#Lineage-specific #pathogenicity, immune #evasion, and virological #features of #SARS-CoV-2 #BA286 / #JN1 and #EG51 / HK.3
Source: Nature Communications, AbstractSARS-CoV-2 JN.1 with an additional L455S mutation on spike when compared with its parental variant BA.2.86 has outcompeted all earlier variants to become the dominant circulating variant. Recent studies investigated the immune resistance of SARS-CoV-2 JN.1 but additional factors are speculated to contribute to…
Structural basis for #receptor-binding domain mobility of the #spike in #SARS-CoV-2 #BA286 and #JN1
Source: Nature Communications, AbstractSince 2019, SARS-CoV-2 has undergone mutations, resulting in pandemic and epidemic waves. The SARS-CoV-2 spike protein, crucial for cellular entry, binds to the ACE2 receptor exclusively when its receptor-binding domain (RBD) adopts the up-conformation. However, whether ACE2 also interacts with the RBD in the down-conformation to…
Immune #escape and attenuated #severity associated with the #SARS-CoV-2 #BA286 / #JN1 #lineage
Source: Nature Communications, AbstractThe SARS-CoV-2 BA.2.86 lineage, and its sublineage JN.1 in particular, achieved widespread transmission in the US during winter 2023–24. However, this surge in infections was not accompanied by COVID-19 hospitalizations and mortality commensurate with prior waves. To understand shifts in COVID-19 epidemiology associated with JN.1…
Structural #basis for the #evolution and #antibody #evasion of #SARS-CoV-2 #BA286 and #JN1 #subvariants https://www.nature.com/articles/s41467-024-51973-8
Here, the authors evaluate the neutralization susceptibilities of BA.2.86 and JN.1 and determine the structural basis for binding to the ACE2 receptor and monoclonal neutralizing antibodies, revealing their evolution and antibody evasion mechanism.
https://www.prevention.com/health/health-conditions/a61423582/covid-summer-wave-2024/
A 'double-humped' summer season. That must be a polite way of saying 'double-fucked' as the United States is taking Covid at both ends.
Relative #vaccine #protection, #disease #severity, and #symptoms associated with the #SarsCoV2 #omicron #subvariant #BA286 and descendant #JN1 in #Denmark: a nationwide observational study https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(24)00220-2/fulltext?rss=yes
Although less effective against the new variants, XBB.1.5 vaccination remains protective and reduces the risk of infection and COVID-19 disease.
Molecular Evolution #MolEvol identified adaptive evolution of #ba286 lineage in August 2023 (reminder: 32 non-synonymous substitutions, including 22 in Spike, and only 11 synonyms) while still at very low frequency. #ba286 has now come to dominate globally 👇
https://ecoevo.social/@firefoxx66@mstdn.science/111964032240034358
Virological characteristics of the #SARS-CoV-2 #BA286 #variant, Cell: https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(24)00005-2?rss=yes
• BA.2.86 is more transmissible than the currently predominant #EG51
• The sensitivity of BA.2.86 to #antiviral #drugs is comparable to that of EG.5.1
• The #replication efficiency of BA.2.86 in vitro and in vivo is lower than that of EG.5.1
• In hamsters, BA.2.86 is less #pathogenic than EG.5.1 and the parental BA.2
#Memory T #cells effectively recognize the #SARS-CoV-2 hypermutated #BA286 #variant, Cell: https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(23)00505-X?rss=yes
• SARS-CoV-2 spike-specific T cells are profiled in healthy individuals and CLL patients
• T cell cross-recognition of mutated BA.2.86 spike epitopes is largely preserved
• BA.2.86-reactive T cells display features of high functional capacity
Postpandemic #memory T #cell response to #SARS-CoV-2 is durable, broadly targeted, & cross-reactive to hypermutated #BA286 #variant, Cell: https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(23)00498-5?rss=yes
-- Spike-specific T cell memory responses are maintained into post-pandemic period
• T cell cross-recognition is preserved against highly mutated variants such as BA.2.86
• Even prior to Omicron infection, reactivity to Omicron sub-lineages is conserved
• Robust nucleocapsid- and membrane-specific T cells enlarge total T cell response
Good Morning SARS2PAians!
I hope you're enjoying the milder weather and staying safe. :canparrot:
__________
VOCs
Nationally, nothing really new. JN.1 everywhere, all over the place. Still over 80% of randomly tested sampling.: https://ibb.co/r6wyHdy
In PA, Same thing, reflecting national levels.: https://ibb.co/b78MGWY
There is nothing so far on the mutation horizon that can compete with JN.1. As always there are a few concerning mutations out there, but sample numbers are low and variant hunters have not sent out any immediate warning signals.
