Ryan Hisner

Headlines often speak of things like a "1% increase" in funding or pay for public servants of public goods, which is totally misleading. Inflation's always more than 1%, so a "1% increase" is plainly a cut in pay/funding.

It would be unthinkable to report GDP or anything else in nominal terms.

Numbers should only ever be reported in real terms. Have you ever noticed that for GDP or any other economic stat, the numbers are always given in real terms, but when it comes to publicly funded things (research funding, teacher pay, etc), they always use nominal figures, unadjusted for inflation?

Study is paywalled. Do we have any idea how it is able to maintain such a large genome? Exceptionally good proofreading? Extraordinary robustness to mutations? Ultra-high rates of recombination capable of purging deleterious mutations? Something else?

Wanted to flag this interesting study led by our collaborators
@kinglabipd.bsky.social suggesting that at least in some contexts, the immunogenicity of H5 influenza vaccines can be improved by mutations that stabilize the HA protein.

See Fede's quick three-post thread for the latest fine details on circulating lineages, something he is THE leading global authority on.

Also, a cool song recommendation at the end by a band I'd listened to years ago but had almost entirely forgotten about.

BTW, is the "impossibility" of a natural FCS insertion still a favorite argument of lab-leakers? I don't follow closely enough to know if it's still a favorite or if it's fallen out of favor, perhaps replaced by some Sinophobic tale congenial to national security types. 3/3
@zachhensel.bsky.social

I still have no idea whether the dominance of G's in SARS-CoV-2 insertions is representative of viral insertions more generally or if this is something specific to SARS-CoV-2 (or maybe just coronaviruses or perhaps RNA viruses with extensive secondary RNA structure). 2/3

Reminder that FCS insertions are not rare or unusual & tend to resemble the OG SARS-2 FCS insert—7/9 nucs are G's in this one, consistent w/the normal G-heavy pattern of that dominates SARS-2 insertions.

1 seq uploaded today of this, which is actually in 7 sequences overall from late 2024. 1/3

Well, that one might well be dead now, which is apparently a more desirable outcome to some researchers than tolerating a remote chance that someone's poo privacy might be violated.

A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation Long-range RNA-RNA pairing impacts the genome structure and function of SARS-CoV-2 variants. To understand the structure and function relationships of different SARS-CoV-2 variants that have emerged d...

Ah, this is the one. I read over it quickly a while ago but need to read again. www.biorxiv.org/content/10.1...

SARS-CoV-2-induced dysregulation in ADAR editing patterns persists post viral clearance in individuals with mild COVID-19 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections remain a public health concern worldwide. Viral antigen triggered innate immune response leads to induction of interferons (IFNs...

This wasn't it but does look interesting in any case. www.biorxiv.org/content/10.1...

There was a recent preprint about ADAR binding something that I thought might be relevant. I posted about it, but the search function here is garbage, so I can't find it.

Yeah, I mean, logically, there has to be some replication/transcription happening prior to DMV formation just to produce the proteins necessary for DMV formation, right?

And while I'm not certain, I think the NSP9-SND1 connection early in infection has to happen outside DMVs as well.

I imagine so, but I don't have any idea why ADAR would strike such small regions so intensely. I really don't know anything about the mechanisms by which ADAR works, so maybe someone with expertise in that area would be able to make sense of this.

Oh, this happened to me during the past school year. I'm always in a hurry, and I had no idea anyone was behind me as I entered the building. Later, I heard from students how another teacher was appalled that I'd "slammed the door in her face."

What Measles Did to My Family My mom always told me that measles was what made my sister sick. I was 8 when she finally explained the whole thing.

Absolutely. Stories like this need to be spread as far and wide as possible. www.voicesforvaccines.org/what-measles...

Adding to the A->G cluster list: two chronic-infection LP.8.1.1 seqs from Ontario, Canada, from June have 10 A->G muts in a 101-nuc stretch. A few other sequences have had similar A->G clusters in this ORF3a region.

Still unsure if this phenomenon is unique to SARS-2 or what the mechanism is.

Nothing known yet. BA.3.2's NTD loops have been shortened so they're more like SARS-CoV-1's, & short NTD loops have been shown to cause increased fusogenicity & infectivity. But it also seems to have a bunch of compensatory mutations to offset instability from short loops, so it may all cancel out.

I think it had something to do with overzealous Firefox privacy protections. I had to exempt BlueSky from digital fingerprinting protections, and now pictures seem to be working.

I will look into Brave though as there are numerous other things about Firefox I'm not crazy about.

Delta Cryptics love Y449R.

I would like for the images I paste into Bluesky posts to show up when I use Firefox. Right now, I have to go back to using Chrome in order to post images here. Example below showing a post using Chrome and another post with the same picture using Firefox.

Post #3 picture.

Post #2 picture.

Apparently, my pictures are not showing up because of some issue with Firefox, which sucks. So until I figure out a way to solve that issue, I guess I have to use Chrome.

Picture for post #1 below.

No, I can't see them either. I'm not sure what went wrong. If they don't appear soon, I'll try posting the figures separately in a reply.

Is there a similar mutational switch out there for BA.3.2 which, once found, will light its fuse and launch it to global dominance? Too soon to know, but as it grows, so does the number of its opportunities to find such mutations.

I wouldn't bet against it at this point. 4/4

Seems clear now that BA.3.2 is not going away anytime soon. Its overall impact so far has been negligible, but at first BA.2.86's was as well. Once it got S:L455S (becoming JN.1) the dam burst & it set off a new wave in the global North. The question now is.... 3/4

This BA.3.2.2 was collected July 15, & is most closely related to the recent South African sequences from May & June.

It has an NSP5 mutation known to be beneficial (ORF1a:K3353R) & 2 new NSP12 mutations, which is unusual. Its 9 synonymous mutations indicate it has been circulating somewhere. 2/4

Wow, BA.3.2 hits its 4th continent with a new sequence from Western Australia.

Reminder: BA.3.2 is a saltation variant resulting from a ~3-year chronic infection. It is very different from and more immune-evasive than all other current variants. 1/4

One great unknown is for how long immunocompetent people can be infected w/SARS-2. This shows such infections can be prolonged, even in nasal swabs, a great contribution.

More difficult mystery: How long can infections can last in other tissues & how much does this contribute to Long Covid? 3/3