#jn1 — Public Fediverse posts

[Correspondence] #Antiviral humoral #immunity induced by #JN1 monovalent #mRNA #vaccines against SARS-CoV-2 omicron subvariants including #JN1, #KP311, and #XEC https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(24)00810-7/fulltext?rss=yes

Our data suggest that the receptor-binding domain of JN.1 S can effectively induce antiviral humoral immunity against JN.1 subvariants and XEC comparable to the full-length JN.1 S.

Robust #antiviral humoral #immunity induced by #JN1 monovalent #mRNA #vaccines against a broad range of #SARS-CoV-2 #Omicron subvariants including #JN1, #KP311 and #XEC

Source: BioRxIV, AbstractAs of November 2024, SARS-CoV-2 Omicron JN.1 subvariants, such as KP.2 (JN.1.11.1.2), KP.3 (JN.1.11.1.3), KP.3.1.1 (JN.1.11.1.3.1.1), and XEC, a recombinant lineage between KS.1.1 (JN.13.1.1.1) and KP.3.3 (JN.1.11.1.3.3), have been circulating in several countries. To control…

https://etidioh.wordpress.com/2024/11/21/robust-antiviral-humoral-immunity-induced-by-jn1-monovalent-mrna-vaccines-against-a-broad-range-of-sars-cov-2-omicron-subvariants-including-jn1-kp311-and-xec/

Neutralizing #antibody #evasion of #SARS-CoV-2 #JN1 derivatives #KP3, #KP311, #LB1, and #XEC

Source: BioRxIV, AbstractThe emergence of SARS-CoV-2 variants poses ongoing challenges to vaccine efficacy. We evaluated neutralizing antibody responses against JN.1 and its derivatives (KP.3, KP.3.1.1, LB.1, and XEC) in healthcare workers who received seven doses of BNT162b2, including XBB.1.5 monovalent vaccine. In COVID-19-naive individuals, KP.3.1.1 and LB.1 showed…

https://etidioh.wordpress.com/2024/11/06/neutralizing-antibody-evasion-of-sars-cov-2-jn1-derivatives-kp3-kp311-lb1-and-xec/

#Impact of #JN1 #booster #vaccination on #neutralisation of #SARS-CoV-2 variants #KP311 and #XEC

Source: BioRxIV, {Excerpt} Conclusion Collectively, we found that the XEC S protein retains the ability to efficiently engage ACE2 and drive cell entry, although entry into Calu-3 lung cells was reduced. Both KP.3.1.1pp and XECpp were generally less well neutralised compared to JN.1pp, indicating elevated immune evasion. Importantly, JN.1-booster vaccination significantly…

https://etidioh.wordpress.com/2024/10/05/impact-of-jn1-booster-vaccination-on-neutralisation-of-sars-cov-2-variants-kp311-and-xec/

#Neutralization and #Stability of #JN1-derived #LB1, #KP23, #KP3 and #KP311 #Subvariants http://biorxiv.org/cgi/content/short/2024.09.04.611219v1?rss=1

We report on the neutralizing #antibody (nAb) #escape, infectivity, #fusion, and stability of these subvariants-LB.1, KP.2.3, KP.3, and KP.3.1.1. Our findings demonstrate that all of these subvariants are highly evasive of nAbs elicited by bivalent #mRNA #vaccine, the #XBB15 monovalent mumps virus-based vaccine, or from infections during the BA.2.86/JN.1 wave.

[Correspondence] Virological #characteristics of the #SARS-CoV-2 #KP311 #variant https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(24)00505-X/fulltext?rss=yes

SARS-CoV-2 #JN1 variant (#BA28611), arising from BA.2.86.1 with spike protein (S) substitution S:L455S, outcompeted previously predominant #XBB lineages by beginning of 2024. Subsequently, JN.1 subvariants including #KP2 (JN.1.11.1.2) & #KP3 (JN.1.11.1.3), which acquired additional S substitutions (eg, S:R346T, S:F456L, and S:Q493E) have emerged concurrently (appendix pp 19–20).2

#Pemivibart is less active against recent #SARS-CoV-2 #JN1 #sublineages http://biorxiv.org/cgi/content/short/2024.08.12.607496v1?rss=1

Pemivibart neutralized both JN.1 and #KP2 in vitro with comparable activity, whereas its potency was decreased slightly against #LB1, #KP23, and #KP3 but substantially against #KP311. Critically, the 50% inhibitory concentration of pemivibart against KP.3.1.1 was ~6 g/mL, or ~32.7 fold higher than that of JN.1.

An upcoming #vaccine from the biotech co Novavax will target #JN1, a #coronavirus #variant that accounted for the bulk of cases in the #UnitedStates this winter. The Pfizer & Moderna shots coming this fall will target #KP2, a newer offshoot of JN.1 that’s been circulating this summer. The #variants responsible for the largest share of cases in the #US right now, #KP3 & #KP311, are closely related to KP.2 & JN.1.

#health #PublicHealth #medicine #COVID

Reduced #Likelihood of #Hospitalization with #JN1 or #HV1 #SARS-CoV-2 #Variants Compared to #EG5 Variant, J Infect Dis.: https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiae364/7717186?utm_source=advanceaccess&utm_campaign=jid&utm_medium=email&nbd=25018031857&nbd_source=campaigner

JN.1 and HV.1 variants may be associated with a lower #risk of severe illness. The severity of #COVID19 may have attenuated as predominant circulating SARS-CoV-2 lineages shifted from EG.5 to HV.1 to JN.1.

#Virological #characteristics of the #SARS-CoV-2 #KP311 #variant http://biorxiv.org/cgi/content/short/2024.07.16.603835v1?rss=1

KP.3.1.1 exhibited a higher Re, higher pseudovirus infectivity, & higher neutralization #evasion than KP.3. These results align with our recent report that #JN1 subvariants with S:S31del (eg KP.2.3 & LB.1) exhibited enhanced Re and immune evasion compared to other JN.1 subvariants without S:S31del (eg JN.1, KP.2, & KP.3), highlighting evolutionary significance of S:S31del in JN.1 lineages.

#Virological characteristics of the #SarsCoV2 #KP3, #LB1 and #KP23 #variants, BioRxIV, https://www.biorxiv.org/content/10.1101/2024.06.05.597664v1?rss=1

Our results suggest that S #substitutions convergently acquired in #JN1 #subvariants contribute to immune evasion, & increase their Re when compared to parental JN.1. LB.1 & KP.2.3 exhibited higher pseudovirus #infectivity & more immune resistance than KP.2. Data suggest that S:S31del is critical to exhibit +infectivity, +immune evasion, & potentially contributes to increased Re.

#Durability of #XBB15 #Vaccines against #Omicron #Subvariants, N Engl J Med.: https://www.nejm.org/doi/full/10.1056/NEJMc2402779?query=TOC&cid=DM2342986_Non_Subscriber&bid=-1971795569

Overall, the XBB.1.5 vaccines were effective against omicron subvariants, although less so against #JN1. Effectiveness was greater against #hospitalization and #death than against infection, and it waned moderately from its peak over time. The ramping and waning patterns were broadly similar to those of the bivalent boosters against BQ.1–BQ.1.1 and XBB–XBB.1.5.3

Update for 5/24/2024!

Good morning SARS2PAians! (well, afternoon by the time I got all this ready)

I hope you are having a BEAUTIFUL and healthy day. 💐💐💐

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VOCs

Nationally, KP.2 is in the lead so far, easily displacng JN.1 variants.: https://ibb.co/JCWtxdr

KP.3 and LB.1 (DeFLiRT) are making FAST gains in the leaderboard, now up to around 5% each nationally.

They are still the top two successful variants that show great potential to take over from even KP.2.: https://ibb.co/kxHkfV1

🔴JN.1.50 is new, and was just designated on 5/18 and though genetically it's as fast as LB.1 and KP.3, it remains to be seen in meatspace how it will spread.

In PA, JN.1 still in the lead here in random sequencing at 20% and KP.2 behind it at 13%.: https://ibb.co/G7Nnft5

Unfortunately KP.3 has been found here. So we now have BOTH very fast DeFLiRT variants here for the summer, KP.3 and LB.1. Take care, keep windows open, clean the air, wear a quality respirator and be aware of social contacts. These two variants might push the numbers up this summer.

In NY/NJ, KP.2 in the lead and look at that LB.1....in second place at 10% of random testing already. Yikes. It's been making very fast gains for a while now there.: https://ibb.co/8xRfkkh

Some parts of Jersey have noticeable upticks of matarial concentraion on WastewaterSCAN.: https://ibb.co/7STgtLZ

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Wastewater

Trying to get as much info as possible here since almsot everything useful is being discontinued. 🙄

SARS2 has been bumped up to MEDIUM nationally on WastewaterSCAN.: https://ibb.co/Wf5MdxN

There are noticeable upticks starting to happen in the Harrisburg and Chester areas.: https://ibb.co/g3HQZp0

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Non-SARS2 Pathogens

Gastro pathogens Noro and Rotavirus are still in the HIGH category on WastewaterSCAN. Please wash hands carefully, wash fruits and veg, and be aware of kitchen cleanliness discipline to avoid cathing these bugs. Mostly because they're just gross 🤢

🔴Concerning H5N1 (HPAI, "bird flu"), we are NOT in flu season, so seeing upticks for Influenza A is extremely concerning.

This is what the FluA graphs SHOULD look like now in a normal post-FLuA season.: https://ibb.co/X4Q8szS

H5N1 is an influenza A. It's been upgraded to MEDIUM on WastewaterSCAN.: https://ibb.co/wKC300x

However, the online tool makes no differentiation between H5N1 and other types of FLuA. It also cannot tell live virus from inactivated virus or its fragments.

