Thread by @1goodtern

It's probably time to talk about bird flu again.
🧵

You may have noticed UKHSA going into intense *we're not panicking mode* about flu here.

They've given a few reasons, including the circulating strains causing more illness and death...

https://x.com/cv_cev/status/1986952422464328170?s=20

But there's something else happening at the same time that has them on red alert.

In the last *week* there have been *fifteen* new outbreaks of highly pathogenic H6N1 bird flu at commercial premises.

All across the country.

experience.arcgis.com/experience/062…

There are other farms also being urgently investigated.

And there has been an intense flurry of new cases of H5N1 bird flu in wild birds.

Mostly migratory geese and swans, but also local populations of a wide variety of birds.
It always breaks my heart seeing each one of these.

So there's a rapidly increasing amount of bird flu around...

And there's a rapidly increasing amount of flu A around...

And that dangerously increases the risk of what's called *reassortment*.

Basically, flu's genome comes in 8 little pieces that get duplicated when it is replicating.

When two strains infect the same cell, those pieces can get mixed and matched.

That’s called reassortment.

Think of it like two people with eight playing cards, discarding some, and merging the rest together into one hand.

(It's different to Covid's genome, which is one long strand. When two covid strains meet, the copying machinery can switch templates mid-way, splicing the two together. That's recombination - not reassortment.)

So, yes, I think UKHSA, on top of everything else, are worried about a reassortment event.

But there's another factor that I suspect they haven't spotted.

Reassortment needs two different flu strains infecting the same person at once, and those strains both need enough time to replicate together in the same cells.

In most people, the immune system clears one infection fast, so the overlap window is short.

But in someone who's immunocompromised, the infection can last longer, viral loads can stay high, and control over replication is weaker.

That gives multiple strains a chance to coexist and swap genome segments.

There's evidence from case studies and animal models that prolonged infection in immune-suppressed hosts can support both reassortment and within-strain evolution.

And we've just had a big wave of covid that *we know causes some short term immune suppression* in most people, and *serious short term immune suppression* in some.

So we've got:
Lots of bird flu
Lots of flu flu
Lots of post-covid infection immune dysfunction

And a public health system that is telling people to wash their hands to deal with airborne illness.

Yes...

https://x.com/cv_cev/status/1986952416944685226?s=20

Oh damn.
I put a typo in there.
H5N1 that's supposed to be.

https://x.com/1goodtern/status/1987225853785149496?t=Px_eF9BNqJ72ejrzqxIf_g&s=19