, so there aren't necessarily telltale signs.
The biggest change in the transmissibility of the virus came from an insertion of 12 nucleotides that created a furin cleavage site in the spike protein of the virus. This is a protein on the surface of the virus that latches onto cells the virus is trying to infect. Latching on is one step, but more important in actually penetrating into the cell, and the furin cleavage site helps a lot in penetrating human cells. So this is the big mutation that made covid as bad as it was in 2019-2020.
Some virologists have looked at the 12 nucleotides and considered it a smoking gun, obviously engineered. The majority don't appear to share that opinion, but it's enough of a debate to take it seriously -- not just wackos on one side of the question.
So who has the stronger case? That's also a matter of opinion, and I actually developed an opinion. To me, it doesn't look engineered. It's a non-standard furin cleavage site, and I think a virologist would go with a standard model rather than trying something somewhat random. Also the nucleotides start in the midst of a codon (the 3-nucleotide triplet that encodes for a specific amino acid). This looks somewhat unlikely for engineering too because the real target is the change in the amino acids, not the codons themselves. The codons are just the means. As an analogy, when we write we don't swap out individual letters but we do swap out entire words with words being analogous to the 3-nucleotide codons.
So that's my tentative conclusion, subject to change with new evidence. Below is a list of sources and briefly what the significance of each one is.
Three sources on CRISPR DNA editing showing how very specific it can be. 1, 2, 3. For RNA there aren't these tools, just some limited nucleotides replacement enzymes and less precise cut and/or paste.
One proposal to NIH is considered by some to be a smoking gun because it proposes tinkering with coronaviruses genome especially the spike protein and adding cleavage sites there. The program, called DEFUSE, covered many additional areas of research too, but it wasn't funded. However some of the research may have been done with alternate funding. Overview here. More detail here. Full text of the proposal here; I found 'cleavage' to be most useful search term to get to the parts on engineering the spike protein. Nothing here showed the specific sequences to be tried. Another paper on engineering of chimeric (combination manipulated genomes) viruses to show that it's a standard procedure in viral research. A 500+ page collection of approved NIH research proposals just to hold on to a valuable link. This isn't pointed to as a smoking gun so I haven't looked extensively at it.
Finally a batch of six papers about the specific nucleotide sequence and related material. Claim it was engineered. Detailed rebuttal of the claim explaining how huge a project it would have been. Claim that the furin cleavage site came naturally from another coronavirus. This paper is notable for the Q&A comments after the paper. The clearest explanation of the actual nucleotide sequence, written by a virologist some people think is complicit in engineering, meaning it could be a coverup. Very helpful timeline showing some of the controversial early discussions on the origin. Lastly an article on the natural mutations of the virus into the omicron variant to give a sense of how the virus can change naturally, which is what I think happened to create the original nasty covid virus.

