T. Ryan Gregory πŸ‡¨πŸ‡¦ Profile picture
Nov 24, 2022 β€’ 24 tweets β€’ 7 min read β€’ Read on X
How could COVID be involved in the pediatric health crisis resulting from a surge in RSV and flu in various places (Canada, USA, Europe)? There are at least three ways. 🧡
First, let me get the "immunity debt" idea out of the way, so I can focus on the alternative (or, more likely, additional) explanations. I have already done some threads on this subject.

In short, the current patterns of infection -- when, how much, and where they are happening, and the number of severe cases -- does not seem to fit a simplistic "immunity debt" explanation. So, what else could be going on this year?
If (and we need more data here) it is NOT simply a matter of way more cases this year with the same percentage of them being very serious, then it would mean that either the severity of infections has increased for many patients. How could that be?
In simple terms, this would suggest that either the virus has changed, and/or we have changed, and/or there is some additional factor increasing the relative number of severe cases. So, what might be different this year? And how could COVID be implicated?
1. Co-infection.

COVID, RSV, and flu are all circulating right now. Being infected with more than one of them at the same time makes things worse.
Here are some papers about co-infection with COVID making RSV and flu infections more severe:

thelancet.com/journals/lance…

pubmed.ncbi.nlm.nih.gov/36112521/

ncbi.nlm.nih.gov/pmc/articles/P…

onlinelibrary.wiley.com/doi/10.1002/pp…
2. COVID infection during pregnancy affects fetal lung development.

thelancet.com/journals/lanre…
This doesn't cause respiratory distress by itself at birth, but it could become relevant when infected with respiratory viruses. "The absence of postna...
3. Immunity theft, in which COVID infection damages the ability of the immune system to fight off other infections.

How could this happen?
One mechanism is by COVID infection affecting dendritic cells.

journals.plos.org/plospathogens/…

frontiersin.org/articles/10.33…

Those cells are important in fighting RSV infections.

mdpi.com/1999-4915/12/1…
Some patients with long COVID show dysfunction in the immune system for at least 8 months post-infection even if the acute case was mild.

nature.com/articles/s4159…
There are other ways that COVID infection can affect immune function, including exhaustion of T cells. This article summarizes these and other ideas that have been discussed by @fitterhappier very well:

thetyee.ca/Analysis/2022/…
So, to summarize, there are three major ways that COVID could very plausibly be making this season much worse:

1. Co-infection with COVID and RSV or flu.
2. Infection during pregnancy affecting fetal lung development.
3. Immunity theft (several mechanisms).
A reduction in population level immunity and thus more susceptible hosts is obviously a factor (though, again, there was lots of RSV last year in many places). But it matters a great deal whether there are other factors.
A very large fraction of people, including children, were infected with Omicron variants over the past year. So, this would be the first season of RSV and flu in which this would be a major factor in most places. The season is starting early and many hospitals are overwhelmed.
It's worth noting that Sweden, which never had lockdowns, had a bad RSV surge last year.

From Nov 2021:

thelocal.se/20211105/rsv-w…
If COVID has made the severity of RSV and flu infections worse, then we need to mitigate the spread of these viruses now to protect children who are more vulnerable. We do not need to let them get infected to pay an immunity debt.
It is also important to consider what this would mean as more and more people get infected (or reinfected) with COVID. What about future seasons? Other viruses? Bacterial and fungal infections?

What we need is data, not assumptions.
One quick clarification. The claim is not that *all* RSV and flu infections are more severe. It's that more of the infections that occur will be severe because in *some* kids COVID has these effects. I don't want people misconstruing the claims made.
Another possible factor besides "immunity debt" or COVID is that the RSV or flu viruses in circulation this year are different and more virulent and/or transmissible. Here's a recent study on RSV variants that result in longer infection, for example.

academic.oup.com/jid/advance-ar…

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More from @TRyanGregory

Dec 5, 2025
Well, it's that time again. Meet "Cicada", BA.3.2* (including descendant RE.*). This one has been underground for years (its ancestor BA.3 hasn't been circulating since early 2022, and didn't do much then either) but is now emerging as a contender for the next major lineage.
Volunteer variant trackers have been watching this one since March, with it popping up around the world throughout November. It's another highly divergent variant (50 spike mutations) that evolved within a chronically infected host.

