Ryan Hisner
@ryanhisner.bsky.social
Teacher. Learner. Investigating mysteries of SARS-CoV-2 evolution. LongDesertTrain on another platform.
Another day, another sequence displaying undeniable evidence of positive selection of molnupiravir-induced mutations (i.e. adaptive mutations—good for the virus, bad for the infected person).
G->A is the classic MOV mutation—and the vast majority of the positive selection is in G->A muts. 1/3
G->A is the classic MOV mutation—and the vast majority of the positive selection is in G->A muts. 1/3
January 16, 2026 at 12:26 PM
Another day, another sequence displaying undeniable evidence of positive selection of molnupiravir-induced mutations (i.e. adaptive mutations—good for the virus, bad for the infected person).
G->A is the classic MOV mutation—and the vast majority of the positive selection is in G->A muts. 1/3
G->A is the classic MOV mutation—and the vast majority of the positive selection is in G->A muts. 1/3
Another weird aspect of BA.3.2 evolution so far: an extraordinary number of NSP1 mutations. NSP1 is only 180 AA, but a new mutation shows up almost every day there, often on top of previous new ones. The @nextstrain.org visual here can't even accommodate all the NSP1 muts—at least 2 are invisible.
January 15, 2026 at 11:54 PM
Another weird aspect of BA.3.2 evolution so far: an extraordinary number of NSP1 mutations. NSP1 is only 180 AA, but a new mutation shows up almost every day there, often on top of previous new ones. The @nextstrain.org visual here can't even accommodate all the NSP1 muts—at least 2 are invisible.
Agree with Josette here. There are only 10 sequences from Germany collected after December 23. Needless to say, this is not sufficient to base a forecast on.
I think it's possible (though uncertain) that the loss of ORF7a might mean there's a ceiling to the current incarnation of BA.3.2. But... 1/3
I think it's possible (though uncertain) that the loss of ORF7a might mean there's a ceiling to the current incarnation of BA.3.2. But... 1/3
I see this happening all the time. A variant seems to go down, looking at the last incomplete week. And a week later, that week has been adjusted to a higher percentage. Like you see happening here in NSW Australia.
January 15, 2026 at 11:36 PM
Agree with Josette here. There are only 10 sequences from Germany collected after December 23. Needless to say, this is not sufficient to base a forecast on.
I think it's possible (though uncertain) that the loss of ORF7a might mean there's a ceiling to the current incarnation of BA.3.2. But... 1/3
I think it's possible (though uncertain) that the loss of ORF7a might mean there's a ceiling to the current incarnation of BA.3.2. But... 1/3
Reposted by Ryan Hisner
Today, Minneapolis. Tomorrow, it could be my town, your town, anywhere. The good news is that people in all the towns care about their neighbors and are organizing to resist this. It will stop when enough of us say no.
January 13, 2026 at 5:52 AM
Today, Minneapolis. Tomorrow, it could be my town, your town, anywhere. The good news is that people in all the towns care about their neighbors and are organizing to resist this. It will stop when enough of us say no.
Reposted by Ryan Hisner
🎥 WATCH | Children’s educator Ms. Rachel urges the US and Israel to end the deliberate suffering of 1 million Palestinian children, calling for the immediate entry of lifesaving shelter and medical aid into Gaza.
Video: Assal Rad via X (@AssalRad)
Video: Assal Rad via X (@AssalRad)
January 14, 2026 at 11:42 PM
🎥 WATCH | Children’s educator Ms. Rachel urges the US and Israel to end the deliberate suffering of 1 million Palestinian children, calling for the immediate entry of lifesaving shelter and medical aid into Gaza.
Video: Assal Rad via X (@AssalRad)
Video: Assal Rad via X (@AssalRad)
Mark Twain was a vehement anti-imperialist, often wielding his "pen warmed up in Hell" against the imperialist warmongers of his day.
"Patriotism... it is a word which always commemorates a robbery...."
"Patriotism... it is a word which always commemorates a robbery...."
"Patriotism... a word which always commemorates a robbery. There isn’t a foot of land in the world which doesn’t represent the ousting & re-ousting of a long line of 'owners' who each, as 'patriots' defended it against the next gang of 'robbers' who came to steal it & did—& became patriots in turn."