It's extremely telling, though, that the highest concentration of FluA is located exatly where herd breakouts have or are occuring, mostly in the middle of the country in the plains corridor.

To reduce the risk of contracting, transmlitting, or allowing H5N1/HPAI to mutate,

🔴🔴🔴DO NOT DRINK RAW MILK.🔴🔴🔴

I don't give a flying fart if it's legal to sell/buy here in PA. Do NOT be that guy. Do NOT encourage this pathogen to mutate and DO NOT endanger your own life or everyone else's by consuming raw or unpasteurized dairy products.

Use caution in handling raw dairy products, especially meat and milk. Pasteurization has been proven to kill FluA and fluA is very sensitive to heat, but please use caution, fully cook raw meat, and use good sanitary habits when working with raw farm products.

As always, some method of source control is always good to help keep these pathogens in check whether they're just annoying and gross OR have a high kill rate.

I hope you stay safe, enjoy the open windows in Spring, and ARE NOT DRINKING RAW MILK.

Have a great week!!

#covid #Covid19 #SARS2PA #CovidIsNotOver #Pennsylvania #PA #JN1 #FLiRT #F456L #R346T #spike_f456l #spike_r346t

#DeFLiRT #S531del

#FLuQE #SQ493E

#KP3 #LB1 #JNOne50

#IFYouAreDrinkingRawMilk__STOP__DOING__IT

#WearAMask #CleanTheAir #WashHands #StayHomeIfSick !

Characteristics of #JN1-derived #SarsCoV2 #subvariants #SLip, #FLiRT, and #KP2 in neutralization #escape, #infectivity and membrane #fusion http://biorxiv.org/cgi/content/short/2024.05.20.595020v1?rss=1

Interestingly, #antibodies in #XBB15 monovalent vaccinated hamster sera robustly neutralized FLiRT and KP.2 but had reduced efficiency for SLip.

Good morning SARS2PAians!

I hope your very cloudy annd humid Spring is going well. 💐💐💐

The only thing I have right now are VOC visuals.

Nationally, KP.2 in the lead at 12% of random sequencing. The FLiRT variants are not far behind and VERy fast variants KP.3 and LB.1 are still making fast gains even after only a few days.: https://ibb.co/309Ygcj

In PA, classic JN.1 is still at the lead here. We don't have KP.3 here but we do have fast mover LB.1 which is now over 5% of random sequencing.: https://ibb.co/CpyDWkH

IN NY/NJ, immune evasive variants LB.1 already at over 7% of testing and KP.3 almost at 5%.: https://ibb.co/LZ1hZM7

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Wastewater

Biobot has released a statement saying they are stopping keeping up their COVID-19 wastwater visuals. There's still WastewaterSCAN but only three sheds are on there.: https://ibb.co/2tYPPcm

https://biobot.io/from-raw-data-to-actionable-insights-biobots-evolution-of-public-data-sharing/

This is another removal of a GREAT tool that helped everyone stay informed, and gave a heads-up when to buckle down on source control issues.

A very good potential replacement for Biobot is Iowa Covid-19 Tracker and I'll start to try to get familiar with that as soon as I can sit down to do it so the vizzes might look very different soon.: https://iowacovid19tracker.org/

I hope to have more info on Friday, and until then have a GREAT week and safe Spring! 💐💐💐

#covid #Covid19 #SARS2PA #CovidIsNotOver #Pennsylvania #PA #JN1 #FLiRT #F456L #R346T #spike_f456l #spike_r346t

#DeFLiRT #S531del

#FLuQE #SQ493E

#KP3 #LB1

#Biobot #IowaCOVIDTracker

#WearAMask #CleanTheAir #WashHands #StayHomeIfSick !

Update for 5/17/2024!

Good morning SARS2PAians!

I hope you are staying healthy during this very cloudy and rainy period! 🌦🌧☁️☔️

VOCs

Nationally, the FLiRT group (in pink on the graph), which is the first group that can cause a rise in summer numbers in a few wweeks, is still pushing closer and closer to the top of the chart. FLiRT variant KP.2 is already at almost 10% nationally in random sequencing.: https://ibb.co/Wxtgg1N

The second group (KP.3, LB.1, JN.1.32) that can push up summer numbers is not far behind and is FAST.

To complicate issues even more:

It's been advised where I'm cruising around for this info that the second group is not only VERY immune-evasive to current variant antibodies, but also returning to a more lung-based symptom set rather a gut-based set. JN.1 is mainly centered in the gut, which makes wastewater monitoring more sensitive and more accurate.

A return to a more lung-based centered illness is a bad thing and will make wastewater testing not-as-sensitive as it was for JN.1 relatives.

In PA, KP.2 is already in the lead of random sequencing results at 16% of share.: https://ibb.co/6XpWGfF

We already have LB.1 here so it's oging to very important to track this fast moving and immune evasive variant.

In NY/NJ, KP.3 and LB.1 in fifth and sixth places on the leaderboard. Their rise is increasing quickly as they're up to over 4% of varaint share, up from 3% a week ago.: https://ibb.co/9gsdZ0W

A 1% increase in such a short amount of time in a field of already very fast variants is noteworthy. In a race of thoroughbreds, varaints like this are the potential triple-crown winners.

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Wastewater

Wastewater levels are still very good (low.) Nationally we're at the same level as last year but not low enough to match 2021 yet.: https://ibb.co/Y3Tv51h

In PA, not much to say. EVERYONE is smashing it. Bucks county area a bit higher than naitonal levels and trending upwards. PLEase use precaution and some sort of source control so these numbers don't go back up.: https://ibb.co/hd2FcNh

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That's all I have this morning, so I hope you have a GREAT week! I apologize for not updating consistently as data is harder to obtain and H5N1 takes over the foreground of virology conversations (as it should, understandable)!!

#covid #Covid19 #SARS2PA #CovidIsNotOver #Pennsylvania #PA #JN1 #FLiRT #F456L #R346T #spike_f456l #spike_r346t

#DeFLiRT #S531del

#FLuQE #SQ493E

#KP3 #LB1

#WearAMask #CleanTheAir #WashHands #StayHomeIfSick !

Update for 5/13/2024!

Good Morning SARS2PAians!

I hope your chilly Spring is going well! 💐💐💐

Just a very quick VOC update as there is absolutely nothing really updated to work with this week 🙄

While numbers are still very very low right now (which is great), the virology world and variant hunters are watching a few new mutations lately.

The two most important coming up are KP.3 and LB.1.

Globally, KP.3 is already in 2nd place, very high in places like the UK and Australia, easily growing past previous JN.1 incarnations AND FLiRT variants.: https://ibb.co/ch19ph8

It carries a very rare mutation (S:Q493E) that enhances its fitness and will enable it to grow much fater than previous JN.1 incarnations.: https://ibb.co/9vx0JTn

It is IMMUNE EVASIVE compared to all current acquired immunity, both by vaccination and infection. It's fast enough and evasive enough to probably bump up numbers in June or July.

In the US, KP.3 is in relatively low numbers right now: https://ibb.co/XpRF6D6

BUT KP.3 is growing very quickly as the previous variant snapshot show when put together:

4/01-- 0.34%

4/05-- 0.44%

4/12-- 0.63%

4/19-- 1.17%

4/25-- 1.55%

5/03-- 1.64%

5/06-- 2.23%

5/12-- 3.20%

(This is fast in a landscape that's already thoroughly saturated very very vast variants.)

In PA, variant sequencers have not seen KP.3 pop up yet (doesn't mean it's not here, sequencing and testing are soooooo loooow but at least it's not showing up on the leaderboard.): https://ibb.co/4YzwNFN

However, LB.1 (from the FLiRT group but with an important deletion {S:531del}) is another very fast variant that is probably enough to bump up numbers too.

The summer will probably be FLiRT + FLiRT children vs. KP.3 (nicknamed FLuQE) + FLuQE children.

Those two mutation classes together wil probably start pushing up numbers again in early June.

Unfortunately that's all I have for now as it's getting harder and harder to find updated info.

I hope your Spring continues to be healthy! 💐💐💐

#covid #Covid19 #SARS2PA #CovidIsNotOver #Pennsylvania #PA #JN1 #FLiRT #F456L #R346T #spike_f456l #spike_r346t

#DeFLiRT #S531del

#FLuQE #SQ493E

#KP3 #LB1

#WearAMask #CleanTheAir #WashHands #StayHomeIfSick !

Update for 5/6/2024!

Good Morning SARS2PAians!

Yes I have an update today aaaaand unfortunately that's kinda never a good thing. You DON'T want to hear from me here!

(I am asking you once again....to please make this hobby of mine obsolete 🙏😔 Filter the air, be aware of social contacts, wear a quality respirator, and wash hands for the gastro stuff.)

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VOCs

We are dealing with FLiRT now, but there are two groups of incoming variants that are becoming concerningly successful in other countires including right next door in Canada.: https://ibb.co/fkG3gpg

One is an earlier-new group consisting of JN.1.32 and KP.3.

Another, far off-new yet, is KW.1 and its child, KW.1.1.

All of these variants have been proven faster than FliRT in Australia, UK, etc. KP.3 is exceptionally fast.

🔴Due to antigenic drift, vaccines and previous infection are NOT as effective to protect you with these upcoming variants.

🔴This does NOT mean vaccines don't work, so do not go spreading that. (You should also be mightily shunned for spreading that.)

Again: Vaccines are safe and effective...but these incoming variants are starting to yet again DRIFT TOO FAR AWAY from the current XBB vaccines.

I've highlighted the upcoming concerning variants in teal, as opposed to the FLiRT group which is in pink. KW.1.1 isn't above the fold yet nationally at 0.16% so I made a note on the image so I remember to keep track of this number.

