Extraordinary claims require extraordinary evidence https://twitter.com/JakobssonLab/status/1338415484757225473

Since sequencing is actually my area of expertise, I may humbly chime in here (among many others) and break down the claims of this paper, why I am sceptical about its conclusions, and what this means in terms of your concerns

The authors report:
1) sequencing reads (just small pieces of DNA that a machine has read) the contain human and SARS-Cov2 DNA right next to each other

2) the RNA of the virus can integrate into the genome under very particular lab conditions

Chimeric sequencing reads (when DNA from two species looks like it's stuck together) can be real or can happen as a result of preparing the DNA for sequencing. There are ways to confirm this is REAL and not a preparation artefact, but the authors haven't done these things

In terms of their lab experiments, the authors took an enzyme that changes RNA (like the virus) to DNA (like our genome) and can put that reverse-transcribed DNA into the genome, and asked a cell line to make MORE of this enzyme than normal

And then they found that the virus's genome was integrated into the genome of the cells

I'm personally not particularly surprised that with this approach, this is the answer they got. This is exactly what the enzyme the told the cell to make more of does.

And that raises questions about how relevant this is to us, we don't normally make that much of it

Additionally, they used a cell line, and cell lines (while great for growing in the lab), have notoriously weird, and often unstable genomes

This is speculation, but I wonder what these types of unstable genomes mean in relation to actual biology. Are they really representative?

Now, to the things you may be worried about

I've seen this paper tweeted with comments about this meaning PCR tests for the virus are not to be trusted, and I've seen tweets regarding the mRNA vaccines

Regarding the implications on PCR tests
1) I dont think this is a worry. As far as I can tell, most PCR tests focus on part of the virus that is on the opposite side of the viral RNA than the part the authors reported as "sticking" to human DNA in the sequencing reads

So even IF their conclusions are sound, it means that a different piece of the viral RNA would be likely to get stuck into our DNA than the part that is used for testing

And besides, for the virus to integrate into our DNA, the virus needs to be present in the first place

The other concern about the mRNA vaccines that I've seen is people suggesting this means the vaccine RNA can get into our genome

Wait, I'm annotating a figure of the viral genome to make a point here

So this is a figure from the preprint, showing that most of the chimeric sequencing reads involved the right hand side of the viral genome

And here I've highlighted the region that (afaik) is used for PCR (brown oval), and the small portion called the Spike Protein (red oval) which is the ONLY portion of viral RNA used in the vaccine

Source for this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293463/#:~:text=The%20genetic%20makeup%20of%20SARS,CoV%20%5B28%2C29%5D.

Time for a summary?
1) seems unlikely the virus is integrating into human genomes
2) If so, I see no evidence the FULL virus is doing so (the virus needs all it's RNA to function)
3) Seems unlikely to interfere with PCR tests
4) Doesn't mean the spike mRNA vaccine will integrate

And also regarding 4- IF, and IF any of the spike mRNA from the vaccine can integrate into out genomes, it is useless without the rest of the virus right there

And if your immune system recognises the spike protein, the cell making it is destroyed & wouldnt spread to other cells

The caveats I should apply to this thread:

My expertise is evolutionary genomics, genome sequencing, and transposable elements (some of these are elements that CAN reverse transcribe and integrate into DNA)

I am not a virologist or immunologist

If I am incorrect on any of these points, please correct me, but keep my expertise and qualifications in mind

I have tried to make this understandable to those without a PhD in genomics, I hope it makes sense!

Also, lastly, I want to say that none of the individual analyses or experiments the authors did have faults to them PER SE, but the conclusions are almost surely over-interpretations that IMO require further support and context than what is in the preprint

I also encourage you to read the comments on the preprint as they cover which types of evidence are "missing" to draw these conclusions https://www.biorxiv.org/content/10.1101/2020.12.12.422516v1#disqus_thread

Here’s another thread with a different hypothesis about the chimeric sequencing reads

The practical implications of which are largely the same as if it’s a sequencing artefact https://twitter.com/mw_fr/status/1338275889268760576

To be clear, by “practical implications” I mean the implications for PCR tests and mRNA based vaccines