Stefan Pöhlmann

187 new SARS-CoV-2 sequences from Germany were submitted to GISAID yesterday, December 6. All from Bavaria, collected between May and November. No BA.3.2 sequences were included, suggesting that, at present, spread of the variant is limited to certain federal states.

BA3.2 has previously been detected in Germany in the federal states Rhineland-Palatinate, North Rhine-Westphalia, and Berlin.

News on BA.3.2. - Now called Cicada and designated Variant Under Monitoring (VUM) by WHO

Here's an animated map showing the spread of the BA.3.2.* variant, nicknamed "Cicada".

The other main hotspots have been South Africa, Western Australia (since July) and Germany (from mid-October).

Locations are approximate - typically country and state/province.
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Another US wastewater detection of BA.3.2.2 (from CDC-NWSS surveillance)

This time from Austin on 11/19

The score:
Wastewater 2
Patient surveillance 0

/6 Next months will tell. In particular, we need to know whether the variant has a reduced capacity to cause disease.

#BA32 🎃

/5 So too strong to die, too weak to cause the waves we are used to. Do we witness the transit of SARS-CoV-2 from a pandemic to an endemic virus? Is BA.3.2 taking the 229E, NL43, HKU1, OC43 and not the JN.1 path?

/4 Capacity to reach and replicate in the lower respiratory tract might be compromised beyond the level we expect for Omicron subvariants.

/3 BA.3.2 might only be able to infect a fraction of individuals at any given time who have the right antibody profile. Further, it has lost some capacity to counter innate defenses (ORF7/8 deletion) and some subvariants show signs of further attenuation (QT repeat gone).

/2 However, this did not happen so far and exactly the opposite might be true.

/1 A JN.1-like development is expected for BA.3.2 - acquisition of mutation(s) that increase ACE2 binding and/or antibody evasion followed by massive global spread.

A BA.3.2.2 sequence from New York (EPI_ISL_20262473) was submitted to GISAID yesterday. Sample collected Nov 17 via airport screening. Travel history: Kenya.

Supports the idea raised by @ryanhisner.bsky.social that this sublineage is circulating widely.

#BA32

The first BA.3.2.2 sequence from South Australia has appeared, collection date November 22.

No major new mutations, though it does get a synonymous mutation (A4576T) that, together with T4579A, creates a more extensive TRS-like motif (previously found in BA.5.2.23).

BA.3.2.* appearing for the first time in the QLD wastewater variant charts. 2 sewage plants: Longholme and Merrimac. Merrimac looks around 15%.
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New BA.3.2.2 from Scotland, EPI_ISL_20261526, collected November 7.

Already two more BA.3.2.2 from Ireland today, both closely related to the first (and both with the ORF1a:∆141-143 deletion also found in most European BA.3.2.1).

Only real change was N:T271S in one of the two. (A29086T was inherited, but C->G muts like this are very rare.)

/4 In sum, one can understand why the above-mentioned losses are tolerable for BA.3.2. IMO, it is less clear, however, how they provide an advantage to the virus.

/3 Similarly, one can speculate that the deletion of one QT repeat in front of the FCS, observed in some BA.3.2 variants, might have a more profound impact on entry into cells in the lower as compared to the upper respiratory tract.

/2 This may be compatible with still appreciable spread in the upper respiratory tract, where IFN responses upon infection seem to be less robust as compared to the lower respiratory tract, with temperature playing a role.

/1 The large deletion removing ORF7/8 together with Δ141–143 in Nsp1 in BA.3.2 likely reduce its capacity to counter the interferon (IFN) system and to interfere with host cell translation, respectively.

BA.3.2 still active in New Zealand.
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Another US BA.3.2 wastewater detection.

This time from Bristol County, RI on Nov 11. It was about a third of the seqs.

I wonder if it was someone who flew back from Australia through SF?
@ryanhisner.bsky.social @snpoehlm.bsky.social @rajlabn.bsky.social

BA.3.2.2 arrived in Ireland - EPI_ISL_20259113

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4 new BA.3.2.2 sequences from South Africa submitted to GISAID today - 4.5% of total sequences from South Africa.
4 new BA.3.2.2 sequences from New South Wales submitted on 24.11., 4.5% of total sequences from Australia.

Now waiting for new sequences from Germany… 👀

This is a very sad day for public health and evidence-based science in general.

Yes, the furin cleavage site is a known virulence determinant, and you’d expect this mutation to at least partially attenuate most variants. Whether this holds true for BA.3.2, however, still needs to be determined.

Info on the 8 new BA.3.2 sequences from Germany:

➡️All are BA.3.2.2, deposited in GISAID.
➡️3 were collected in late October, 5 in November.
➡️Samples originate from Rhineland-Palatinate, North Rhine-Westphalia, and Berlin.

#BA32

Overview of global BA.3.2 sequences, plus reference to 8 new sequences from Germany

BA.3.2 has been detected again in the USA.

8/ The deletion of a single QT repeat preceding the furin-cleavage site is notable. In wild-type virus, one would expect some degree of attenuation, but BA.3.2 may act differently. We’ll see.

See previous thread by @ryanhisner.bsky.social

bsky.app/profile/ryan...