Nationally, JN.1.7 and JN.1 are a tthe top of the board. JN.1.32 at 2.23% and KP.3 also at 2.23%. KW.1 at a little under half a percent. These numbers might be higher in actual meatspace because there is not nearly enough labwork/sequencing available to make laser-focused predictions.: https://ibb.co/bRpvDP7

In PA, we do not have group 2 of the far-off variants yet here but we do have KP.2. Gotta watch this one.: https://ibb.co/3kPMBwM

In NY/NJ, whoa, KP.3 already clocking in at over 3%, in the top 10 of random sequencing already. I haven't been watching this one so when I have more time I'll go back and check this one out.: https://ibb.co/qM7C4CY

KP.2 already at over 10%. That's fast, and antigenic drift is absolutely not helping here as any protection we might have had against this new stuff is starting to slip away.

We might be in for a bump up in numbers this spring, as something similar last year happened too.

Just giving everyone a heads-up on what we might be in for this spring/summer.

We can keep it in control by practicing some very comon-sense, easy things!

Have a safe spring!! 💐💐💐

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Wastewater #Pennsylvania #PA #JN1 #FLiRT #F456L #R346T #spike_r346t #spike_f456l

#KP2 #KP3 #JNOne32 #JN132 #KS1

#KW1 #KW11

#WearAMask #CleanTheAir #WashHands #StayHomeIfSick !

Good Morning/Afternoon SARS2PAians!!

I hope you are enjoying this GORGEOUS Spring weather 💐💐💐

1/2 Update for May 3, 2024!

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:all_the_things: State of the Subreddit/Fediverse posts:

There's not much new to report for COVID right now except some closely watched new mutations, so basically TL;DR is that COVID levels are very very low, enjoy it but please keep source control safety always on the backburner.

So. I don't mean to only have this as a once-a-week thing but it's kind of turning into that. I also don't mean to have people waste their time checking in here if I don't post, but I'm always hesitant to call it a once-a-week-thing as COVID is so volatile and mutations can always manifest something very weird in a short amount of time.

I have no idea when info will be available so I'm keeping it a "twice-a-week thing", Monday and Friday but sometimes I just don't have enough info/anything new/time for a Monday, so Friday is always much better for a full post for me.

I hope you continue to find this informative useful and I suuuuuper apologize if you check in and I don't post. 🙏

But even better, go check out the links for yourself and follow people smarter than me for COVID stuff!

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VOCs

Nationally, JN.1 and JN.1.7 still at the top of the leaderboard. FLiRT variants JN.1.4 and KP.2 keeps chipping away at their lead.: https://ibb.co/JqWkBSD

KP.2 seems to be the fastest mover of the whole FLiRT mutation block and the one the virology world is keeping their eyes on.

In PA, we don't have KP.2 showing up on Rajnarayanan's Tableau site so far, whcih is good but we still have quite a few FLiRTs here.: https://ibb.co/vP5yH4G

In NY/NJ, we can see here KP.2 has climbed above all the other FLiRTs, is in 4th place at >8% and is right behind JN.1 now.: https://ibb.co/ZzLcRxJ

The WHO is now looking to JN.1 being the next mutation that will be the base of the newest COVID vaccine.: https://www.who.int/news/item/26-04-2024-statement-on-the-antigen-composition-of-covid-19-vaccines

🔴PLEASE GET VACCINATED if available. Don't be a tuff guy. Go get it.

Upcoming fast variants are KP.3 and JN.1.32👀, which are not FLiRTs but very fast. I have them highlighted in teal on the charts as they are both already up to almost 5% of national sequencing.

In PA, we have JN.1.32 in low but measurable amounts at a little over 3% of random sequencing and these two variants wil have to be watched.

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CDC

CDC has stopped requiring reporting COVID hospital admissions, hospital capacity or hospital occupancy data at the beginning of May. 🙄 This plus nowhere near enough testing and sequencing makes this....hard to keep up with the virus.

"Effective May 1, 2024, hospitals are no longer required to report COVID-19 hospital admissions, hospital capacity, or hospital occupancy data to HHS through CDC’s National Healthcare Safety Network (NHSN). CDC encourages ongoing, voluntary reporting of hospitalization data. Data voluntarily reported to NHSN after May 1, 2024, will be available starting May 10, 2024, at COVID Data Tracker Hospitalizations."

"The source of hospital information on the COVID Data Tracker home page will change from the National Healthcare Safety Network (NHSN) to COVID-NET. Instead of displaying national counts of new hospital admissions, it will show COVID-19 hospitalization rates per 100,000 people. More information on COVID-Net is available on COVID-NET Laboratory-confirmed COVID-19 Hospitalizations."

https://covid.cdc.gov/covid-data-tracker/#datatracker-home 🙄

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Other Pathogens

WastewaterSCAN now has SARS2 as LOW! YEAH! :canparrot:

Also FluB and RSV! Woohoo! :canparrot:

Still HIGH though are FluA, Human Metapneumovirus (HMPV), parainfluenza, and gastro bugs Noro and Rotavirus.: https://ibb.co/By0g9Xt

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H5N1 follows in second post......

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Wastewater #Pennsylvania #PA #JN1 #FluB #Influenza #Norovirus #HMPV #FLiRT #F456L #R346T #spike_r346t #spike_f456l

#H5N1 #CleanFeedNOW

#WearAMask #CleanTheAir #WashHands #StayHomeIfSick !

Good Afternoon SARS2PAians!

I hope your spring is healthy and productive! 💐💐💐

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VOCs

Nationally, the most concerning variants are, as I posted last week, the FLiRT variants that have specific mutations enabling fast transfer. JN.1.4 and KP.2 are already almost at 10% of variant share but remember the amount of testing and sequencing right now is dismal and it makes everything harder to evaluate.: https://ibb.co/KDt0Bh4

FLiRT variants are highlighted in pink on my screenshot. Expect these to push further and further near the top in the next few weeks (and the CDC NOWCAST confirms this prediction.)

In PA, we still have a few FLiRTs here and you can already see them starting to move toward the top of the variant chart.: https://ibb.co/kc9CQyZ

In NY/NJ, FLiRTs KP.2, JN.1.4, JN.1.16.1, and JN.1.18 already account for ~20% of random sequencing.: https://ibb.co/TrcS9rW

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Wastewater

The GOOD news is COVID is stil fairly low; we've gone below the higher level of two years ago, and are at the lower level of last year at this time!: https://ibb.co/Q83BR3k

We still must watch to see if the FLiRT crew push this metric upwards.

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CDC

The new hospital admits map has changed. High increases all through Central PA excepting Centre Co. and also over tehre in Mercer Co. Philly and Pitt looking very good!: https://ibb.co/Xp8tCJV

The Inpatient Beds Map looks pretty good, some increases in McKean, Potter, and Cameron counties and also around Somerset and Cambria Cos.: https://ibb.co/fD7JYTf

ICU beds over all showing stability, with lots of counties in Central PA and the old coal region on the decrease! Some increases from Lycoming over to McKean though.: https://ibb.co/jMTdyCT

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NOWCAST

The CDC Nowcast is now including multiple fast-moving FLiRT variants in its tracking: KP.2, KP.1.1, KQ.1, JN.1.18.: https://ibb.co/wBY45FV

According to current estimates, these variants combined account for over a third of illnesses already.

These are moving FAST.

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NonSARS2 Pathogens

More good news: according to WastewaterSCAN, there are now lots of pathogens considered LOW nationally!

Just be warned that they are still showing HIGH in the Northeast, like FluB, which is LOW nationally but regionally still HIGH. Hopefully these numbers will lower even more as the Spring enables more outdoor/well ventilated activity.: https://ibb.co/vYGmTd1

__________
H5N1

H5N1 particles have been found in dairy milk, and are assumed to be inactivated due to the pasteurization process.

We MUST demand healthy cows, testing and tracking of sick herds, and transparency from the meat and dairy insustries.

This is not necessarily to keep H5N1 out of dairy products.

The more IMMINENT concern than being found in dairy milk is letting this thing percolate until it gains new mutations, whether to infect swine or enable human-to-human transfer.: https://ibb.co/FVbNnky

Some things you can do that are obviously proactive and not panicking about this:

🔴Demand clean feed for cattle and swine.

🔴Demand transparent testing, tracing of cattle illness.

🔴Demand high levels of sampling and sequencing of sick herds.

🔴AVOID raw dairy products. Seriously, people, DO NOT contribute to this thing by consuming raw dairy products, even if your State allows its sale (and Pennsylvania DOES as far as I know!)

🔴Try ultra-pasteurized milk, it's the most common milk sold in European countries.

Here's a nifty guide that compares pasteurized/ultra-pasteurized/UHT (ultra high temperature) methods of treating dairy products:

https://www.britannica.com/technology/pasteurization

🔴Avoid undercooked or rare meats. Meats must be heated to 162 degrees for at least 15 seconds to destroy pathogens like tuberculosis.

🔴Switch to providers that are not battery farms and practice humane farming. This is NOT just to be kind to animals (although that's a huge bonus), it is PRACTICAL and keeping herds not densely packed will lessen disease transmission. So far, H5N1 has a 50% kill rate even in non-bird species and we MUST keep outbreaks of it controlled.

I hope you have a FANTASTIC, well-ventilated, healthy and fun Spring!! 💐💐💐

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Wastewater #Pennsylvania #PA #JN1 #FluB #Influenza #Norovirus #HMPV #FLiRT #F456L #R346T #spike_r346t #spike_f456l

#H5N1 #CleanFeedNOW

#WearAMask #CleanTheAir #WashHands #StayHomeIfSick !

