Someone on twitter asked me

What does it really mean when people say that covid can alter your dna?

Like i get it in theory but i dont understand how it would work

and another person asked

Do you have any thoughts on horizontal gene transfer

Many viruses have a chance of inserting themselves in the DNA of a cell without actually triggering cell death or furthering replication. It is supposed to be rare in coronaviruses. Most of the ones that do this are known to be retroviruses

It seems to happen in some people with sars-cov-2 so when their cells die, the segments of viral dna are released. This is a suspected failure mode of PCR

The PCR failure thing is heavily pushed by conspiracy theory types to say that viruses don't exist. I don't hold that stance. Its fascinating because the DNA implantation does suggest that PCR itself may be flawed more than people believe

I think viruses can be friendly and helpful. There are viruses that live in mucus that specifically target and destroy pathogenic strains of bacteria. ("bacterialphages"). So the idea that viruses don't exist is absurd to me. But I can see why people would have doubts about PCR tests tho. Been thinking about this from before the pandemic hit.

There are all sorts of stories of weird faux pandemics thanks to faulty testing. So I'm inherently cautious here. There's a really illuminating story about Dartmouth Hitchcock's faulty whooping cough pandemic that is worth reading. I lived near this place for a while and some of my family have worked at it.

This has been termed "The false positive paradox"

Even a test with a very high 99% specificity (1% chance of false positives), when used to screen asymptomatic populations with a low background rate of actual infection, will yield high levels of false positives.

I am uncertain about PCR as a test myself. It does seem to have a much higher failure rate than is touted, and the amplification step they use does seem to be a bad way to actually measure infectious genetic material as a way to confirm someone is 'positive'. Some of the PCR techniques are better than others because they are designed to be used as diagnostics, but even then they wouldn't be able to distinguish genetic transfer from viral infection.

This is why I've been focusing on other signals besides just the PCR tests. With it being so hard to get testing done early on, we used head fevers as a proxy measure of infection. I also was hoping to see the data from waste-water plants. The CDC has only just recently started pushing this data out. The more signals we have, the easier it is to trust that the results from a test kit aren't a false positives.

I'd really like a reliable way to measure if someone is a carrier and able to transfer a virus without showing major symptoms. I don't think a single test is gong to work if the DNA can be modified like this, so it seems foolish to not also explore other ways of measuring. It has been an issue since the dawn of infectious disease research. Like the case of Typhoid Mary', who was a carrier of the disease that wasn't has heavily impacted. She apparently went on to spread it for a long time.

Some people believe this means there never was a virus and it is all human DNA, but I believe this is a mistake. That being said I do think the gene transfer effect happens more often than is commonly believed, but not so often it would explain it happening every time like purported by the conspiracy.

It's not even a new idea really. Horizontal Gene Transfer effects from viruses are also suspected as the cause of many virus derived cancer mutations. This has been a very rapidly improving area of research and is one of the reasons why I pay so much attention to DNA repair processes.

Been some research into it in the past, but not as much as I think there should be

How this impacts the person's gene expression? I am not sure. I do know if it happens to trigger any of the HERV-* pathways in the genes, it tends to be problematic.

I'm interested in HERV-* pathways because it is suspected of being a cause of triggering neurological disorders. In particular, strange ties to Multiple Sclerosis.

The research is still the first evidence of this retrovirus presence, in the severe COVID-19 patients' respiratory tract and plasma. The HERV-K presence — which also occurs in other diseases, such as cancer and multiple sclerosis — can be used as a biomarker associated with severity in COVID-19 cases. Its early detection could reinforce certain strategies use, such as anticoagulants and anti-inflammatory drugs

A lot of times these transpositions from virus to host are actually beneficial to the host' survival, so they get passed on thru evolution. I suspect many of these viral stretches of DNA are actually activated to induce hibernation. Its fascinating to think our bodies do this to learn patterns against disease.

My hunch is this is what 'long covid' is -> that HERV mechanism being triggered as a defense mechanism developed by an old virus in our genome.

But that is one of my unfounded crankpot ideas. I can't prove it, and its one of a number that might be possible.

I believe this is the term for the process that ends up triggering the host dna modification

I also suspect that this process is more normal than we realize and is perhaps a mechanism that drives horizontal gene transfer between bacteria etc.

I think part of the problem is we don't look for it because we don't have good mental models of how bacteria share genes and mate.

It these effects can cause changes in gut bacteria in fascinating ways.

Like how there was a carbohydrate digestion enzyme transferred from seaweed bacteria into the human gut bacteria in some people.

That mechanism has been investigated as a way to spread antibacterial resistance. So it's worth thinking about more critically than simply looking at it under the vaccine/virus lens.

CRISPR is one mechanism involved here, tho I am not sure how often viruses use it.

I don't know the rest of them. They are often used for intentional gene editing, particular ones that target "germ line" if they are meant to be passed on. We are still fairly 'green' at this process and I suspect there are more out there we don't know about.

Humans have mechanisms that fight this process in our own cells. But sometimes it doesn't work. People are trying to figure out how to stop this effect to enable gene therapy with it.

I personally think disabling CRISPR defense is very dangerous. There was a study that showed bacteria themselves use CRISPR as part of a combative process.

Some bacteria are resistant to it as well. It may be more widespread than believed.

Now, do Vaccines cause this? This idea keeps me up at night.

Horizontal Gene Transfer what?