January 11, 2026 at 9:05 PM
Mark Twain was a vehement anti-imperialist, often wielding his "pen warmed up in Hell" against the imperialist warmongers of his day.
"Patriotism... it is a word which always commemorates a robbery...."
"Patriotism... it is a word which always commemorates a robbery...."
Observation on SARS-CoV-2 mouse-adapted viruses: The mutations that occur in these seem to me to more about adapting to lung tropism than adapting to mice.
A large fraction of the mutations are the same ones you see in bronchoalveolar-lavage (BAL) samples from chronically infected humans. 1/4
A large fraction of the mutations are the same ones you see in bronchoalveolar-lavage (BAL) samples from chronically infected humans. 1/4
January 10, 2026 at 11:08 PM
Observation on SARS-CoV-2 mouse-adapted viruses: The mutations that occur in these seem to me to more about adapting to lung tropism than adapting to mice.
A large fraction of the mutations are the same ones you see in bronchoalveolar-lavage (BAL) samples from chronically infected humans. 1/4
A large fraction of the mutations are the same ones you see in bronchoalveolar-lavage (BAL) samples from chronically infected humans. 1/4
Reposted by Ryan Hisner
My own last, unreturned, correspondence with GISAID, after a months-long project building a version of Taxonium that would run within the walled garden (the dispute was over whether it could link out to e.g. the source code)
January 7, 2026 at 1:22 PM
My own last, unreturned, correspondence with GISAID, after a months-long project building a version of Taxonium that would run within the walled garden (the dispute was over whether it could link out to e.g. the source code)
8/77 new seqs from New South Wales are BA.3.2, & several feature interesting spike muts:
• T19I + G72W (2) (1 w/E1202G)
• A123V (1) (+ ORF6:Q57*)
• T124I (1)
T19I & T124I both remove glycans—& we've seen T124I before in an unrelated BA.3.2 from South Africa.
1/4
bsky.app/profile/ryan...
• T19I + G72W (2) (1 w/E1202G)
• A123V (1) (+ ORF6:Q57*)
• T124I (1)
T19I & T124I both remove glycans—& we've seen T124I before in an unrelated BA.3.2 from South Africa.
1/4
bsky.app/profile/ryan...
The spike mutations are T124I, N478T, & T678I.
N478T is a reversion to the ancestral AA, meaning it's gone from T-->K-->N-->T in this lineage.
There and back again.
S:478 has been by far the most active AA residue in recent months. We've seen K, T, I , E, R, N, L, M, and Q there of late. 2/6
N478T is a reversion to the ancestral AA, meaning it's gone from T-->K-->N-->T in this lineage.
There and back again.
S:478 has been by far the most active AA residue in recent months. We've seen K, T, I , E, R, N, L, M, and Q there of late. 2/6
January 2, 2026 at 5:38 PM
8/77 new seqs from New South Wales are BA.3.2, & several feature interesting spike muts:
• T19I + G72W (2) (1 w/E1202G)
• A123V (1) (+ ORF6:Q57*)
• T124I (1)
T19I & T124I both remove glycans—& we've seen T124I before in an unrelated BA.3.2 from South Africa.
1/4
bsky.app/profile/ryan...
• T19I + G72W (2) (1 w/E1202G)
• A123V (1) (+ ORF6:Q57*)
• T124I (1)
T19I & T124I both remove glycans—& we've seen T124I before in an unrelated BA.3.2 from South Africa.
1/4
bsky.app/profile/ryan...
The first SARS-CoV-2 sequence uploaded in 2026 is....
...a BA.3.2.2 from New York sampled from a traveler from Japan.
This is the first BA.3.2 sample w/any connection to Japan. There have been no non-travel BA.3.2 collected in the US (yet).
From the Western Australia S:P1162L branch. 1/9
...a BA.3.2.2 from New York sampled from a traveler from Japan.
This is the first BA.3.2 sample w/any connection to Japan. There have been no non-travel BA.3.2 collected in the US (yet).
From the Western Australia S:P1162L branch. 1/9
January 1, 2026 at 10:46 PM
The first SARS-CoV-2 sequence uploaded in 2026 is....
...a BA.3.2.2 from New York sampled from a traveler from Japan.
This is the first BA.3.2 sample w/any connection to Japan. There have been no non-travel BA.3.2 collected in the US (yet).