Evaluating #Humoral #Immunity Elicited by #XBB15 Monovalent #COVID19 #Vaccine, Emerg Infect Dis.: https://wwwnc.cdc.gov/eid/article/30/6/24-0051_article

We report boosting of #IgG (2.1×), #IgA (1.5×), and total IgG/A/M (1.7×) targeting the #spike receptor-binding domain and neutralizing titers against WA1 (2.2×), XBB.1.5 (7.4×), #EG51 (10.5×), and #JN1 (4.7×) variants.

Good Afternoon SARS2PAians!

It's going to get a bit chilly the next few days , butin spite of that I hope you're haivng a great Spring! 💐💐💐

🔴Reminder: If you've built a Corsi-Rosenthal box, you can get lots of seasonal allergy relief by running it! CR boxes have many, many practical uses besides just controlling air particles that carry pathogens.

There was nothing much new to post on Monday plus I had a bunch of family things to handle (and doing this, admittedly takes time) so I apologize again for not posting. But you know the saying "no news is good news" and that defintiely applies to these updates.

I'm going to try and update the link list ASAP.

I hope you still find all this useful and informative. I hope the medical community finds these accurate and reliable.

__________
VOCs

While we are experiencing a MOST welcome lull in COVID numbers right now, disease modelers are predicting a bump up in numbers at the end of this month.: https://ibb.co/YpnpfMF

This is due to a variant block that have specific mutations. Together they are nicknamed the FLiRT group and are named so because their most important mutations are located at S:F456L and S:R346T within the structure of the pathogen.

🔴Right now FLiRT mutes have an 8% advantage even over JN.1. That's fast.: https://ibb.co/NshJLK6

The most important VOCs out there right now are the variants that have the FLiRT designation, and I've highlighted these mutes on these screenshots in pink.

Remember that there is nowhere near the amount of national testing or sequencing that should be implemented, so it makes trying to predict growth activity more difficult.

Nationally, lots of FLiRT mutations out there. It is unknown whether they are fast enough to cause a wave altogether, but they're fast enough to compete with JN.1 to eventually take over quite a bit of the current leaderboard.: https://ibb.co/S7kCkpH

In PA, we have quite a few FLiRT mutation here but these mutes are in relatively low numbers, so far.: https://ibb.co/bdhJwKv

In NY/NJ, FLiRT mute JN.1.4 already in second place on the leaderboard at over 9% of random sequencing. The other FLiRT variants will undoubtedly catch up.: https://ibb.co/ZBgYP2G

Here you can see FLiRT's innate growth advantage compared to JN variants.: https://ibb.co/3swYQ4r

Here you can see JN.1's innate growth advantage compared to older variants.: https://ibb.co/DfH6j53

__________
Wastewater

Nationally we're still on the bottom of the lull. This might be the lowest point of the whole year as our numbers ongoing could match 2022/2023, where we had quite a bump up in the middle of the summer (because, reminder: COVID doesn't have a "season", it can bump those numbers up anytime it gets lucky with a new mutation!).: https://ibb.co/3mVzfx9

In PA, wastewater still low pretty much everywhere which is great. MontCo SMASHING it, going way below national levels!!: https://ibb.co/TbrQgk7

__________
CDC

The counties showing high increase in hospital admits has shifted around. Now the counties with the highest increases are along the NY border and down in the Southwest corner surrounding Greene Co. Adams and York also showing high end increases. Philly corner showing moderate increases.: https://ibb.co/cQRgbwM

The % inpatient beds map looks very good! stable or decreasing everywhere, except some increases in Columbia Co up going Northeast to Wayne Co.: https://ibb.co/Q8JMZvh

Staffed ICU beds in the vast majority of counties steady or going down...except Columbia, Luzerne and Wyoming in the eastern half of the State and Centre, Clearfield and Jefferson in Central PA.: https://ibb.co/5kXgcYR

__________
Other Pathogens

We're still high in non-SARS2 respiratory pathogens according the WastewaterSCAN. FluA, FluB, and Human Metapneumovirus (HMPV) are still HIGH.

Gastro stuff is very high too, Norovirus and Roitavirus.

🔴Keep the air clean, be aware of social contacts and wear a quality respirator in crowds and in places where air filteration is suboptimal. Stay home of you are sick to beat the respiratory stuff.

🔴WASH HANDS with warm water and soap for at least 20 seconds to beat Noro and Rota. Rinse off fruits and veg before you eat them. Be aware of food handling safety in the kitchen. Don't send kids to school with this.

Mostly because...Noro and Rota are not only extremely contagious, they're also just...gross. 🤢

I hope you have a GREAT and safe Spring!! 💐💐💐

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Wastewater #Pennsylvania #PA #JN1 #FluA #FluB #Influenza #Norovirus #Rotavirus #HMPV #FLiRT #F456L #R346T #spike_r346t #spike_f456l

#WearAMask #CleanTheAir #WashHands #StayHomeIfSick !

Good Morning SARS2PAians!!

I apologize for not typing up a thing for you all on Friday, I got caught up in family stuff. I hope you had a GREAT and SAFE weekend!!
:canparrot:

__________
VOCs

Nationally, JN.1 still at a solid >40% of randomly sequenced samples.: https://ibb.co/s9rZzPq

KP.2 is the next variant to watch and has already had some FAST gains in the past few days.

in PA, both JN.1.16 and KP.2 have already been sequenced here. Control the spread of these potentiall troublesome two mutations by employing SOME form of source control!: https://ibb.co/rtKWn48

in NY/NJ, JN.1 and JN.1.4 at the top as usual but KP.2 already at 1.31% of random sequencing.: https://ibb.co/XDTdCJ8

__________
Lineage News

While other lineages with lab-estimated growth did not seem to contribute to the leaderboard as much as JN.1 continues to do that, its descendant KP.2 is showing extremely fast growth both in lab estimates (with a high confidence level, so this lab data will probably translate more readily into real-world trouble) AND in actual numbers of sequences found.: https://ibb.co/3kyD7Bc

It still has a bonkers high growth advantage rate considering genetics alone and has moved quickly up a couple ranks in actual practice, on the sequencing leaderboard already.

It'll definitely be one to watch.

__________
Wastewater

Nationally, COVID levels continue to decline in wastewater. This will only get better once these cold snaps are done! We're still at a point where we're very high compared to previous years, though.: https://ibb.co/DY8LNMB

Previous years comparison: https://ibb.co/pw8WLjH

Regionally, all regions are declining in found SARS2 material in wastewater. We are still at the highest concentration in the Northeast compared to everyone else, though.: https://ibb.co/8sj4BpS

In PA, Chester Co. is SMASHING IT and levels are absolutely tanking for now! But Bucks, Luzerne, and Lackawanna's levels are still a bit above naitonal averages. Use source control to improve this data point!: https://ibb.co/s65h3yG

__________
CDC

The New Hospital Admits map is showing significant increases in Juniata Co. curving down to Somerset Co and Bedford Co., and also over in Lawrence Co. The rest of the map is pretty good, with overwhelmingly reductions in hospital admits in most counties!: https://ibb.co/sKnLV5X

Staffed Inpatient Beds are showing significant increases in Juniata, Mifflin, Huntingdon and Elk Cos with the rest of our counties stable or slightly decreasing.: https://ibb.co/Yyj4MRr

Quite a lot of ICU bed use increases. From Greene at the southweasternmost corner, all the way diagonally up to Bradford and Susquehanna Cos, increasing levels all the way. Don't be this statistic, folks. Get those XBB/flu/etc. shots.: https://ibb.co/LYkXcKJ

Sadly there have been 1,064 COVID deaths in PA in the last three months and while this number has gone down a bit since last time I posted this, our state remains in the highest category of the 3 month data cycle.: https://ibb.co/8m5SDBY

__________
Non-SARS2 Pathogens

Well, if you want to stick around to read this, I'll post this part up last.

While SARS2/COVID continues to steadily decline, the one pathogen that's still at quite a staggeringly high rate is Norovirus, the "24-hour stomach bug".

Levels of this are still EXTREMELY high, and are slow to start going down, as they had around this time last year.: https://ibb.co/Kqny3QJ

PLEASE WASH HANDS with soap and water. Hand sanitizer is not enough. Norovirus is extremely resistant to alcohol and heat sterilization due to a tough "shell" surrounding the virions.

You MUST wah hands with warm water and soap for 20 seconds to actively contribute to controlling Norovirus.

Wash fruits and veg before you eat them, even if you don't eat the peel (example: clementines, oranges, and grapefruit.)

Don't serve or prepare food if you are sick!

This thing is just gross. 🤢 Make sure everything's clean before you sit down to eat!

Using source control will make numbers for ALL pathogens go downward so we have a healthy (and not gross) Spring! 💐💐💐

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #JN1 #Influenza #Norovirus #Noro

#KP2

#WearAMask #CleanTheAir #VaccinesSaveLives #WashHands #Wastewater #StayHomeIfSick #SourceControl #USESourceControl #COVIDSourceControl

#XBB15 monovalent #mRNA #vaccine #booster elicits robust neutralizing #antibodies against #XBB subvariants and #JN1, Cell Host Microbe: https://doi.org/10.1016/j.chom.2024.01.014

• An XBB.1.5 booster markedly enhanced neutralization of SARS-CoV-2, including JN.1
• An XBB.1.5 booster induced similar antibody titers to XBB infection
• Omicron infection followed by XBB.1.5 booster yielded the highest antibody titers
• Our findings supported recommendations for broad use of the updated XBB.1.5 booster

Update for 3/8/2024!

Good Morning SARS2PAiains!!

I hope you're ready for that time change on Sunday! 🕐🕐🕐

This is a wonderfully short update. I mean, it doesn't look short, but it kinda is. 🤪

There's no new CDC stuff.

