SARS-CoV-2 variants

We are also still only offered JN.1 in Australia. Vaccines targetting LP.8.1 look like a much better fit against XFG.

Here are the leading countries reporting the XFG.* "Stratus" variant. 🧵

Here are the leading countries reporting the NB.1.8.1 "Nimbus" variant. 🧵

Here's the latest variant picture for the "Global - Other" countries, to late August. The NB.1.8.1 "Nimbus" variant remained dominant, growing to 59%. XFG.* "Stratus" fell slightly to 35%. #COVID19 #SARSCoV2 #GlobalOther #NB_1_8_1 #Nimbus #XFG #Stratus 🧵

Here are the leading European countries reporting XFG.* "Stratus". Ireland hit 93%, the highest I’ve seen so far in Western Europe. 🧵

Here's the latest variant picture for Europe (excluding the UK), to late August. The XFG.* "Stratus" variant continued to dominate, but may have peaked at around 80% frequency. NB.1.8.1 "Nimbus" fell to 9%. #COVID19 #SARSCoV2 #EUR #LP_8_1 #XFG #Stratus #NB_1_8_1 #Nimbus 🧵

Here's the latest variant picture for the United Kingdom, to late August. The XFG.* "Stratus" variant remained dominant, growing strongly to 80%. NB.1.8.1 "Nimbus" fell back to 11%. #COVID19 #SARSCoV2 #UK #XFG #Stratus #NB_1_8_1 #Nimbus 🧵

Here's the latest variant picture for Canada, to late August. XFG.* "Stratus" continued to dominate, but fell back to 62%. NB.1.8.1 "Nimbus" grew strongly to 30%. #COVID19 #Canada #NB_1_8_1 #Nimbus #XFG #Stratus 🧵

Here's the latest variant picture for the United States, to late August. The XFG.* "Stratus" variant continued it’s dominance, finishing at 77% frequency. NB.1.8.1 "Nimbus" was flat, finishing at 12%. #COVID19 #SARSCoV2 #USA #XFG #Stratus #NB_1_8_1 #Nimbus 🧵

The recent rebound in the JN.1.* +DeFLuQE variant now seems mostly driven by the PE.1.4 sub-lineage, which has also been successful lately in Australia. 🧵

Here's the latest variant picture for New Zealand, to early September. NB.1.8.1 "Nimbus" has continued to dominate, finishing at 57%. It looks under serious threat from JN.1.* +DeFLuQE, which finished at 36%. #COVID19 #SARSCoV2 #NZ #NB_1_8_1 #Nimbus #DeFLuQE 🧵

For Australia, JN.1.* +DeFLuQE is showing a healthy growth advantage of 3.9% per day (27% per week) over NB.1.8.1 "Nimbus". That predicts an recent crossover (the data routinely lags). 🧵

The recent rebound in the JN.1.* +DeFLuQE variant was driven by the PE.1.4 sub-lineage, with support from some sub-lineages. PE.1.4 is an Australian-born descendant of MC.10.2.1, which had a long run of dominance over XEC in NZ (up to the arrival of Nimbus). 🧵

BA.3.2.* continues to be reported in the wastewater analysis for Perth. bsky.app/profile/mike... 🧵

BA.3.2.* (arising from a chronic case with many mutations) appears to be well established in Western Australia now, rising as high as 46%. Note the sample volume is very low, so it’s hard to have confidence in that result. 🧵

Here's the latest variant picture for Australia, to late August. NB.1.8.1 "Nimbus" has continued to dominate, but fell back to finish at 47%. It looks under threat from the rebound in JN.1.* +DeFLuQE, which grew to 32%. #COVID19 #SARSCoV2 #Australia #NB_1_8_1 #Nimbus #DeFLuQE 🧵

Here are the trends across all the International Traveller samples. From that perspective, XFG.* "Stratus" fell sharply to 50%, while NB.1.8.1 "Nimbus" was grew sharply to 46%. 🧵

Here's the latest variant picture with a global scope, to late August. XFG.* "Stratus" fell to 61%. NB.1.8.1 "Nimbus" grew slightly to 26%. #COVID19 #SARSCoV2 #Global #NB_1_8_1 #Nimbus #XFG #Stratus 🧵

Australian COVID-19 weekly stats update: The risk estimate increased slightly to 0.3% “Currently Infectious”, or 1-in-389. That implies a 7% chance that someone is infectious in a group of 30. #COVID19 #SARSCoV2 #Australia 🧵

I lean toward skeptical right now. It could be real, but I suspect it's either a coinfection or contamination. It would need to have numerous breakpoints, and some aspects of the sequence—like the (artifactual) frameshift at S:243 suggest some reads are registering the BA.3.2 deletion & some not.

I’m sorry to hear that. I imagine the risk for novids / lowvids steady ratchets up with each new variant, so 5.5 years and 12 or so waves is a creditable effort.

BA.3.2.* rebounded to 10% in the wastewater, so a further +440 to my estimated BA.3.2.* infections in Perth. That takes my estimated total past 2,100. Meanwhile, a possible BA.3.2 / NB.1.8.1 recombinant was shared in the clinical sample data from WA ... very worrying if true ...

Coeur d'Alene, ID continues to have by far the highest SC2 levels among the 192 wastewater SCAN sites. Guess where it is coming from? 1/

We hebben een nieuw record... 25,41% van de mensen met klachten die getest zijn bij de infectieradar vorige week, is positief getest op SARS-CoV-2. Het vorige record (23,39%) stamt uit oktober 2024. Er is gemeten sinds eind 2022. Let op, er hebben NIET een record aantal mensen klachten/Corona!

EPI_ISL_20175638 is the first possible recombinant with Jn.1 if real and not artifact or contamination or coinfection it would be BA.3.2.2/NB.1.8.1/BA.3.2.2/NB.1.8.1 getting from 245 to 439 in the spike from NB.1.8.1 and getting back orf7ab/Orf8 and acquiring Orf9b:I5T all from NB.1.8.1