__________
Wastewater
Nationally, SARS2 matierial found in wastewater starting to take an unpleasant upturn again. 😓: https://ibb.co/PQkNZs6
Regionally, the decline in levels has evened out again across all non-Eastern regions, and levels are rising in our area.: https://ibb.co/XWGNB1r
In PA,levels rising slightly in Bucks and ChesterCo areas but heeeeeey Lackawanna, please stay safe and use some form of source control! Levels are waaaay up over there.: https://ibb.co/8XLYRgb
The PA Wastewater dashboard has levels staying level for now except in the West Chester area.: https://ibb.co/C0BX4tY
__________
CDC
The New Admits map is looking pretty good, except in the center fo the State and again in SchuylkillCo and the rest of the old coal region west of there, where level increases are substantial. Seems like this rather isolated area still has cases filtering through the health system.: https://ibb.co/vDM2rRL
Lancaster Co also showing significant increases.
The Inpatient Bed map also looking better, with some elevated counties up by Potter Co there, also somewhat in Berks. Nothing substantial which is.....OK.: https://ibb.co/12hc0HV
ICU bed use increased substantially in the center of the State (along I-80-ish) in CentreCo and counties west oif there, with smaller increses east of there too.: https://ibb.co/DMskC0W
Berks showing isngificant increases in ICU use. Berks/Lancaster seem to be having a tough time this winter. Please be safe there, get your most current COVID vaccinations and use source control! Don't become a statistic!
Overall, the northern half of the US, including PA, is doing fairly well in controlling ILIs (influenza-like infections).: https://ibb.co/RvkZ8Hw
Keep practing SOME form of source control (wearing a quality respirator, staying home when sick, do NOT send sick kids to school, avoiding large crowds, aware of social contacts, run those air purifiers, wash hands often to control non-SARS stuff like flu/norovirus etc.) and if we all do SOMETHING then we can keep this controlled for the arrival of Spring! 💐
#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater
Update for 2/02/2024!
Good Morning SARS2PAians!
I hope you're staying dry with all this winter rain! (Sorry I haven't mirrored on Fedi for a while, i had major important stuff going on.)
There's no new CDC stuff today, but also not much new info to write about in total, JN.1.11 doesn't seem to be taking off right now, and numbers are still doing very well in spite of colder weather (when air cleaning and freshening is a bit more difficult).
THIS IS GOOD! I don't want to have any more news here ever! 🎊
__________
VOCs
Nationally, nothing different yet. JN.1 and JN.1.4 still at the top. JN.1.11 still way down at 0.13% and though it's in 5 states and a few more sequences have been found, it hasn't risen above 1% yet.: https://ibb.co/wgZHftH
__________
Wastewater
Nationally, the decline is starting to level off a bit. Hopefully it continues down after more data is collected.: https://ibb.co/MkcDDX5
Regionally, the West is ticking a bit upwards while everyone else is levelling off.: https://ibb.co/kXdhcTJ
In PA, the 5 stations reporting to Biobot are still doing fabulously. Luzerne and Lackawanna still quite above the national average though.: https://ibb.co/M1KzWJy
According to PA's own wastewater monitoring site numbers are holding steady through the state except thre's an uptick in Franklin Co and over by Pottstown.: https://ibb.co/n3hfVrY
FranklinCo: https://ibb.co/VCb9Z9N
Pottstown: https://ibb.co/0Jg6Gy8
Please use caution to keep these numbers from going back up and causing life, learning, and financial loss.
I just want to shoutout Erie Co since I lost track of there, Erie doesn't report to Biobot but it IS on the PA Wastewater dashboard.
It's not only that Erie's numbers are low, it's that (except for a post-holiday small rise) the absolute baseline there is going down!! Look at that. : https://ibb.co/RyVt4bn
That's amazing. Every county, State, and territories' chart should look like this.
:canparrot: :canparrot: Thank you Erie! :canparrot: :canparrot:
Another short update is a good update. Please keep using caution especially with at-risk people and in large public gatherings. Wear a quality respirator in places where there is tightly enclosed space with little ventilation (elevators, restrooms, large public closets, etc.)
Keep that air fresh and clean and we'll be fantastic by Spring! ❄️❄️🌷
#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater
Update for 1/22/2024!
Good Morning SARS2PAians!