There are no new wastewater updates and we are continuing to approach lower levels of previous years as spring gets closer.: https://ibb.co/QfPr8NJ

__________
Lineage News

There's no new immediate variant news as JN.1 is still the only thing all over the place so far.

There are some new varaints being watched as JN.1 (and specifically JN.1.11) seems really capable of producing descendants that worry virologists:

❗️JN.1.16: Concerningly infectious even over very wide areas in China; Lots of this currently being uploaded from what I gather in USA too, already in 9 states.

❗KP.1.1 (which is JN.1.11.1.1.1): this has a potential nuts-level of growth rate going by genetics alone.

❗KP.2 (which is JN.1.11.1.2): seems closely related to JN.1.16 that I was, in my very very unprofessional opinion, concerned about last update.

❗KP.2.1: widespread already in East Asia.

KP.x.y has an extraordinary growth rate only considering mutations but we'll see how any of this checks out in actual biological results.

__________
NON SARS PATHOGENS

There is still a very high amount of total pathogens all around.: https://ibb.co/3sxWQ3C

Respiratory pathogens are still high according to WastewaterSCAN:

❗SARS2

❗RSV

❗Flu A

❗Flu B

❗Parainfluenza, which has been upgraded to HIGH since last update.

Gastro stuff is still very high too!:

❗Norovirus

❗Rotavirus

Noro is thankfully declining at UPark but still in the very high range.: https://ibb.co/CMSGsjg

If we keep using common sense ways to control it, it prevents DAYS of learning/financial loss and potential hospital visits for dehydration. And...it's just gross to deal with. 🤢

Fpr respiratory illnesses, wear a quality respirator, be aware of social contacts, mask/respirator up in crowds and in low ventilation areas (low ceilings, restrooms, elevators, etc.), keep the air clean, get those COVID and flu shots, and STAY HOME if you are sick!

For the gastro stuff, don't prepare food when sick. Don't depend on gloves for sanitizing either! Wash fruits and veg before you eat them.

Wash hands with soap and water for 20 seconds.

❗Hand sanitizer and heat does not work well against Norovirus because the individual virions are very very tough to kill. You MUST wash hands with soap and water.

For all pathogens, cover coughs and sneezes in the elbow crease and not your hands.

We're almost there! :canparrot:

It's Goose flyover season! :cangoose:

We're gonna have a great Spring, and simple, common sense consideration and source control is how we get there! 💐💐💐

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #JN1 #FluA #FluB #Influenza #Norovirus #Noro #Rotavirus

#JN1Sixteen #JN116
#KP1One #KP11
#KP2
#KP2One #KP21

#WearAMask #CleanTheAir #VaccinesSaveLives #WashHands #Wastewater #StayHomeIfSick #SourceControl #USESourceControl #COVIDSourceControl

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! ❄️❄️🌷

#JN1Eleven

#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! 😷❄️❄️❄️

#JN1Eleven

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater

𝗟𝗔𝗧𝗘𝗦𝗧 𝗨𝗞 #COVID19

🧪𝗖𝗮𝘀𝗲𝘀 — weekly
🔻6,117

🧮𝗧𝗼𝗽 𝗩𝗮𝗿𝗶𝗮𝗻𝘁𝘀
#JN1 #HV1 #EG51

🏥𝗛𝗼𝘀𝗽𝗶𝘁𝗮𝗹 𝗔𝗱𝗺𝗶𝘀𝘀𝗶𝗼𝗻𝘀 — weekly
🔻3,298

🕯️𝗗𝗲𝗮𝘁𝗵𝘀 — weekly
🔺301

🕯️𝗧𝗢𝗧𝗔𝗟 𝗗𝗲𝗮𝘁𝗵𝘀
🔺235,028

➡️http://PMP-Magazine.com/covid-19-today/

#COVIDisNotOver 😷

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 ❄️❄️❄️)

#JN1Eleven

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater

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

Update for 1/8/2024!

Good Morning SARS2PAians!

I hope your holidays are continuing to be joyful and safe. 🎊🎊🎊

__________
VOCs

Nationally, JN.1 firmly in the lead at over 32% of leaderboard share. This number is most likely a LOT higher (as per the CDC NOWCAST) as the last few weeks of sequencing are incomplete.: https://ibb.co/YTBcv9J

The most current CDC NOWCAST estimates JN.1 at almost 62% of share.: https://ibb.co/HFcmSRC

It is EXTREMELY important to practice some form of source control in the next few weeks and when school starts.

In PA, JN.1 at 28% of random sequencing, almost reflecting national levels.: https://ibb.co/4VR9Pwv

In NY/NJ, JN.1 at 46.89% of leaderboard share. It's getting close to the 50% of shares to get to to know whether this will cause an actual surge and not a takeover of share.: https://ibb.co/Pgf37bk

A surge strains hospitals (not only from COVID, but also fluA, fluB, RSV, etc. etc. etc.) and requires extra care and source attention from the public. Please wear a quality respirator in public so this doesn't happen in the next few months.

__________
Pennsylvania hospital systems are already REQUIRING masks and putting strict entrance standards on +C19 carriers.: https://6abc.com/penn-medicine-face-mask-policy-philadelphia-pa-covid-rsv/14284086/

PHILADELPHIA (WPVI) -- With COVID-19, RSV, and flu cases rising, another hospital system in Philadelphia is taking extra precautions.

Starting Monday, Penn Medicine says in certain departments like emergency and waiting rooms, everyone two and older is required to wear a mask.

Visitors who tested positive for COVID-19 or have symptoms are not allowed to enter any facility even with a mask.

Other health systems across the region, including Main Line Health and Cooper University Health Care, have revised their mask policies due to the rise in cases.
__________

Wastewater

Nationally, C19 material in wastewater still climbing nationally. You can see where we were last time I posted, at 800 copies/mL by the blue line there I drew. We're now well on our way to 1300 copies/mL.: https://ibb.co/0cwFJyv

Regionally, if there's a "more-than-vertical" way to increase, the Northeast is almost there. Other regions lag behind. You can see here, too where we were last time at 800 copies/mL by the line I drew.: https://ibb.co/gmFjQJr

The Northeast is now in the second highest level of the whole pandemic.: https://ibb.co/Y2JTgKZ

In PA, only 5/11 sheds have anywhere near current data. Bucks and Chester are doing rather well handling this current rise. Lackawanna, Luzerne and MontCo going vertical. PLEASE do the source control.: https://ibb.co/n0LDZLF

__________
CDC

EDvisits have increased moderately in most States, including PA.: https://ibb.co/Nxpc7C8

Lots of new C19 hospital admits for PA. The vast majority of the state is showing substantial rise except for Warren and McKean Cos down to Centre Co.: https://ibb.co/dcPTfw4

Don't be this statistic and keep those hospitals clear. Get your C19 vaccine, whether mRNA or Novavax. You'll still have to wait 2 weeks for full effect but it's better than nothing. Once these kids start school, hoooooo boy.

Staffed inpatient beds on the rise, moderately, all through the State. High levels in Berks, Lancaster, Elk, Wayne and Lackawanna Cos.: https://ibb.co/7JwQ4S2

ICU beds on a sharp increase through the State, the southwestern corner, Fulton circling around to Jefferson, circling around again over the NJ border to Columbia and Wayne Cos.: https://ibb.co/xfh2Hx4

__________

Please practice some form of source control, and mask up when those kids go back to school! Run those Corsi-Rosenthal boxes you have. Open a window if at all possible. Be aware of social contacts. Do takeout instead of dine-in. Go virtual at work if you can. Stay home if you're sick. Test test test! :canparrot: :canparrot: :canparrot:

If we work together we can keep cases down to manageable level and keep our medical facilities working well. 😷😷😷

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater

Update for 1/5/2024!

Good Morning SARS2PAians!

There's not much new data as of yet, and I don't have much time to post this morning.

There's no new Biobot wastewater data, that will be updated Jan. 9th.

There's also no new CDC map data and the NOWCAST has not been updated at the time I posted this.

__________
VOCs

The Tableau site is regularly updated after the holidays again, however.

Nationally, JN.1 flying high at over 31% of random sequencing.: https://ibb.co/Qf1vD0t

In PA,, a little slower pace but it's still at over 28% of leaderboard share.: https://ibb.co/sCmQtbH

In NY/NJ, JN.1 at over 45% of share and this is only going to go up when kids go back to school.: https://ibb.co/DkJbCXs

Please take this highly evasive, transmissible variant seriously. The latest XBB vaccine will help sorta-ok-marginally against severe disease and health care system strain but this variant is many, many mutations away from anything we currently have, so source control is best.

Wear a quality RESPIRATOR. This is increasingly VITAL as it gets colder, making leaving windows open less ideal.

__________
Wastewater

Biobot isn't updated yet but CDC has its own wastewater info page.: https://www.cdc.gov/nwss/rv/COVID19-nationaltrend.html

Nationally, most of the contiguous States are at VERY HIGH levels. We in PA are in more moderate levels of SARS2 spread and it will be more important than ever to practice source control against JN.1 to maintan this. It will prevent straining health care systems from not only increasing FluA, FluB, etc. but also people that just didn't care to get vaccinated.: https://ibb.co/RCYyNY3

Previous vaccination formulas DO NOT protect against JN.1 at all due to antigen drift.: https://zeroes.ca/@[email protected]ial/111664708844139916

Please get the XBB version ASAP if you didn't get one.

In PA, numbers match national levels so there's no real difference here. The last 2 weeks are shaded grey as they are incomplete, so the massive dropoff in wastewater on the end there is not due to declining levels but rather data gap.: https://ibb.co/FJK3BxN

PLEASE NOTE that we are in the midst of the SECOND largest increase in wastewater SARS2 material, and even if cases aren't reflecting this in data, those cases are still out there.