From the Western Australia S:P1162L branch. 1/9
...a BA.3.2.2 from New York sampled from a traveler from Japan.
This is the first BA.3.2 sample w/any connection to Japan. There have been no non-travel BA.3.2 collected in the US (yet).
From the Western Australia S:P1162L branch. 1/9
I'm not a big music video guy, but this one for the song "I Say Fever" by Ramona Falls is easily my favorite music video ever.
vimeo.com/423208503
vimeo.com/423208503
January 1, 2026 at 3:58 PM
I'm not a big music video guy, but this one for the song "I Say Fever" by Ramona Falls is easily my favorite music video ever.
vimeo.com/423208503
vimeo.com/423208503
Reposted by Ryan Hisner
In less diplomatic language, GISAID is power mad and is jeopardising worldwide monitoring of current diseases, and possible future pandemics, by restricting information to researchers on entirely spurious grounds.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 7:10 PM
In less diplomatic language, GISAID is power mad and is jeopardising worldwide monitoring of current diseases, and possible future pandemics, by restricting information to researchers on entirely spurious grounds.
Very proud to be a co-author on this comprehensive preprint on the novel, growing saltation lineage BA.3.2, together with @tuliodna.bsky.social, @darrenmartin.bsky.social, Dikeledi Kekana, and lead author @graemedor.bsky.social. 1/11
bsky.app/profile/tuli...
bsky.app/profile/tuli...
SARS-CoV-2 continue to surprise us with evolutionary jumps. In this pre-print, we describe the Identification and genomic characterisation of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa. A thread 🧵 www.medrxiv.org/content/10.6...
Identification and genomic characterisation of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa
In November 2024, a highly divergent BA.3-related SARS-CoV-2 lineage, designated BA.3.2, was detected in South Africa, marking the first appearance of a BA.3-derived lineage in over two years. Phyloge...
www.medrxiv.org
December 29, 2025 at 8:49 PM
Very proud to be a co-author on this comprehensive preprint on the novel, growing saltation lineage BA.3.2, together with @tuliodna.bsky.social, @darrenmartin.bsky.social, Dikeledi Kekana, and lead author @graemedor.bsky.social. 1/11
bsky.app/profile/tuli...
bsky.app/profile/tuli...
Reposted by Ryan Hisner
1/4 Mutations in the SARS-CoV-2 spike N-terminal domain (NTD) and receptor-binding domain (RBD) can drive antibody evasion. BA.3.2 is a saltation variant with a heavily mutated spike and strong resistance to antibody-mediated neutralization, but the relative roles of NTD vs RBD were unclear.
December 26, 2025 at 11:00 PM
1/4 Mutations in the SARS-CoV-2 spike N-terminal domain (NTD) and receptor-binding domain (RBD) can drive antibody evasion. BA.3.2 is a saltation variant with a heavily mutated spike and strong resistance to antibody-mediated neutralization, but the relative roles of NTD vs RBD were unclear.
BA.3.2 emerged in Nov 2024 after ~3 years of intrahost evolution with >50 new spike AA muts, but since then, it's changed very little.
Could the mutagenic drug molnupiravir (MOV) galvanize BA.3.2 into pursuing new evolutionary paths? A new 89-mut BA.3.2 sequence hints that it could. 1/11
Could the mutagenic drug molnupiravir (MOV) galvanize BA.3.2 into pursuing new evolutionary paths? A new 89-mut BA.3.2 sequence hints that it could. 1/11
December 24, 2025 at 10:03 PM
BA.3.2 emerged in Nov 2024 after ~3 years of intrahost evolution with >50 new spike AA muts, but since then, it's changed very little.
Could the mutagenic drug molnupiravir (MOV) galvanize BA.3.2 into pursuing new evolutionary paths? A new 89-mut BA.3.2 sequence hints that it could. 1/11
Could the mutagenic drug molnupiravir (MOV) galvanize BA.3.2 into pursuing new evolutionary paths? A new 89-mut BA.3.2 sequence hints that it could. 1/11
In the 2-week period from Dec 3 to Dec 16, 6/25 SARS-CoV-2 sequences collected in Slovenia were BA.3.2 (and 6 of 17 sequences collected since Dec 7).