Warmer temperatures are ahead, finally, after this bitter cold spell.❄️❄️❄️
__________
VOCs
There's not much new info out there and of course JN.1 and its child JN.1.4 still dominate the variant leaderboard, so this update will be brief as I have family stuff to do this morning anyway.
It's all going to be about closely watching JN.1.11 (JN-one-eleven).
It's now in 5 states as now it's been found in Washington State, and is spreading blazingly fast in India.
JN.1.11 is now accounting for 0.13% of all random sequencing in the US, up from 0.8%. (Yes, it matters to watch it at those low numbers. Low numbers become top leaderboard numbers eventually!).: https://ibb.co/q92Mccf
__________
CDC
The new hospital admits map looks very much improved since last time. Still some increased activity in Philly, Pike Co, and Lawrence Co. Significant increases in Tioga.: https://ibb.co/n6YqkGj
The Northeast US still struggles with lots of occupied inpatient beds. Lots of increases here as COVID filters through the medical system. Increases from Wayne Co down southwest through Huntingdon Co, over to Jefferson Co and up to Potter and McKean.: https://ibb.co/cyzjP7j
ICU Beds now rising through the State too, especially in Berks, Lancaster, Franklin Co up through to Centre, and the northwest corner of the State excluding Crawford Co.: https://ibb.co/wNWptSH
The 3-month death metric unfortunately remains high in most states including PA, and if you compare to last week, this number is increasing steadily in a lot of States.: https://ibb.co/9TNjnkW
We are sadly experiencing over 300 deaths a month from COVID, 1004 deaths in the past 3 months alone.
❄️❄️❄️Don't become a statistic! Please keep wearing those quality respirators, keep the air clean, be aware of social contacts, and get those vaccinations! 😷❄️❄️❄️
#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater
Update for 1/19/2024!
Good Morning SARS2PAians!
So. How 'bout that snow? ❄️❄️❄️
Please be cautious and don't travel today if you don't have to! (And don't travel even if you do have to, if you can help it!)
There's no new CDC map stuff today.
__________
VOCs
Nationally, JN.1 at the top of the leaderboard at over 32% of sequencing.: https://ibb.co/vsK3j09
Please remember ALL sequencing is very slow so these numbers are delayed by weeks. Its child JN.1.4 in second place at over 16%.
In PA, JN.1 and its child mutation JN.1.4 at the top of the chart, reflecting naitonal levels.: https://ibb.co/Bcp6Skk
In NY/NJ, numbers also reflect national levels, ans the first few successful lineages are JN.1, JN.1.4, and HV.1.: https://ibb.co/WBk99sG
XDD is a recombinant that has potential to keep up with and even surpass JN.1.
__________
Lineage News
I want to bring your attention to two potentially problematic new mutations: Previously mentioned XDD (a recombo of EG.5.1.1 and JN.1,) and also especially JN.1.11.
Note: That is J-N-ONE-ELEVEN, and I'll hashtag it here on the Fediverse as #JN1Eleven so it won't get confused with other names like JN.1.1.1 or JN.11.1. Understanding the correct lineage name is vital in tracking!
JN.1.11 has a bonkers high estimated fitness (ability to reproduce, infect, take over the lineage leaderboard etc.) based on genomic info alone.: https://ibb.co/J28MbXh
It was only sequenced this month and is already in 5 countries: India, USA, Singapore, Israel, and the UK.
It's already in at least 4 US States: TX, CO, MD and NC.: https://ibb.co/vDhvmX2
Reminder that the JN.x.y series also as a whole has a bonkers high estimated fitness and binding ability based on genomics alone that you can see here on the ACE2/Immune Escape estimation graph.: https://ibb.co/cJ7dLRT
Numbers in wastewater are starting to go down from the original JN.1, but the trouble with this JN.1 clan is it mutates quickly AND all of it is fast. It has the potential to raise the absolute baseline high and keep it there so it never goes down IF we all do not practice some form of source control.
Schools as they open will contribute to rising cases and increased absences all over the place, for kids AND for adults. The way to combat this is source control.
__________
Wastewater
Nationally, SARS2 in wastewater starting to decline.: https://ibb.co/ftKcw5N
Regionally, the Northeast on a sharp downturn and the rest of the regions holding steady or ever so slightly declining.: https://ibb.co/KbjPYLR
Please don't get comfy with this until we know how schoolkids are going to fare.
In PA, the 5/11 Biobot up-to-date sheds are showing a promising downturn, ChesterCo and BucksCo down to meeting the national average level again.: https://ibb.co/0MTv8cm
MontCo is back to smashing it going BELOW national levels!
