BA.2 continues to do its thing in Denmark. The two most recent days of sequencing (January 20 & 21) recorded 74.2% BA.2 (285 of 384 cases). 1/9
The exponential increase in the proportion of BA.2 cases continues in the UK.
The apparent slowdown in growth in the past several days is entirely due to 0 of 8 sequences being BA.2 over the past four days & should therefore be ignored. 2/9
Similar exponential increase in the percentage of BA.2 cases in the US.
Again, the illusory plunge over the last five days is entirely due to a very small number of sequences and should be ignored. 3/9
My home state of Indiana had recorded zero BA.2 cases before last night's update, when six cases were recorded in the most recent week of sequencing, indicating a substantial percentage of BA.2. Major caveat: sample size very small. 4/9
Germany's BA.2 path is similar to what Denmark's was early on. A recent report found that 30% of cases in Berlin were BA.2, so as has been the case elsewhere, large cities with lots of international travelers are leading the way. 5/9
Japan finally has enough BA.2 to provide a decent indication of it's path. Surprise!—it's upward.
(Once again, the tiny sample sizes in recent days mean the illusory plunge at the end should be ignored.) 6/9
Not much sequencing in Portugal, but in the most recent day of sequencing, which was two weeks ago, all eight cases sequenced were BA.2. 7/9
Spain, like Portugal, has poor genetic surveillance, but is seeing a similarly steep rise in BA.2.
Small sample size makes this a pretty unreliable estimate, however. 8/9
Most of the other countries whose graphs I posted in a previous BA.2 update have seen little change. Not much has changed in Sweden, but I'll include it here since it has among the highest level of BA.2 among countries with decent sequencing. 9/9
I was rushed when putting together this thread and made a mistake in the number of BA.2 cases recorded in Indiana. There have actually been 12 BA.2 sequences in the most recent 8 days of sequencing, not 6. This gives Indiana the highest percentage of BA.2 of any US state.
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• BA.2.87.1 - Appeared suddenly Sept 2023, spread across South Africa, & was detected in WW in Thailand. Then basically disappeared after Dec 2023 (apart from 1 seq collected in May 2024 from Eswatini). Emerged just when JN.1 was sweeping—bad timing. 2/
• BA.2.83 - One of several BA.2 saltation variants that emerged in late 2022. First appeared in India, then in Denmark, Canada, and Australia. Could not compete with BA.2.75 and BA.5 though and disappeared without making any real impact. 3/
A mysterious, unusually diverse saltation lineage descended from KP.3.1.1 (last seen early 2025) has circulated at a low level for ~8 months in Ontario (see 🧵on next post).
Seemed a local anomaly, but @solidevidence just spied a weird spike in NYC WW—& it's the same one!
1/14
Wildly diverse branch of MC.10.1.7 (KP.3.1.1 descendant, died out early 2025) in Ontario.
It's apparently been circulating at a low level for the past year. ≥6 different people are represented here.
I think this must involve one or more chronic infections + transmission. 1/7
• Busy 630 loop: ∆621-622 + NVFQ->IFPMAE at S:641-644.
• 2-nuc muts: W452K + D839K.
• Ultra-rare S2 insertion: ins791P
M:H155N, ORF1a:R3164H, & ORF3a:255-256 deletions cluster in chronics, often w/S:D936H/Y or ORF1a:L3201P. Intriguingly, D936Y was in the last seq. 2/7
More info on this unusual branch can be found on the Github page for undesignated lineages, which Fede Gueli tirelessly and selflessly keeps up to date.
Another fantastic preprint on BA.3.2's propensity for children, this time from @yunlong_cao & co.
They not only confirm the findings of David Ho's lab (that kids have ~0 antibody response to BA.3.2) but dig into the details of exactly why kids are so vulnerable to BA.3.2.
1. Kids vaccinated before being infected have robust antibodies against BA.3.2
2. Unvaxed adults much more vulnerable to BA.3.2, esp. compared to mRNA-vaxed adults.
Read @yunlong_cao's 🧵 & very readable paper for details. 2/4
There's still one major paradox here I can't wrap my head around: countries with the highest vaccination rates & the lowest proportion of children appear—very low sequencing makes hard conclusions difficult—to have the highest proportion of BA.3.2. 3/4
New data from David Ho's lab showing that while adults & kids have ~equal antibody responses to XFG & NB.1.8.1, children have essentially no neutralizing antibodies to BA.3.2.
This seems to largely solve the BA.3.2 + kids mystery. 1/14
If you've missed the story about how BA.3.2 (a novel, divergent saltation variant) is hugely overrepresented in sequences from children, this was my original (very quick) analysis, which subsequent data extended & confirmed. 2/
More details from this preprint. 50 is the limit of detection (i.e. zero). Nearly all kids under 7 had no detectable nAbs to BA.3.2, despite robust nAb titers against NB.1.8.1 & XFG.
I've tried to make sense of BA.3.2's penchant for kids by considering its unique spike: more compact, more closed, & more antibody-evasive than any other variant.
But I think another feature of BA.3.2 is responsible: its wholesale deletion of ORF7a, ORF7b, & ORF8 (∆ORF78).
2/
∆ORF78 is rare but not unheard of; it was in several late XBB variants (GW.5.1.1, FW.1.1, GE.1.2, etc) & a few branches of other variants. I've long thought these late XBB had an advantage in some population subsector, but I didn't suspect kids. 3/