Stefan Poehlmann

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

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

But: protection against severe disease/death — where T cells play a key role — is expected to remain strong.

📄 PMID: 40480242 | DOI: 10.1016/j.lanmic.2025.101165
📄 PMID: 40484018 | DOI: 10.1016/S1473-3099(25)00308-1

Based on initial studies, BA.3.2 evades neutralizing antibodies from JN.1-based boosters more effectively than other current variants (see below). This may reduce protection against infection.

The figures do not appear as intended - this might be a problem with my computer.

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

Yesterday I wondered on X why no new BA.3.2 sequences were popping up. Well, here’s a fresh one: EPI_ISL_20094964 from Western Australia.

Looks like this variant is still making its rounds globally - just as we feared.
#BA32 #SARSCoV2 #VariantTracking

BA.3.2, an emerging SARS-CoV-2 variant, has been detected in Mozambique - adding to cases in South Africa and, more recently, Germany, the Netherlands, and the United States. Where will it turn up next?
#BA32

Expanding on the S:A852K/S:D843G/NTD-deletion connection described in the thread below, there's one other extremely rare BA.3.2 mutation with an uncanny connection to D843G—S:K795T, seen in just 53 sequences ever prior to BA.3.2. 1/4

For completeness: another BA.3.2 sequence from Gauteng, South Africa — possibly from the same individual.
EPI_ISL_20075832, sampled May 30, 2025, from an 11-year-old girl during baseline surveillance.
#COVID19 #VariantWatch #BA.3.2

BA.3.2 isn’t gone yet — a new sequence from a patient in South Africa has been deposited, EPI_ISL_20075682. Sample from an 11-year-old girl, taken June 12, 2025, during routine pneumonia surveillance.
#COVID19 #BA.3.2 #VariantWatch

An antibody against PRCV and TGEV cross-neutralizes FCoV-23.
#SpikeProtein #ViralEntry #Coronavirus #CatHealth

4/5 D0 deletion isn't new: in pigs, loss of D0 in TGEV gave rise to PRCV, shifting tropism to the respiratory tract. In FCoV-23, D0 deletion enhances cell-cell fusion and accelerates entry — and thus provides an advantage to the virus.

3/5 Domain 0 (D0), unique to alphacoronavirus spikes, is lost upon FCoV-23 infection in cats.

2/5 The study shows that FCoV-23 uses APN/CD13 as a receptor and reports the cyro-EM structure of the RBD–receptor interface.

1/5 The alphacoronavirus FCoV-23 causes peritonitis in cats. The virus arose via recombination with a canine coronavirus.

Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics - Nature The molecular mechanisms of cell entry for the recently identified highly pathogenic feline coronavirus FCoV-23 are characterized in detail.

Important insights into FCoV-23 cell entry from the @veeslerlab.bsky.social

Freely available: www.nature.com/articles/s41...

Please add me to the list. Thanks

👀 Important insights into TMPRSS2 usage by Omicron subvariants

If that's the case, never mind that N17 glycan. It's not there because S:1-22 gets left behind in the ER.

I want to go into the amazing work of @enyaqing.bsky.social on inter-domain spike interactions at this point, but I've spent hours on this & have too much else to do, so I'm signing off. 16/16

BA.3.2 update: another sequence from the Netherlands, June 18 collection.

It belongs on the same branch as the GBW travel sequence below it (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. 1/9

🧬 New BA.3.2 sequence from the Netherlands
🧾 GISAID ID: EPI_ISL_20064494
📍 Donor age: 71
📅 Sample date: 18 June 2025

#SARSCoV2 #Genomics #BA32 #COVID19 #GISAID

Quick update on BA.3.2. Another BA.3.2.2 (the S:K356T, S:A575S branch) from arrived 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

5/5
The most recent BA.3.2 sequence includes one new spike mutation.
It’s unlikely to boost transmissibility much -
but this underscores the need for ongoing genomic surveillance.
#COVID19 #ImmuneEvasion

4/5
Compare with BA.2.86: it circulated "quietly" in 2023 until a single spike mutation gave rise to JN.1, which became widespread in 2024.
BA.3.2 could follow a similar path - if it acquires (a) mutation(s) that enhance transmissibility.

3/5
BA.3.2's spike mutations help it evade neutralizing antibodies with high efficiency -
but that immune escape apparently comes at a cost: reduced entry into certain host cells.
🔗 doi:10.1016/j.lanmic.2025.101165
🔗 doi:10.1016/S1473-3099(25)00308-1

2/5
Why care about BA.3.2?
Most variants differ from their ancestors by just a few spike mutations. BA.3.2, however, shows extensive spike divergence - likely from long-term infection of an immunocompromised patient.
#ViralEvolution

1/5
The recent detection of BA.3.2 suggests it's still circulating at low levels. Though rare for now, this variant could have important implications for SARS-CoV-2 evolution.
Also see recent insights from @ryanhisner.bsky.social
#COVID19 #Variants

Get well soon!

Final takeaway: BA.3.2 definitely not dead & now detected in international travel surveillance for the first time.

However, the particular branch this ocean-hopping sequence is from seems unlikely to be the one to break through due to its deleterious ORF1a:∆141-143 deletion. 10/10