Try to go virtual if you can. Crack open a window. Practice SOME form of source control until the Spring!

If we all work together we can prevent life, learning, and finanical fallout in the next few months! :canparrot: :canparrot: :canparrot:

Stay safe from COVID and also that wacky storm coming our way tomorrow! ❄️❄️❄️

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater

[Correspondence] #Virological characteristics of the #SARS-CoV-2 #JN1 #variant https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00813-7/fulltext?rss=yes

-- JN.1 harbours Leu455Ser and three mutations in non-spike proteins (appendix pp 17–18). Spike protein mutation Leu455Ser is a hallmark mutation of JN.1: we have recently shown that HK.3 and other flip variants carry Leu455Phe, which contributes to increased transmissibility and immune escape ability compared with the parental EG.5.1 variant.

Update for 1/2/2024!

Good Morning SARS2PAians!

I hope you're having a GREAT and SAFE new year! 🎊🎊🎊😷

There's no new wastewater for today.

__________
VOCs

Nationally, JN.1 is now the top variant in random testing with an easily-gotten 26% of variant share.: https://ibb.co/JrVrwsT

In PA, JN.1 is now the top varaint in PA, too with 23% share.: https://ibb.co/Pcrc2cv

In NY/NJ, JN.1 has ALREADY reached 40% of random sequencing 👀 and that was before 100,000 people hung out together unmasked in Times Square. 😓: https://ibb.co/ZhghSmQ

The closest new competitor to JN.1 is GE.1.2.1, a descendant of XBB.2.3, but it still falls a bit short of JN.1'a relative growth rate. JN.1.1.1 also falls a bit short but is still so fast it warrants monitoring.: https://ibb.co/9Yhn37n

This NOWCAST was from two weeks ago, so should be updated this Friday. You can see the absolutely explosive rate of JN.1's growth.: https://ibb.co/0qYtpB1

We will know how much of a surge it will cause once it hits 50% share of national sequencing, after which hosiptals and other care centers could experience strain.

DON'T CONTRIBUTE TO THIS.

Wear a respirator.

Keep the air clean.

__________
CDC

You can see on the CDC At-A-Glance graphic, we're heading (not unexpectedly) in the wrong way after the holday season.: https://ibb.co/61yR8Jk

Emergency Department visits rising along most populous/coastal/border States.: https://ibb.co/QYzSJM6

Most Eastern states and metro areas in most other States have substantially increased in new hospital admits.: https://ibb.co/3CHBpQb

Don't let this get worse, folks. Wear a quality respirator. Stay home. test and retest. Keep the air clean!

The old coal region including and west of Schuylkill south toward the MD border is holding steady.

Tioga and the southwest corner is still hoiding out there, doing OK with numbers reducing.

Inpatient Beds holding steady and actually decreasing through msot of the state with some rising around Easton, around CentreCo. and up by Potter Co.: https://ibb.co/dW26YRs

ICU bed use reducing in a lot of areas but increasing significantly in Huntigdon, Mifflin and Juniata Cos.: https://ibb.co/wsc4jmp

More states are experiencing increases in deaths over a 3-month period. This is very much caused in part by refusal to take latest vaccinations causing waning immunity.: https://ibb.co/Sf3rk0K

4% of deaths in PA in the past week were from COVID. GO GET XBB VACCINATED.

__________

With an increase of caution now we can prevent fallout in the health system in the next month or two! 😷😷😷😷😷

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater

Update for 12/29/2023!

Good Morning/Afternoon SARS2PAians!

I hope your holiday season is joyful and safe. ❤️️❄️❄️❄️

TL;DR: I'm going to do a lot of yelling in this, but I want you to have a GOOD new year and not a BAD one! ❤️️

Unfortunately there's no new VOC info from the Tableau site as it has not been updated since the 23rd. I'll try to make this issue with as much VOC data I can collect without it.

__________
VOCs

Raj Rajnarayanan's Tableau data hasn't been updated since 12/23 so I'll try to make do with other sources.

Worldwide, JN.1 is absolutely the dominant variant/mutation set right now, even if it hasn't filtered through everywhere less populous yet.

Mike Honey's ( :fediverse: Fediverse: https://aus.social/@mike_honey_) Covid variant tracker tracker shows a strong crossover for JN.1 nationally.: https://ibb.co/0hTvz6P

JN.1 is horribly close to an estimated 50% of national sampling, after which we will know if it's going to cause a surge and not just take over the leaderboard. (There is no way something this fast will NOT cause a surge in my very very non-med non-stat-guy opinion.)

In PA, the JN.1 crossover is slower, steadier, but we have enough to deal with here because of the high numbers of RSV, Noro, etc.: https://ibb.co/FwJJbJF

Babies and the elderly are in particular danger from RSV. Don't spread it! Wear a quality respiratoir, stay home, and keep the air clean!

__________
Wastewater

Wastewater monitoring continues to be absolutely essential in tracking pathogens during this extrmely volatile season.

Nationally, C19 signal in wastewater keeps rising. We're not even started with this, folks. PLEASE use some source control in this high pathogen season.: https://ibb.co/tYQDWyh

Regionally, all regions rising, Northeast going almost vertical, and what I thought would be a nice respite in the Midwest is now also turning into a strong rise. 😓: https://ibb.co/q52nqDm

In PA, 5/11 sheds reporting current info to BIOBOT. Of those 5 sheds, all of them have a general trend of rising absolute baseline.: https://ibb.co/89xxPdk

Luzerne going VERTICAL and MontCo now matching national trend. Chester and Berks are really trying hard. Keep at it!! Source control will help everyone in the long run!

University Park now reports to WWSCAN (https://ibb.co/tbrzPg4), making it the third shed that reports there along with Dauphin and Chester. Here again you can see Chester trying to handle it, but the absolute baseline is still rising.

Dauphin and UPark sheds going vertical.

WastewaterSCAN also shows C19 levels as HIGH in all regions.: https://ibb.co/hst7ZRy

WWS also shows RSV (https://ibb.co/DDgpYfX) and Norovirus (https://ibb.co/NtYPX4G) (which is the "24 hour stomach bug" that is picked up from unclean surfaces like improperly washed restaurant flatware) as HIGH in all regions, with Noro high in our region.

__________
CDC

Lots of new hospital admits in Central PA excluding CentreCo.: https://ibb.co/G9WGKSc

Most counties holding steady for %change in bed use, but some counties showing significant increases: Fulton, Franklin, Luzerne, Wyoming, Columbia, Tioga.: https://ibb.co/sFZdmQL

ICU bed use rising significantly in a LOT of counties.

People NOT getting bivalent and XBB VACCINATIONS are going to make this skyrocket next month, foilks.: https://ibb.co/58whZh7

Significant rise in FranklinCo and counties West of there along the MD border; in the Northeast especially all north of Luzerne; Berks; Crawford and counties east of there.

Southwest corner of the State looks very good for now.

Stop this nuimber from going up, guys. Don't be part of this statistic. Get those vaccinations.

Also flu. Don't be that guy clogging up health facilities on others who also need them.

Diagnosed C19 Emergency admits rising in the Northeast and the South. Moderate increase in PA.: https://ibb.co/52SJX7G

___________
Side Note: Immune Dysregulation is Not New

Permanent immune system disability from pathogens is not unheard of, which is the actual reason measles is so deadly and not just its initial acute symptoms.: https://ibb.co/1mNvwq9

BBC link: https://www.bbc.com/future/article/20211112-the-people-with-immune-amnesia

C19 also disables the immune system with each bout of it. REPEATED INFECTIONS DOES NOT HELP YOUR IMMUNE SYSTEM. Your immune system is not a muscle and pathogens are not deadweights.

It's not just about acute symptome. We need to think long-term.

I hope your holiday celebrations are joyful with a focus on social contact tracing and source control. The fallout in January and February will not be as bad, folks!!

Stay safe! ❄️❄️❄️

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater

Update for 12/22/2023!

Good Morning SARS2PAians!

I hope you are having a SAFE holiday season. (Sorry I missed mirroring Monday's post on the Fediverse.)

There's no new CDC map info for today.

__________
VOCs

Nationally, HV.1 still at the top of the leaderboard in random sequencing, with JN.1 catching up FAST at over 15%.: https://ibb.co/5RM1Ncf

In PA, quite a looong list of variants found here. HV.1 at the top at 28%, and JN.1 also catching up here at 12%.: https://ibb.co/F8gvjDH

In NY/NJ, JN.1 has easily taken over the leaderboard at 26% of share in NY/NJ. "Variants? What other variants?": https://ibb.co/G0kQBsj

If you have plans to see the ball drop on 5th in person this year, you reeeeaally might not want to do that. Seriously.

The WHO has now categorized JN.1 as a Variant of Interest, separated out from the BA.2.86 clan it came from.: https://www.cidrap.umn.edu/covid-19/who-designates-jn1-separate-covid-19-variant-interest

:ms_arrow_right: "The WHO recommended universal masking in health facilities, with appropriate masks, respirators, and other personal protective equipment for health workers caring for patients who have suspected or confirmed COVID. The group also urged improved ventilation for health facilities."

The concern is not only JN.1, but also STILL rising levels of FluA and FluB, and also RSV not at low levels yet. All these together could potentially strain health care facilities in the new year if we do not choose some form of source control and help one another now.

__________
Wastewater

Nationally, SARS2 levels still rising.: https://ibb.co/HFggZ4y

Regionally, levels going up FAST in the Northeast, with the Midwest declining.: https://ibb.co/86fx1nx

In PA, only 5/11 sheds are current. Of those sheds, Berks is going vertical and Lackawanna is rising fast. The absolute baselines of all 5 are rising though some sheds seem to be working at controlling outbreaks.: https://ibb.co/7NBCTGp879

__________
If we all do some form of simple source control this winter (wear quality respirators, s tay home when sick, test test test, avoid unnecessary trips, open a window, keep the air clean, take out instead of dine-in, etc.) IT ADDS UP and quite honestly we have a lot less miserable and very much more merry January and February this year.

