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 !

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 5/6/2024!

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 Afternoon SARS2PAians!

I hope you had a clear and safe view of the eclipse on Tuesday!!!

I hope you also have a great and safe Spring now that warmer weather is finally here!
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VOCs

Nothing much new to report on new variants (which is why I didn't post on Monday...absolutely nothing was updated at all...wastewater, CDC, variants, etc.).

JN.1 and JN.1.4 still at the top of the leaderboard.

The fastest two variants now in the US are JN.1.18 and KP.2 (which is a descendant of JN.1.11.1) and though the two are making gains every update, they don't seem to be near as fast as JN.1 was.: https://ibb.co/zFNhBF7

There are no new imminently concerning variants on the horizon right now.

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Wastewater

National level is still MEDIUM on WastewaterSCAN but we're now approaching where we were at this time last year. Still a ways to go to get to LOW levels but at least it isn't going up for now.: https://ibb.co/yR8ttZ1

Wastewater is showing SARS2 actually increasing in the UPark area.:https://ibb.co/K2MWY4G

PLEASE use quality respirators, be aware of social contacts, and KEEP THE AIR CLEAN!

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Other Pathogens

WastewaterSCAN has us at MEDIUM for SARS2 but there's still a LOOOOOT out there that is HIGH.: https://ibb.co/R6R5jDM

FluA, FluB, Human Metapneumovirus(HMPV) and gastro pathogens Norovirus and Rotavirus are still HIGH nationally.

In PA, the highest by far is Noro, but also FluA and FluB is very high.

Wear respirators to control SARS2 and WASH THOSE HANDSIES to control the gastro stuff!

UPark has got some work to do with pathogen control. Levels are going up/lagging behind on handling SARS2, FluA, FluB, HMPV, Noro.: https://ibb.co/YcvPpJg

Please get a handle of this stuff, UPark.

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H5N1

A condensed version of the current state of H5N1:

H5N1 IS NOT NEW.

So far, the only human cases of contracting H5N1 are through direct contact with infected animals.

So far, scientists are still unsure of how H5N1 affects cattle. THIS IS in fact, NEW.

Cattle cases have been found in 8 states.: https://ibb.co/YcvPpJg

The vast majority are in Texas. 40% of Panhandle cattle have been infected, and that area produces 82% of Texas' milk. This is LOTS of room for new mutations to develop.: https://ibb.co/yFr2Rm1

New Mexico
Idaho
North Carolina
Ohio
Michigan
Kansas
South Dakota.

These states are not in the paths of migratory birds so contaminated FEED is suspected. The feed is contaminated by practices that are LEGAL in the US but BANNED in Canada and Europe....mainly, feeding bird waste to cattle.

Feed for swine was DEREGULATED in 2018 and MUST be re-regulated to protect swine from H5N1. They are genetically similar to humans and can easily percolate a mutation that spreads to humans.: https://ibb.co/NxdSJm7

Feed for all farm animals must be regulated and animal waste must be kept out of farm animal food.

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Like COVID, H5N1 has the ability to gain new mutations from new hosts. THIS IS NOT A NEW CONCEPT.

Some things to watch for that are NOT CURRENT but are progressively bad:

--Cattle-to-cattle transmission proven.

--Contaminant-to-swine (pigs) develop.

--Swine-to-Human acquired.

--Human-to-human transmisison proven.

The first three have to somehow happen before the fourth happens. None of these things seem to be imminent but that progression will mirror pathogens like Spanish Flu.

I keep spending a lot of time on this because I cannot stress enough that H5N1 in humans has a 50% kill (case fatality) rate so far. A vaccine does exist for H5N1 for both humans and birds, but the human version is not stored in mass quantities for now.

Some things we can do together to lessen the chances of allowing H5N1 to mutate:

Lobby for CLEAN animal feed for swine, cattle, and fowl.

Buy dairy products from smaller, more humane farms. Grass-fed cattle and free-range chicken eggs are more expensive, but better than battery farming products where thousands of animals are squeezed together.

Buy ultra-pasteurized dairy products (most of our cream is ultra pasteurized anyway).

Insist that farm birds are vaccinated against H5N1.

I can't stress enough that farm feed must be HUMANE and REGULATED. This is not political, this is literally to stop a highly pathogenic disease from becoming capable of infecting humans.

Contaminated cattle feed is exactly how the prion infection called Mad Cow Disease begun.

Clean feed and happy farm animals make better, cleaner, and healthier products!

__________

There are always simple things we can all do to prevent the possibility of dangerous pathogen mutations!

Source control is the most important part to keeping life, learning, and financial loss to a minimum.

I hope you all continue to have a great Spring!

#covid #Covid19 #SARS2PA #CDC #CovidIsNotOver #Pennsylvania #PA #JN1 #KP2 #FluA #FluB #Influenza #Norovirus #Rotavirus #H5N1 #HMPV

#WearAMask #CleanTheAir #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!!

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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

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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.

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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

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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

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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