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Nick Rose Profile picture
@Asinickle1
Nov 10 • 2 tweets • 1 min read • Read on X
@LongDesertTrain Right, it wasn't what I set out to find, but in the graph below, x axis is "Days the variant spent in the host before emerging" where each blue dot is one chronic variant that spread enough to be detected multiple times. There's a clear gap in the middle. Image
@LongDesertTrain Not sure if it's just coincidence due to the timings of when fit variants emerged and suppressed the emergence of potential chronic variants, or if there's some inherent reason these mid-range chronic variants are unlikely to be very fit.

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More from @Asinickle1

Nick Rose Profile picture
Nov 4, 2023
I think I'm seeing most people agree that JN.1 is the fastest variant at the moment, possibly by a substantial amount. So I'm glad that got recognized! Ile-de-France is the hotspot and my model predicts that sequences collected there Oct on 30 will be 50% JN.1. (1/N) Image
Right now my model has JN.1 at a 128% weekly growth advantage over the background in Ile-de-France from Aug 14-Oct 16. Confidence interval is 80%-200%.
This appears to be slightly slower than if you measure JN.1 in France as a whole. (2/N) Image
In order to sanity check my model and the quality/consistency of data coming from Ile-de-France, I used a log scale graph with 4 lines, which I'll try to explain a bit... (3/N)
Read 9 tweets
Nick Rose Profile picture
Oct 24, 2023
New data for JN.1 today. I've also changed my model to only include full weeks of data for large regions (England, France.) - I'll explain more in the thread, but my model is back to seeing JN.1 as very fast and largely consistent in my 3 tracked regions. (1/n) Image
For England, I am using data that @OliasDave has access to through CLIMB, which is more complete than what is on GISAID. I am now cutting off the most recent incomplete week. Thanks @JosetteSchoenma for talking me into this! Should result in more accurate consistent data. (2/n) Image
@OliasDave @JosetteSchoenma For Ile-de-France, I don't need to cut off the incomplete week hopefully. My model is sensitive to when inherently different populations are included from one week to the next, but if only the sample size is changing that's fine. Oh, but I also modified the data on this... (3/n) Image
Read 7 tweets
Nick Rose Profile picture
Oct 21, 2023
I'm trying to make sense of how much we can believe the data coming out of France which shows JN.1 is very fast.
It's still early on so there's not great comparisons, but I'll show some of what I found in this thread.
First - JN.1 is well distributed in France, meaning that the sequences aren't all coming from one cluster. Additionally the region that had the first sequence has the most JN.1 sequences today.
Here is a summary of the population of French regions, and how many JN.1s they have. Image
The only other country with enough JN.1 for it to make sense to look at is UK - but the sequences are all in England, so I'll just look there. Image
Read 5 tweets
Nick Rose Profile picture
Oct 20, 2023
France uploaded more data, including 8 new JN.1 sequences. Note that the "week" of 10/9 only has data for a single day.
To me, JN.1 (and therefore BA.2.86*) is increasingly likely to be the most significant/inportant development for the virus since Omicron. Image
Here is my model. The blue line is after today's upload, and red is before.
The x axis is growth advantage, but please note that the scale is logistic -- 1% covers more pixels on the left side than the right.
Y axis is relative likelihood -- higher = more likely Image
My higherbound now excludes the possibility that JN.1 is as fast as Omicron was. The lower bound still might be enough to make JN.1 be the fastest variant today. The highest likelihood guess puts it as faster than all historical variants excluding the initial Omicrons.
Read 5 tweets
Nick Rose Profile picture
Oct 18, 2023


I believe this is the first data on JN.1, the apparently fast child of BA.2.86.1.
It is measured to be the most immune evasive variant that was investigated (and its a good list).
To me, it appearing as the most immune evasive variant strengthens the current data that suggests it is the fastest growing variant.

Also though, even though the measured growth advantage JN.1 has in France under my model would make me suspect XBB will not catch up...
...the lab data makes the gap between the two look more surmountable. XBB has already been able to improve its immune evasion by more than the measured gap between it and JN.1. Can it do it again? Currently its binding affinity is much better than JN.1's.
Read 4 tweets
Nick Rose Profile picture
Aug 17, 2023
I want to talk a bit about what we know of the potential speed and spread of the BA.x/potential Pi variant explained here.
There are still only three sequences that have been identified. Two from Denmark that were submitted on 8/14 and collected on 7/24 and 7/31 respectively. One from Israel, submitted on 8/13 and collected on 7/31.
These are all from different and unrelated patients.
...meaning that there is not just a single cluster in Denmark, and the variant is likely in many countries since there is no reason to believe the variant originated in Denmark/Israel. It must be at least fit enough to be recently competitive; Re was at least recently above 1.0.
Read 15 tweets

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