burying the lede

[mellowtigger]

"Burying the lede." This idiom is one of my favorites, because the obscure spelling gives it an air of mystery. It really just means that the most significant statement is kept out of initial sentences for an important story. Since I'm talking about this idiom in particular, we'll pretend that today's post has nothing whatsoever to do with a certain topic that I promised to avoid for 6 months.

For example, suppose you were investigating potential side effects of a brand new kind of vaccine. Perfectly reasonable thing to do. New technologies might have unexpected consequences, right? Sure. So you work in your lab to answer that question. As you write up your findings (which are ONLY about the lab environment and NOT actual whole human people (yet)), you mention a few paragraphs in: "Oh, sure, we know the virus can add itself to human dna, so we were just curious if the more limited vaccine could do the same thing." As everyone already knows, of course.

"A recent study showed that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the genome of human cells [25]. This gives rise to the question of if this may also occur with BNT162b2, which encodes partial SARS-CoV-2 RNA."
- https://www.mdpi.com/1467-3045/44/3/73/htm

Whoa.  Whopper of the decade.  Talk about burying your lede!

I'll gladly queue up for my next vaccine.  FAR better to gain exposure to the least influential bits, rather than both it and the nastier bits of the whole virus.  When this knowledge finally goes mainstream, I look forward to the next relevant Plague Poem on this topic.

Comments

[darkoshi]

This appears to be the study that one refers to:
2021/05/06: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166107/

Other related ones;
2021/07/12: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8274596/
2021/08/03: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8379926/
2021/10/29: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8554740/

I only skimmed through them.
Makes me wonder though, if parts of the COVID virus can end up getting added to your DNA, how often it happens with other viruses too.

[mellowtigger]

Famously, HIV does this rna-to-dna conversion.
https://pdb101.rcsb.org/motm/33

Generally, this activity is done by retroviruses, hence the name ("backwards virus"). So far, it appears to be a very short list of viruses known to do it.
https://www.health.state.mn.us/diseases/retrovirus/index.html

[darkoshi]

Ah, I see.

[mellowtigger]

P.S. This detailed rebuttal from your middle link is hopefully a little good news?

"The very low frequency of identified chimeric events (Table 1) suggests that SARS-CoV-2 integration into the host genome is unlikely. Given that the HEK293T-L1 model increases detection of “rare integration events” and L1 can retrotranspose any polyadenylated cellular RNA (2) and “insertions” are found preferentially in protein-coding exons, a bias unknown to L1 endonuclease insertions (3), these findings are likely spurious. Additionally, 2 of the identified 61 chimeric nanopore genomic DNA (gDNA) reads contain human DNA from separate chromosomes (chr1,chr22 and chr18,chrX, respectively), suggesting a portion of chimeric gDNA nanopore reads have arisen due to infrequent technical artifacts, such as base-calling software not recognizing an open-pore state between distinct molecules."

[darkoshi]

Yes, I thought perhaps so too. But the study you linked to seems convincing as well, so I suppose we'll have to see if it gets any rebuttals like the first one or not.

[mellowtigger]

Yeah, that's the part that worries me. Two different studies found the same result. Result replication is usually a "good" sign that something is done right. Maybe the objection applies to both circumstances equally? I just don't have the skills for that kind of analysis. :( These days, everyone needs a pet microbiologist in their back pocket for convenient consultation. :)