According to the PA DOH wastewater site (thank you so much to a supercool Fediverse reader that pointed this site out for me!!...thank you lemon❤️️) sheds in CentreCo, near Philly and in MonroeCo are experiencing increases in tested SARS2 material.: https://ibb.co/BgDtfH0
On WastewaterSCAN, levels are still HIGH nationally for SARS2, RSV, and Norovirus (which is the "24hr stomach thing" from tainted surfaces/food). Make sure your utensils and eating places are cleaning things properly...this stuff's just gross 🤢: https://ibb.co/LSnpD2j
We are not out of the woods yet with this illness season. PLEASE practice some source control as this blazing fast JN.x.y clan takes over and can push numbers way up if we get hit with multiple very fit variants at once.
NOWCAST
The latest NOWCAST from CDC is out. JN.1 estimated at 85% of cases this week! 👀🚀👀🚀👀🚀: https://ibb.co/LS53WZH
Lots of junk out there and JN.x.y is some seriously fast business. Please :canparrot: doooooooooo the source control :canparrot: and we can prevent life, learning, and financial loss and have an easy transition into spring! 😷😷😷
(And be careful out there today too ❄️❄️❄️)
#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater
#Macau, Serviços de Saúde apelam aos residentes para prestarem maior #atenção à #prevenção do vírus #influenza e da #COVID19 devido ao crescimento dos casos em Macau https://www.gcs.gov.mo/detail/pt/N24ALK8Q5a #EG5 #BA286 #JN1
Good Morning SARS2PAians!
I hope you have a restful and powerful holiday today! ✊
Thre's not much new info out today. No Tableau stuff, no wastewater.
__________
CDC
CDC has released new per-county information, though.
The new hospital admits map has improved quite a bit for now, the post-holiday pre-school timeslot. Cases are still substantially increasing in the counties along south of I-80, and north up to Potter and McKean Cos.: https://ibb.co/zSCd72n
Also in Crawford, Franklin and Fulton Cos.
The map showing inpatient beds has gotten only slightly better, still a LOT of counties showing substantial and high increases.: https://ibb.co/ZxS1yYN
A direct result of waning immunity considering most people not getting current vaccines...XBB or even their bivalents from last year.
Substantial increases east of Potter Co, east of Luzerne Co, in Berks, and east of Juniata.
ICU bed occupation near the Philly area and surrounding counties has considerably lessened since last update where this area in particular was experiencing high levels.: https://ibb.co/n8vsDst
Now everywhere else but Philly and surrounding counties are showing substantial and high levels. Again, those counties are the same already mentioned...East of Juniata, east of Luzerne, Berks, and along the western half of the NY border counties. Also in Mercer Co.
C19 Emergency Dept visits are nationwide on the low side except here in the Northeast.: https://ibb.co/mbdkxDq
Unfortunately, as of Jan.11th, there have been 1,026 deaths from Covid-19 in PA in the past 3 months. (PLEASE NOTE this number keeps rising monthy.): https://ibb.co/xmjvw2d
PA, and in fact the majority of states, are in the highest CDC percentage category of states with COVID deaths in a 3 month roling period.
__________
JN.1 News
Along with 11 NYC public hospitals, mask mandates have returned to NYC EMS for their fire/ambulance emergency services.: https://www.msn.com/en-us/health/other/mask-mandate-returns-for-fdny-fire-ambulance-personnel-amid-rise-in-covid-other-viruses/ar-AA1mVNAu
China is issuing stern warnings about JN.1, but I want to draw attention to the last paragraph of this article in particular: https://news.cgtn.com/news/2024-01-14/China-warns-on-possible-rebound-of-COVID-19-JN-1-subvariant-1qmE7pROeGY/p.html
""High-risk groups like pregnant women, children and the elderly should prioritize annual influenza vaccination and maintain healthy habits," Wang advised. He further stressed the importance of understanding that contracting one type of respiratory illness does not guarantee immunity against others in the short term."
Please, folks, keep up with all available respiratory vaccinations, not just COVID.
Encourage children to mask up with quality respirators when they go back to school. If we are cautious until the Spring it's going to save us going through some things in the long run!! 😷😷😷
:canparrot:
#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater
Good Day Fediverse, SARS2PAians!
A bit late for me to mirror this on the Fediverse (sorry), but here's the 1/12/2024 update!
There's no new CDC hospitalization data today.
