Share this page!

Enter URL or ID to Unroll

You can paste full URL like: https://x.com/threadreaderapp/status/1644127596119195649
or just the ID like: 1644127596119195649

How to get URL link on X (Twitter) App

  1. On the Twitter thread, click on or icon on the bottom
  2. Click again on or Share Via icon
  3. Click on Copy Link to Tweet
  4. Paste it above and click "Unroll Thread"!
  5. More info at Twitter Help
Ryan Hisner Profile picture
@LongDesertTrain
Jan 25, 2022 • 9 tweets • 5 min read • Read on X
Scrolly
As Omicron has washed over the US, infecting perhaps 25% of the population already & likely to reach 40% by mid-February—see thread by @trvrb below—it has driven down almost all other respiratory pathogens, with one curious exception I’ll get to later. 1/9
This is not entirely unexpected. Viral infections trigger both innate and adaptive immune responses that can prevent infection by other viruses. Behavior changes likely contribute to this pattern as well. 2/9
There have been some claims that rhinovirus infection protects against SARS-CoV-2 infection. As you can see in the graph below, SARS-CoV-2 and RV prevalence seem almost perfectly inversely related in recent months. 3/9 news.yale.edu/2021/06/15/com…
Rhinoviruses typically peak in spring & fall & are lower during winter, when influenza, coronaviruses, HMPV, RSV, & other viruses thrive, suggesting these viruses & RVs compete & inhibit one another in some way. Great article on RVs by @MackayIM below. 4/9 virologydownunder.com/rhinovirus-ram…
One would expect more closely related viruses to compete most vigorously. The rapid displacement of one SARS-CoV-2 variant by another in this pandemic seems to confirm this. 5/9
The history of influenza also suggests closely related viruses undergo intense competition. It’s thought H3N8 dominated in late 19th c. but was replaced by H1N1 in the 1918 pandemic. H1N1 in turn was displaced by H2N2 in 1957, which vanished when H3N2 appeared in 1968. 6/9
Curiously, H3N2 has persisted through the emergence of H1N1 in 1977 (possible lab leak) & pH1N1 in 2009. The paper linked to below suggests this is because the 2 major proteins on their surfaces are quite different & antigenically distinct. 7/9 journals.asm.org/doi/10.1128/mB… 6/
This makes the one exception to the downward trend in all non-Omicron respiratory pathogens all the more remarkable. As Omicron has risen, everything else has fallen—except the seasonal coronaviruses, which have risen in step with Omicron. 8/9
OC43, NL63, and 229E have all contributed to the recent rise in seasonal coronavirus cases. (HKU1 has been absent for nearly 2 years now.) I don’t have any idea why this would happen. I’d love to hear what others’ hypotheses are though. 9/9

• • •

Missing some Tweet in this thread? You can try to force a refresh
　

Keep Current with Ryan Hisner

Ryan Hisner Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @LongDesertTrain

Ryan Hisner Profile picture
Jul 30
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 Image
It was collected July 15, & is most closely related to the recent S African seqs 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 Image
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 Image
Read 4 tweets
Ryan Hisner Profile picture
Jul 7
BA.3.2 update: another sequence from the Netherlands, June 18 collection.

It belongs on the same branch as the GBW travel seq (tree gets confused by ORF7-8 deletion). Also, there are 3 artifactual muts in the GBW sequence (as usual), so the branch is shorter than it looks. Image
Bottom line, in my view: BA.3.2 has spread internationally & is likely growing, but very slowly. If nothing changes, its advantage vs circulating lineages, which seem stuck in an evolutionary rut, will likely gradually grow as immunity to dominant variants solidifies... 2/9
So far, this seems like a slow-motion version of what we saw with BA.2.86, which spread internationally & grew very slowly for months. But then it got S:L455S & exploded, wiping out all competitors. Will something similar happen with BA.3.2? I think there's a good chance... 3/9 Image
Read 9 tweets
Ryan Hisner Profile picture
Jul 2
Quick BA.3.2 update. Another BA.3.2.2 (S:K356T+S:A575S branch) from South Africa via pneumonia surveillance.

This means that 40% of SARS-CoV-2 sequences from SA collected since April 1 (2/5) and 50% collected after May 1 (1/2) are BA.3.2. Its foothold seems strong there. 1/3
2 interesting aspects of the new BA.3.2:
1. ORF1b:R1315C (NSP13_R392C)—This mut is in all Omicron *except* BA.3. So this may well be adaptive.

2. S:Q183H—First known antigenic spike mut seen in BA.3.2, not a major one, but one we've seen before—eg, LB.1/JN.1.9.2.1 2/3 Image
I think the unusually long branches in the BA.3.2 tree indicate 2 things:
1. Slow growth globally—fast growth results in many identical sequences, if surveillance is sufficient

2. Undersampling—BA.3.2 most common in poorer world regions with little sequencing of late. 3/3
Read 5 tweets
Ryan Hisner Profile picture
Jun 29
BA.3.2 update, Chapter: "I'm Not Quite Dead, Sir"

A new sequence from a traveler to the USA from the Netherlands was uploaded yesterday, with a collection date of June 17. 1/10 Image
This was a BA.3.2.1, the branch with S:H681R + S:P1162R (not S:K356T + S:A575S).

An updated, annotated version of the BA.3.2 Usher tree pictured below.

This sequence has the first new spike mutation since BA.3.2 emerged in November 2024—S:V227L. 2/10 Image
It has an extremely rare NSP5 mutation, ORF1a:T3487S (NSP5:T224S), only in 4 of ~17 million SARS-2 seqs

Intriguingly, 3 of these 4 share something in common w/this BA.3.2.

The first—and most remarkable—is a BA.2 from England that, like BA.3.2, has the ORF7ab-ORF8 deletion. 3/10 Image
Read 11 tweets
Ryan Hisner Profile picture
Jun 27
@yaem98684142 @TBM4_JP This analysis is extremely flawed.

There is nothing abnormal about BA.2.86 appearing in multiple countries shortly after discovery. This has been the norm lately w/reduced surveillance. 1/
@yaem98684142 @TBM4_JP The mutational spectrum analysis is poorly done. It cites a single study looking at the mutational spectrum in *three* immunocompromised individuals. Needless to say, this sample size is WAY too small. 3/
@yaem98684142 @TBM4_JP Furthermore, the IC people examined did not give rise to highly divergent variants with a large number of spike mutations. They appear to have accumulated a very modest number of mutations, with few substitutions in spike. The sequences themselves are apparently not published. 4/
Read 7 tweets
Ryan Hisner Profile picture
Jun 19
Interesting recombinant showed up today from Texas. It's a mixture of B.1.595, BA.1, and some flavor of JN.1. Most of the genome is from B.1.595. The ancestry of this one is clear: it directly descends from a B.1.595 sequence collected in January 2023, also in Texas. 1/11 Image
When the B.1.595 was collected this infection was >1 yr old, w/no sign of Omicron. BA.1 ceased circulating ~1 year prior.
Now a BA.1 spike appears w/just 5 changes from baseline BA.1, none in the RBD—S12F, T76I, Q271K, R765H, S939F.

This is a zombie BA.1 spike. 2/ Image
There are only a few signs of JN.1, & they're scattered. In ORF1a, we see JN.1's V3593F, P3395H, & R3821K, but the NSP6 deletion btwn these—universal in Omicron—is absent. In
M has JN.1's D3H + T30A & E19Q (in JN.1 & BA.1), yet A63T—also in both BA.1 & JN.1 is absent. 3/11 Image
Read 11 tweets

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us!

Send Email!

:(