Read 6 tweets
Oct 5, 2025
There is growing interest in possible links between SARS-CoV-2 and cancer. I strongly recommend this video series with @arijitchakrav which discusses why it might be even worse.

🧡

Part 1:

Part 2:

Part 3:

Read 4 tweets
Jun 12, 2025
Two new variants are competing for dominance: NB.1.8.1 and XFG. We recently nicknamed NB.1.8.1 "Nimbus", and it's pretty clear that XFG deserves a nickname as well. Keeping with the meteorological theme, XFG = "Stratus".

Here's some more info about Nimbus and Stratus. 🧡

1/
There are two main ways by which divergent variants may evolve within single hosts: evolution during chronic infection and recombination during simultaneous infection with more than one variant. Nimbus (NB.1.8.1) and Stratus (XFG) have both mechanisms in their ancestries.

2/
Stratus (XFG) is a recombinant of LF.7 x LP.8.1.2 -- both of which descendants of BA.2.86, which itself had evolved within someone infected for ~2 years.

LF.7 = JN.1.16.1.7 = BA.2.86.1.1.16.1.7

LP.8.1.2 = JN.1.11.1.1.1.3.8.1.2 = BA.2.86.1.1.11.1.1.1.3.8.1.2

3/ Stratus ancestry diagram summarizing the info given in the main text.
Read 10 tweets
Jun 6, 2025
Nimbus (NB.1.8.1) is getting a fair bit of attention, but it's not the only SARS-CoV-2 variant worth watching. Here's a link to info about a few more, all of which have arisen either through within-host evolution during chronic infection and/or within-host recombination.

🧡

1/
First, a reminder that Nimbus (NB.1.8.1) is a triple recombinant with both BA.2.86 and XBB ancestry -- that is, it has multiple recombination events and chronic infections in its evolutionary history. Here's a thread I wrote about it:



2/
Another that is very competitive is XFG, which is a recombinant of two Pirola lineages (LF.7 x LP.8.1.2).

Head over to BlueSky to see the post by Josette Schoenmakers on the XFG vs. NB.1.8.1 battle for dominance.



3/bsky.app/profile/josett…
Read 4 tweets
May 27, 2025
Meet "Nimbus", aka SARS-CoV-2 variant NB.1.8.1.

🧡

1/ Diagram showing the ancestry of Nimbus (NB.1.8.1). The evolution of NB.1.8.1 has including three recombination events, including XBB (Kraken) and BA.2.86 (Pirola) lineages.
Evolutionary tree of SARS-CoV-2 variants showing the small fraction of diversity covered by every variant with a Greek letter except "Omicron", and the enormous diversity within "Omicron", including Nimbus NB.1.8.1.
The last variant to receive an informal nickname was BA.2.86 "Pirola" nearly two years ago, back in August 2023. Since then, it has been a prolonged "variant soup" phase, with descendants of BA.2.86 arising, gaining prominence, and then falling in frequency.

2/ Tweet from August 18, 2023 with the nickname "Pirola" for BA.2.86.
A prolonged variant soup phase involving the Pirola clan does not mean there was no within-host evolution occurring. It just meant that nothing had gotten back into the general population that could compete with the many, many descendants of BA.2.86.

3/
Read 14 tweets
Apr 29, 2025
Btw folks, what happened is that QuΓ©bec saved us all from Poilievre. Bloc voters went Liberal this time to keep him out.

Ontario, not so much. Big gains for the Cons.

BC was where the NDP did best last election, and this time it went Lib and Con.
So, we essentially traded a Liberal minority with progressive parties being very influential to a Liberal minority with a huge Conservative opposition and minimal progressive representation.

The fact that 41.4% voted Con (vs. 43.5% Lib) isn't a good sign either.
Yes, I'm relieved that it's not Poilievre as PM and I'm glad he lost his seat. But beyond that, we're not in a very good place overall. The major rightward shift isn't going to be good, especially when the Liberals eventually lose to the Conservatives.
Read 4 tweets

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