Don't let people rooting for the virus discourage you. EVERY small act of source control in this holiday season matters with a variant as fast as JN.1! ❄️❄️❄️

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater

"A COVID variant known as JN.1 has been listed as a separate "variant of interest" by the World Health Organization (WHO)."

"The omicron sub variant was previously classified under its parent strain, BA.2.86, which prompted concern among some scientists earlier this year due to its high number of mutations."

#COVID19 #COVIDvariant #JN1 @auscovid19

Source: https://abcnews.go.com/Health/covid-variant-jn1-listed-variant-interest-world-health/story?id=105782742#:~:text=A%20COVID%20variant%20known%20as,its%20high%20number%20of%20mutations.

Update for 12/15/2023!

Good Morning SARS2PAiains!

There's no new CDC stuff today.

__________
VOCs

Nationally, HV.1 at over 27% of random testing, and JN.1 catching up more every day, now at over 10% nationally.: https://ibb.co/TmgNzjM

This thing is FAST, and also immune evasive. PLEASE stay home and wear a quality respirator to keep souce control down.

In PA, HV.1 reflecting national levels almost right on at 27%, JN.1 coming outta nowhere to over 6% and second place in random testing.: https://ibb.co/6Rmhy14

I want to bring to your attention the last variant in the list, XDD, which is a recombo of two already fast variants (EG.5.1.1, or HK, and JN.1). It's at .51% but probably won't stay there with holiday gatherings and work environments that ignore source control.

This thing is fast, too, so PLEASE be sure to use caution this month into next month.

In NY/NJ, HV.1 at over 27%, but JN.1 at over 16% already👀 👀 👀. Not enough to start chipping away at HV.1 right now, but......soon.: https://ibb.co/4890HZS

According to Biobot, RSV has most likely hit its peak but FluA and FluB are STILL on the rise.: https://ibb.co/2nt8Hbh

We don't want a mess in January...please practice some form of source control.

__________
Wastewater

Nationally, SARS2 wastewater concentration stil rising.: https://ibb.co/DWP0Fr9

Regionally, the West has been adjusted downwards, but the Northeast, Midwest and South still rising.: https://ibb.co/wrZRZrn

In PA, only 5/11 stations anywhere near current. Luzerne and MontCo going vertical. Lackawanna on a plateau (good) so we'll see if it declines there (BETTER!): https://ibb.co/tPGth19

__________
Research

Dr. Eric Topol has posted important research from The Lancet about C19 vs. Flu outcomes.: https://ibb.co/6b1ct7F

Direct Mastodon/Fedi link: https://mstdn.social/@erictopol/111581476647325603

Takeaways:

50% post C19 higher death rate.

Worse C19 outcomes for all organ systems and disability except lung.

Higher burden of health loss on the POST ACUTE PHASE than in the acute phase for both. (Which means acute severity is NOT the only real danger!)

Screenshot of research findings: https://ibb.co/cgqKWx8

Paper is at: https://thelancet.com/journals/laninf/article/PIIS1473-3099(23)00684-9/fulltext

Stay safe out there and have a GREAT holiday season!!! ❄️❄️❄️

Have a safe winter and if we all contribute to source control, we can have a GREAT post-holiday season!! ❄️❄️❄️

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater #Lancet

Update for 12/11/2023!

Good morning SARS2PAians!

I hope you are staying dry with all this rain the past few days. 🌧🌧🌧

__________
VOCs

Nationally, HV.1 at over 26% of random sequencing, and now JN.1 starting to catch up, almost at 7%. ANY of the JN.1s are fast, fit, and can contribute to more post-holiday illness at this point.: https://ibb.co/JvqVQzS

In PA, HV.1 at 27% of sequencing. Right behind it is FL.1.5.1 (6%), JD.1.1 (5%). JN.1 almost at 3% and weirdly, BA.2.86.1 more successful right now at almost 5%.: https://ibb.co/VJxZ3jG

In NY/NJ, HV.1 in the lead at over 28% and JN.1 catching up FAST at over 12% now 👀 👀 👀: https://ibb.co/c3Zcjkh

__________
Test2Treat.org

There's a new resource available for C19/Flu needs for the uninsured or underinsured, run by the NIH, in partnership with other resources.

Test2Treat.org offers C19/Flu telelhealth sessions and also can ship free test kits to those who register when they are NOT positive when signing up.: https://www.test2treat.org/s/?language=en_US

Here's the FAQ for the site so you can read through.: https://www.test2treat.org/s/faqs?language=en_US

__________
Wastewater

Nationally, wastewater shooting upwards FAST.: https://ibb.co/YkD8kZG

It's already on the highish end of overall concentration excluding the original Omicron wave.: https://ibb.co/FXxXsX7

Regionally, All regions on a strong upswing. Midwest and Northeast going vertical.: https://ibb.co/vVf2MMM

In PA, 5/11 sheds have current info on Biobot. ALL of those sheds are showing increasing concentration, and 4/5 of them increasing exponentially. PLEASE use SOMETHING to control infection at the source so we don't have major fallout in January. Wear a quality respirator, keep windows craked open, clean the air, get those updated XBB vaccinations, and be aware of your social contacts throughout thie early winter.: https://ibb.co/TcQtrzw

__________
CDC

Lots of new hospital admits throughout the State, as most counties are showing substantial increases.: https://ibb.co/yXFzJYc

Philly, Central PA, and Crawford and Tioga counties showing decreasing numbers.

Most counties are stable with inpatient bed numbers but increases here and there. Mostly along I-80 and the southern area there surrounding Bedford Co.: https://ibb.co/jWhxVnG

ICU beds showing substantial increases in the counties surrounding Centre Co, and Franklin and Fulton Co. Moderate increases in Philly area and along the northwestrn border.: https://ibb.co/1bvZwT7

PA is showing a moderate increase in the number of diagnosed ED visits, along with bordering States Ohio and NJ.: https://ibb.co/McwCQjg

Unfortunately as of 12/7 there have been 833 COVID deaths in the past 3 months.: https://ibb.co/c2nSMwC

I notice this number has increased in PA the past few months. (~400->~600->~800.)

Most States are showing substantial COVID death increases over the past 3 months.

___________
If we take some simple precautions NOW, the post-holiday season will be more enjoyable and involve a lot less life, learning, and financial loss!

Stay dry this week! 🌧🌧🌧

Have a safe winter and if we all contribute to source control, we can have a GREAT post-holiday season!! ❄️❄️❄️

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #Flu #Influenza #RSV #Wastewater #Test2Treat

Update for 12/8-9/2023!

Good morning SARS2PAians!

I hope your early winter is going well! ❄️❄️❄️

There's no new CDC county info today.

__________
VOCs

Nationally, HV.1 still at over 25% of random sequencing. JN.1 right behind it at a distant 5% but we'll see how well it fares against a variant that is clocking in at a very similar speed.: https://ibb.co/fYDyhcW

XDD is a variant discovered a few weeks ago that is a recombo of EG.5.1.1 (which ="HK") and JN.1, and is clocked as faster or equally as fast as JN.1 in theory, and must be closely watched.

In PA, HV.1 at over 20%. FL.1.5.1 at over 10% of random sequencing. JN.1 is at 1.33%, still weirdly not climbing as fast. I see lots more people wearing masks as they are out and about so even a few people doing this will greatly help control things into January.: https://ibb.co/hWZXfg5

In NY/NJ, HV.1 at over 27% of random sequencing. JN.1 behind at 10% already 👀 👀 👀: https://ibb.co/HNhBRV8

__________
Wastewater

Nationally, wastewater SARS2 material increasing greatly through last time I posted it.: https://ibb.co/L6960t5

Regionally, SARS2 increasing or leveling in all regions, with the Midwest and northeast going almost vertical.: https://ibb.co/HH3NB2v

In PA, the few stations that are current are showing increases. Chester and Luzerne increasing exponentially! Bucks going vertical. MontCo doing soooooooo fantastic this whole time and now quickly catching up to national averages.: https://ibb.co/Z8GJtZ2

According to WastewaterSCAN, the Dauphin shed is also very steadily increasing concentration, too.: https://ibb.co/86F2K41

Please consider wearing quality respirators or tight-fitting surgical masks in these areas if you are out and about!

WastewaterSCAN shows SARS2, RSV and Norovirus (the "24 hr stomach flu") as all HIGH.: https://ibb.co/zXCqSGR

SARS2 HIGH in all regions.: https://ibb.co/LQN0JTB

All of these can contribute to ER cases and hospital stays. PLEASE use caution this winter as JN.1 plows through these leaderboards.

__________
CDC

The CDC NOWCAST has been updated for today, breaking out JN.1. You can see the bonkers estimated growth of this variant in chart form: https://ibb.co/LzBSY9S

and according to region in map form!: https://ibb.co/n8s7jj4

Guysssssssss please use some form of caution now before the rest of the major holidays. GET THOSE XBB VACCINATIONS. It's not bullet-proof but it's shown to help enough with JN.1 to get ASAP.

Wear those quality respirators. Keep careful track of who you hang out with through the winter to contribute to source-of-infection control. Test test test, repeatedly if needed as infective levels aren't always picked up by rapid tests.

Have a safe winter and if we all contribute to source control, we can have a GREAT post-holiday season!! ❄️❄️❄️

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives #XDD #RSV #Norovirus #Wastewater

Very short update for 12/4/2023!

Good morning SARS2PAians!

I keep checking the Tableau variant leaderboard and other stuff and nothing is updated yet.