__________
VOCs
Nationally, JN.1 solidly in the lead with over 27% leaderboard share in random sequencing.: https://ibb.co/7QdWsxz
In PA, HV.1 in the lead...but not by much, 16% vs. 17%. Weird.: https://ibb.co/rd18RCq
But, I would think that if JN.1 isn't blazing fast here like in other places, especially being close to densely infected metro areas like NY and Jersey, we're doing something right.
We're wearing respirators, keeping close watch of social contacts, and keeping the air clean.
Everyone can snd should practice SOME form of source control. IT WORKS! 😎
IN NY/NJ, JN.1 at 37% of share.: https://ibb.co/tDsZqTS
JN.1.4 is one of a few upcoming variants that have potential to compete with JN.1 but will most likely not actually take over. The JNs will probably just take over more and more of the share from everything else below it.
There's nothing that can take over JN.1.
Yet.
___________
Wastewater
Nationally, SARS2 wastewater is starting to level off a bit.: https://ibb.co/nMgxSvz
Don't get comfortable, the kids still have to go back to school.: https://ibb.co/FnFLrzc
Regionally, the Northeast is still going slightly up but the growth is slowing. The rest of the regions are stable and not rising.: https://ibb.co/2YV5D0Z
In PA, 4/11 sheds reporting naything close to current, and those sheds are all going vertical. The small drop at the end is usually due to incomplete data and not an actual drop in material.: https://ibb.co/2YV5D0Z
If you look at the cumulative data through this whole thing, you can see easily that in BucksCo and in the other current data sheds (Lackawanna, Luzerne, MontCo) that this is the second highest rise in material throughout the pandemic.
BucksCo: https://ibb.co/DCCGwrz
Other sheds: https://ibb.co/brCcRQF
And the concentration is VERY HIGH at over (EDIT:) 2000m/L.
This rise is NOT due to persistence in the gut and extreme shedding through GI issues, but rather due to actual reinfections.: https://ibb.co/5KK6LR9
:ms_arrow_right: Maria Van Kekhove, a director at the WHO, tweeted:
"What is driving circulation is an evolving virus (now JN.1 represents >50% of sequences shared for global analysis) that is reinfecting people in all countries, limited or no public health and social measures used to limit exposure, and many other factors"
__________
CDC
The most current At-A-Glance graphic still has the country trending the wrong way.: https://ibb.co/RbGdvDv
Most states are in HIGH, VERY HIGH or EXTREME levels of Influenza-Like Illnesses (ILI), a combo of a bunch of things like COVID, FluA, FLuB, parainfluenza, colds, etc.: https://ibb.co/L1n896y
Please take caution now because this could make us all go through some things when these kids go back to school.
Wear a respirator, have those kids wear them. :canparrot:
Clean the air, use those CR boxes/HEPA filters! :canparrot:
Keep track of social contacts :canparrot:
Ventilate when possible/weather permits :canparrot:
Keep unnecessary travel to a minimum :canparrot: (<---i love this parrot LOL)
If we use caution now the back-to-school fallout won't disrupt the health care system, and we'll all be much happier! 😷😷😷
#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater
-- #JN1’s #spike protein has just 1 more #mutation than #BA286’s spike. That mutation, called #L455S, enhances the virus’ ability to bind to the angiotensin-converting enzyme 2 (#ACE2) #receptor, SARS-CoV-2’s doorway into cells, Nicole Doria-Rose, PhD, chief of the Humoral Immunology Core at the NIAIDs’ Vaccine Research Center, noted in an interview with JAMA.
📢http://CoVariants.org Update📢
23G (XBB.1.5.70)
23H (HK.3) &
23I (BA.2.86)
are now available on CoVariants! They are visible as part of Per Country & Per Variant plots, on the shared mutation page, & on their individual pages
1/8
Humoral immune #escape by current #SARS-CoV-2 #variants #BA286 and #JN1 December 2023 https://pubmed.ncbi.nlm.nih.gov/38214083/?utm_source=Feedly&utm_medium=rss&utm_campaign=None&utm_content=1tcbYKHhYJMVv9EYVIXTv68QlnI8VGVDqIu1-nD9hvHuYbKgNG&fc=None&ff=20240112095729&v=2.18.0
-- We tested live virus neutralisation of sera taken in Sept 23 from vaccinated and exposed healthy persons (n = 39). We found clear neutralisation escape against recent variants but no specific pronounced escape for BA.2.86 or JN.1. Neutralisation escape corresponds to recent variant predominance but may not be causative of the recent upsurge in JN.1 incidence.