No interesting amino acid mutations, but one BA.3.2 has a 5' UTR deletion, which you almost never see: ∆191-208 (or ∆193-210). 1/3
No interesting amino acid mutations, but one BA.3.2 has a 5' UTR deletion, which you almost never see: ∆191-208 (or ∆193-210). 1/3
December 23, 2025 at 5:41 PM
In the 2-week period from Dec 3 to Dec 16, 6/25 SARS-CoV-2 sequences collected in Slovenia were BA.3.2 (and 6 of 17 sequences collected since Dec 7).
No interesting amino acid mutations, but one BA.3.2 has a 5' UTR deletion, which you almost never see: ∆191-208 (or ∆193-210). 1/3
No interesting amino acid mutations, but one BA.3.2 has a 5' UTR deletion, which you almost never see: ∆191-208 (or ∆193-210). 1/3
How many people even know there was a terrorist attack on the CDC where a deranged antivaxxer fired hundreds of rounds at CDC buildings and killed a police officer? This was a minor news story for about one day, then forgotten. It feels like it never happened.
"[RFK jr.] may as well have shot the bullets himself [...] and I hold him and his colleagues personally responsible for that violence and the death of that officer", says Daskalakis.
Their rhetoric dehumanizing people who do public health created the environment that led to the attack, he says.
Their rhetoric dehumanizing people who do public health created the environment that led to the attack, he says.
December 23, 2025 at 4:29 PM
How many people even know there was a terrorist attack on the CDC where a deranged antivaxxer fired hundreds of rounds at CDC buildings and killed a police officer? This was a minor news story for about one day, then forgotten. It feels like it never happened.
The most valuable viral research tools—@nextstrain & CovSpectrum—are being destroyed—not only blocked from new data but now forbidden from even sharing info from the PAST. Why?
Because GISAID is run dictatorially by a con man, paranoid egomaniac, & liar named Peter Bogner. 1/
Because GISAID is run dictatorially by a con man, paranoid egomaniac, & liar named Peter Bogner. 1/
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
December 22, 2025 at 5:00 PM
The most valuable viral research tools—@nextstrain & CovSpectrum—are being destroyed—not only blocked from new data but now forbidden from even sharing info from the PAST. Why?
Because GISAID is run dictatorially by a con man, paranoid egomaniac, & liar named Peter Bogner. 1/
Because GISAID is run dictatorially by a con man, paranoid egomaniac, & liar named Peter Bogner. 1/
Reposted by Ryan Hisner
1/ In the first half of 2025, I wondered whether BA.3.2 would return at all. A few weeks ago, I considered that it might present a gradual shift toward endemicity rather than achieving global dominance.
December 17, 2025 at 1:22 PM
1/ In the first half of 2025, I wondered whether BA.3.2 would return at all. A few weeks ago, I considered that it might present a gradual shift toward endemicity rather than achieving global dominance.
Reposted by Ryan Hisner
This is the most interesting thing I've seen in ages. If intra-cellular membrane-less hydrogen ion gradients are biologically meaningful/useful things then so too might be membrane-less gradients of everything else - from bigger ions with discrete point-sources through protein complexes.
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
December 17, 2025 at 3:36 PM
This is the most interesting thing I've seen in ages. If intra-cellular membrane-less hydrogen ion gradients are biologically meaningful/useful things then so too might be membrane-less gradients of everything else - from bigger ions with discrete point-sources through protein complexes.
BA.3.2 is approaching 30% of all sequences in Germany and Luxembourg, & it's likely at least that high in Western Australia. Only The Trump admin's defunding of the CDC has prevented non-wastewater detection of BA.3.2 in the US.
Still no supercharging new mutations, but steady growth continues.
Still no supercharging new mutations, but steady growth continues.
Three more BA.3.2 wastewater detections this week. Rhode Island, New Hampshire, and California.
Wastewater: 8
Patient detections: 0
Wastewater: 8
Patient detections: 0
December 18, 2025 at 3:46 AM
BA.3.2 is approaching 30% of all sequences in Germany and Luxembourg, & it's likely at least that high in Western Australia. Only The Trump admin's defunding of the CDC has prevented non-wastewater detection of BA.3.2 in the US.
Still no supercharging new mutations, but steady growth continues.
Still no supercharging new mutations, but steady growth continues.
With 30 new BA.3.2 sequences from the Netherlands and Denmark uploaded today, this is beginning to have a look of inevitability about it.