The only thing updated as I post this are some CDC health care maps.

This update will be brief and I'm sure there will be more info available on Friday.

Lots of new hospital admits all across the State for the lastest CDC county update from the end of November, along with some areas decreasing. It's either-or.: https://ibb.co/NT5yvR3

Decreasing the most around Centre Co, Harrisburg, the southwesternmost corner, and up by Bradford/Susquehanna.

Almsot everywhere else stable or showing substantial increases.

Staffed inpatient beds filling up a bit in the center of the State and along the southwestern border with Maryland and W Virginia. Everywhere else stable.: https://ibb.co/Pj2hskV

Staffed ICU beds showing a lot of increases, border-to-border, right in the center of the State from Tioga all the way down to Bedford and Somerset, and over East to the old coal region (Schuylkill Co and counties east of it.).: https://ibb.co/1KY5KPL

PA showing moderate increases in ED visits on average, and there are many states surrounding us and in the general Northeast showing substantial ED visit increases.: https://ibb.co/6N6g6Fv

That's all I have for this morning, stay safe and Friday will probably have better variant info! 🍁❄️❄️

Stay safe!!!!! 🍁❄️❄️

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives

Update for 12/01/2023!

Good evening Fediverse SARS2PAians!

It's getting super chilly out there! I hope your early Winter is going healthy. 🍁❄️❄️

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VOCs

Nationally, HV.1 still at the top with over 25% of random sequencing. JN.1 almost at 5%.: https://ibb.co/z7F23GR

There are quite a number of upcoming variants faster than HV.1 out there, (JD.1.1, JG.3, JG.3.1, etc.) and they're highlighted on the chart screenshot. Not as fast as JN.1 but together they'll easily drive out the XBBs.

It's not just JN.1 on its own that's going to cause a problem....it's the comnibation of ever faster and faster varaints that will create a high tide that will never lower if we don't do some common sense things for each other (respirators, clean air, staying home) and attack the source of viral infection.

In PA, HV.1 at over 25%. JN.1 at almsot 2%. You can see the XBBs are all the way at the BOTTOM of this graph already.: https://ibb.co/Fk1qcgN

In NY/NJ, HV.1 at 28% of random sequencing, and JN.1 blazing riiiight behind it, in 2nd place already, at almost 9% of sequencing. Crikey this thing is fast. Yikes.: https://ibb.co/0XhGGW3

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Wastewater

Nationally, proportions are still being adjusted upwards a bit every time the levels are posted.: https://ibb.co/WpWkXtL

Regionally, all regions showing levels staying the same or increasing. Especially the Midwest which is going vertical right now.: https://ibb.co/0XhGGW3

I don't have the graph prepared for the PA sheds...there's only a very few updated to current data. Most sheds are waaaay behind with reporting.

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Research news

Bloom Lab has shared some important vaccine info on BlueSky about the latest version of the COVID vaccine that features XBB.1.5.: https://ibb.co/SdSKQC9

Turns out that the updated XBB booster is acceptably effective against the newest variants (BA.2.86.x.y). It's power is cut a bit by antigenic drift but overall it remains VERY advantageous to get a vaccine as XBB varaints are still very much around!

Viral geneticist Federico Gueli has shared information from other researchers that clearly show the immense growth advantage of JN.1. (The text and arrows on the screenshot are my own additions). In my humble non-pro, armchair opinion, there is no way something this fast will NOT cause a wave.: https://ibb.co/6D96R5G

JN.1 has a 50% (which means very good, not 50% "iffy") chance of becoming the leading variant even BEFORE the late December holidays which means......we're not gonna have a good time in January if we don't control it now.

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CDC

Here's the screenshot of the latest CDC NOWCAST. You can see the fast growth JN.1 (still not separated from BA.2.86) is clocking in here.: https://ibb.co/yRSB93L

Lots of new hospital admits statewide. in fact the only counties that are NOT showing levels staying the same or increasing are the old coal region (Schuylkill and counties immediately west of it) and the northern tier counties from Tioga Co. to over to Pike.: https://ibb.co/7XQCVGY

(EDIT: I accidentally wrote "decreasing" and changed it to "increasing".)

To me, looks like essentially a new wave of hospital admits that are going to filter through the terrible and unfortunate admits--> inpatient bed --> ICU pipeline.

Inpatient beds very stable throuhgout the State, increasing substantially in Elk Co.: https://ibb.co/5rmXhFX

Staffed ICU beds overall in a decline, with most substantial inceases in a few counties: Tioga, Huntingdon, Mifflin, Juniata, Crawford.: https://ibb.co/GJfFwch

Deaths over a 3 month period are substantial in most states. Unfortunately, we have lost 759 Pennsylvanians to COVID in the last 3 momths.: https://ibb.co/SwrV1Fw

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Using common sense methods for source control is more important this time of year than ever. Respirators, clean air, vaccines, and staying home if sick all work together to prevent life, learning, and financial loss now and in the new year!

Stay safe!!!!! 🍁❄️❄️

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives

Update for 11/27/2023!!

TL;not going to read: This whole update is basically "Here comes JN.1. Get ready."

Good morning SARS2PAians!!

There are no new CDC or Biobot data today.

The CDC will put out a new Variant Proportions/NOWCAST chart today including BA.2.86 (which includes JN.1) but I will not be able to be where I need to be to grab it for you when it's released as I have lots of stuff to do today.

(Side note, the latest Biobot national levels graph has yet again been sliiiiiightly adjusted upwards.)

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VOCs

It's all about the VOCs the morning even without the rest of the info. JN.1 is fast, folks. SUPER fast. PLEASE get those xbeebee shots in, flu shots, and get yourself some quality respirators (at least a well-fitted head-loop KN95 or better) and run those CR boxes.

Nationally, HV.1 still at a massive lead with over 25% presence in random sequencing.: https://ibb.co/k6nhDMh

JN.1 (which this update is about more than ANYTHING else) is already at 3.71% of random sequencing. I can't reiterate how fast it is.

This thing went from 0 to 45% of sequencing in Singapore in one month, and Singapore is more disciplined with mask wearing and communal viral control than the West is.: https://ibb.co/s5gnh4X

It's nowhere near what original Omicron was (OG Omicron was at 700% growth rate compared to the absolute baseline) but the problem here is it is faster than HV.1 AND has massive immune escape abilities, and can REINFECT super-easily.

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It's bonkers but it MUST be mentioned that there are estimated faster BA.2.86 mutations than JN.1 right around the corner (JN.5.1, XDD) and if we don't want a high tide that never lowers, we MUST keep infections down through the winter.
__________

Don't want to get infected twice in one season? Don't want mass calloffs at your workplace because everyone is sick at once?

WEAR A QUALITY RESPIRATOR.

In PA, JN.1 is HERE and over 2%. It's going to make PA go through some things if we do not excercise some basic, common-sense ways to control spread.: https://ibb.co/9ZRD6mJ

In NY/NJ, JN.1 is already at almost 6% of random sequencing. It's in fourth place after HV.1, FL.1.5.1, and HK.3.: https://ibb.co/3CmB65v

Mask up, New Yorkers and Jerseyans.

I know I'm yelling. But again, if we COOPERATE and use some common sense methods to control the source of spread, it will prevent much life, learning, and financial loss during and after the holiday season.

Stay safe and healthy, PAians. 🍁❄️❄️

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #BA286 #JN1 #HV1 #WearAMask #CleanTheAir #VaccinesSaveLives

PA update for 11/3/2023!

Good Morning SARS2PAians!

I hope your Fall is going great. 🍁

There's no new CDC stuff today.

__________
VOCs

Nationally, HV.1 still in the lead by very far and away at over 18% of random sequencing.: https://ibb.co/BnYKThh

A few potentially fast variants are creeping up the ladder. JG.3, HV.1.1, JG.3.1, and of course potentially very troublesome JN.1 (=BA.2.86.1.1) are above the "fold" and are all theoretically clocked faster than BA.2.86.

In PA, not a lot of sequencing done here but no troublesome varaints found. That doesn't mean they're not out there but at least they're not prevalent enough to come up the sparse sequencing we do have.: https://ibb.co/q0yDj3Y

In NY/NJ, HV.1 now at over 20% of random sequencing. Very fast variants JG.3, JG.3.1, and JN.1 all very close to 1% already. BA.2.86.1 slowing down a bit but still at almost .5%.: https://ibb.co/thMgBz9

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Wastewater

Nationally, wastewater creeping up again.: https://ibb.co/Ms4ytWf

Regionally, the Midwest and South keep getting adjusted higher and higher. Northeast hitting a plateau, still stuck in very high levels.: https://ibb.co/gtMq654

in PA, 5/9 stations (excluding Dauphin and Erie) still overall climbing upwards.: https://ibb.co/WtLLb6W

Butler and Indiana seems to be handling it!!

MontCo is SMASHING IT!!! Yous are below national levels again!

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Flu Comparison

Just want to remind everyone that flu levels are still absolutely minimal for PA and its surrounding States so far. If there's people sick, if it's not a teeny bit of rhinovirus (which actually is the common cold), it's COVID.: https://ibb.co/47G7f73

It's not the flu. It's COVID.

Please be honest with everyone around you about your illness and STAY HOME/WEAR A QUALITY RESPIRATOR if you or your household contracts COVID.

Test often as rapid tests might not pick up levels that can still infect you the first few days of illness.

We can prevent life, learning, and financial loss if we just do some common-sense things for each other.

Continue to have a SAFE and great Fall!! 🍁🍁🍁❄️

#covid #covid19 #CovidIsNotOver #WearAMask #CorsiRosenthalBox #BA286 #JN1 #HV1 #Pennsylvania #PA #StayHome #Wastewater #SARS2PA