Nick Rose

[Nick Rose @Asinickle1]

@SolidEvidence Is there evidence towards it having or not having spike mutations G151S (r), R190S, T547K, D839K, A958S, D1146G, i1169F?

[Nick Rose @Asinickle1]

@LongDesertTrain @SolidEvidence Someone should contact the submitting lab I think, to let them know about the NYC wastewater appearance

[Nick Rose @Asinickle1]

@SolidEvidence Very much appreciated that it's possible to monitor things this way!

[Nick Rose @Asinickle1]

@jQcWWnq98LPRw5Z I'd doubt it's a legitimate recombinant until there's a 2nd sequence. You'll usually be right if you make that bet.

[Nick Rose @Asinickle1]

@shay_fleishon Agreed... the whole system that came into place during the pandemic, where massive amounts of data could be gathered and shared globally, and meaningful insights could easily be gained from the overwhelming data... it was one of our most valuable improvements. Now it's broken.

[Nick Rose @Asinickle1]

@siamosolocani @BenjMurrell I feel that the technological infrastructure and the systems that were created to support identifying new variants and tracking their spread/growth was one of the most tangible achievements to come from the pandemic.
It made me proud of humanity... why did GISAID throw it away?

[Nick Rose @Asinickle1]

@siamosolocani @LongDesertTrain https://t.co/5MTvGrmmyo

BA.1.1 was able to acquire the mutation, apparently gaining an advantage

[Nick Rose @Asinickle1]

@Nucleocapsoid @yunlong_cao @LongDesertTrain I think that if it was just about RBD up/down, then it wouldn't explain why NB.1.8 is more evasive in the general population than XEC is, but the opposite in JN.1* vaccinated mice
I'd expect RBD-Down is always more evasive?

[Nick Rose @Asinickle1]

@Nucleocapsoid @yunlong_cao @LongDesertTrain And Yunlong's studies show NB.1.8.1 has better RBD affinity than XEC but the same whole spike affinity, which should imply NB.1.8.1 is more closed. But I wonder if S:K478i slightly arranges the spike to expose some residues that are well targeted by JN.1 immunity

[Nick Rose @Asinickle1]

@Nucleocapsoid @yunlong_cao Why do you say it's an RBD-up mutation? My understanding was the opposite. And XEC.25.1 has more evasion than XEC in the same figure.

[Nick Rose @Asinickle1]

@Nucleocapsoid @LongDesertTrain It growing slow/not at all means it's under a lot of pressure - it can barely survive.
I think it likely isn't infecting enough people to find the advantageous mutations/for those mutations to spread enough to not die out.

[Nick Rose @Asinickle1]

@Txukun_kurioso @TRyanGregory Only NB.1.8.1 is very fit and has hit prevalence of ~90% in a large region, such as Hong Kong .

[Nick Rose @Asinickle1]

@TRyanGregory https://t.co/DELGN7xRm6

You can track the global growth/prevalence of Nimbus using this link.

[Nick Rose @Asinickle1]

@LongDesertTrain XFG looks really strong in the paper too, and is currently on track to be a top variant by growth advantage too

[Nick Rose @Asinickle1]

@T_Brautigan @PriscillaFalzi1 @famulare_mike @LongDesertTrain @siamosolocani @wolfeagle1989 B.1.640.1 might have been a disaster if not for Omicron emerging right then..

[Nick Rose @Asinickle1]

@T_Brautigan @LongDesertTrain @siamosolocani I think these can be interesting for recombination though. Especially in the delta->omicron phase, there were a few successful lineages that recombined Omicron RBD with a non-circulating chronic Delta

[Nick Rose @Asinickle1]

@T_Brautigan @LongDesertTrain @siamosolocani Since it didn't get RBD mutations (missing the universal F456 mutation), and no R346T or Q493E, I think there's too much immunity against it though

[Nick Rose @Asinickle1]

@JuanKPV1 @SolidEvidence Err, concentration isn't the right word. They have all the variants add up to 1.0, and BA.3.2's value was around 0.005

[Nick Rose @Asinickle1]

@JuanKPV1 @SolidEvidence The month with the highest wastewater concentration had it at around 0.5%, so I /think/ that implies around 1/200 cases? At that frequency it might be rarely exported, and if it doesn't spread so well then it could struggle to get a foothold elsewhere and get sequenecd