Still waiting for a recombinant that restores ORF7a, ORF7b, and ORF8 (all entirely deleted in BA.3.2).
Still waiting for a recombinant that restores ORF7a, ORF7b, and ORF8 (all entirely deleted in BA.3.2).
Three more BA.3.2 detections from US wastewater. Rhode Island (different sewershed, but near the previous one), Vermont, and Florida. All from CDC NWSS data.
Looks like it might be getting a foothold in New England.
@snpoehlm.bsky.social @ryanhisner.bsky.social @siamosolocani.bsky.social
Looks like it might be getting a foothold in New England.
@snpoehlm.bsky.social @ryanhisner.bsky.social @siamosolocani.bsky.social
December 11, 2025 at 10:24 PM
With 30 new BA.3.2 sequences from the Netherlands and Denmark uploaded today, this is beginning to have a look of inevitability about it.
Still waiting for a recombinant that restores ORF7a, ORF7b, and ORF8 (all entirely deleted in BA.3.2).
Still waiting for a recombinant that restores ORF7a, ORF7b, and ORF8 (all entirely deleted in BA.3.2).
Reposted by Ryan Hisner
It would be great if we could see recent trends in these two mutations, but @chaoranchen.de's Cov-Spectrum, @nextstrain.org, & other vital resources have been blocked by the narcissistic con man who wields total control over the world's most important viral genetic database. 4/4
December 9, 2025 at 12:09 PM
It would be great if we could see recent trends in these two mutations, but @chaoranchen.de's Cov-Spectrum, @nextstrain.org, & other vital resources have been blocked by the narcissistic con man who wields total control over the world's most important viral genetic database. 4/4
3/77 sequences from the latest Netherlands upload are BA.3.2 as well as 4/86 seqs from Queensland, Australia, consistent w/the steady, slow growth we've seen in Germany, the UK, Ireland, & much of Australia. 1/4
Nederland (het @rivm-nl.bsky.social) heeft vandaag weer 1 BA.3.2.1* (Noord-Holland) naar GISAID geüpload en voor het eerst ook 3 BA.3.2.2*, waarvan er de laatste tijd al meerdere o.a. in Duitsland zijn gezien.
De BA.3.2.2* zijn gevonden in Limburg, Brabant en Noord-Holland.
Uit 77 samples.
De BA.3.2.2* zijn gevonden in Limburg, Brabant en Noord-Holland.
Uit 77 samples.
o.a.in
December 9, 2025 at 12:09 PM
3/77 sequences from the latest Netherlands upload are BA.3.2 as well as 4/86 seqs from Queensland, Australia, consistent w/the steady, slow growth we've seen in Germany, the UK, Ireland, & much of Australia. 1/4
Reposted by Ryan Hisner
In my 2 cent view BA.3.2.2 is clearly the fastest as of today.
After it we have XFW family, XFG.10.4 (435S), QF.1.1.1 and XFG.23.1.3 (both with 1174V), then XFG with 679R/680P and NB.1.8.1 + 445P, XFZ(.1) and XFG.1.1 with XFG.14.1 and XFG.6 being almost there
underdogs XFJ.3.1.1 and LF.7.11.
After it we have XFW family, XFG.10.4 (435S), QF.1.1.1 and XFG.23.1.3 (both with 1174V), then XFG with 679R/680P and NB.1.8.1 + 445P, XFZ(.1) and XFG.1.1 with XFG.14.1 and XFG.6 being almost there
underdogs XFJ.3.1.1 and LF.7.11.
December 6, 2025 at 1:36 PM
In my 2 cent view BA.3.2.2 is clearly the fastest as of today.
After it we have XFW family, XFG.10.4 (435S), QF.1.1.1 and XFG.23.1.3 (both with 1174V), then XFG with 679R/680P and NB.1.8.1 + 445P, XFZ(.1) and XFG.1.1 with XFG.14.1 and XFG.6 being almost there
underdogs XFJ.3.1.1 and LF.7.11.
After it we have XFW family, XFG.10.4 (435S), QF.1.1.1 and XFG.23.1.3 (both with 1174V), then XFG with 679R/680P and NB.1.8.1 + 445P, XFZ(.1) and XFG.1.1 with XFG.14.1 and XFG.6 being almost there
underdogs XFJ.3.1.1 and LF.7.11.