With DeFLuQE variants dominant or taking over now in most places, it is time to ponder which variant will drive the next wave.

A leading candidate at this stage is samples that combine the mutations for DeFLiRT + DeFLuQE: Spike S31del, F456L, R346T and Q493E.

These first started appearing from mid-May in British Columbia, and are still quite rare (I got 27 samples). But there does indeed seem to be signs of growth in Spain and the US.

AFAIK no specific lineage has been designated yet for this combination.

#COVID19 #DeFLiRTxDeFLuQE #DeFLiRT #DeFLuQE
🧵

Good Afternoon SARS2PAians!

I apologize for my late post today and not posting at all last week. The situation did not change all that much last week so there was not that much new info to go on anyway.

Also, most virologists are slowly getting more absorbed into the more potentially devastating H5N1 pandemic currently playing out in the animal kingdom, which is totally understandable but...still takes away from SARS2/C19 discussion. 😣

🔴Just a quick reminder that if you need to keep windows and doors shut during this 🔥HEATWAVE🔥, you might want to start using or build a Corsi-Rosenthal Box as keeping houses and businesses tightly shut against the elements is diametrically opposed to virus control.

__________
VOCs

There are no recent drastic changes in the COVID19 landscape so far.

Nationally, KP.2.3 in the lead, and quite a few mutations based on KP.3 right after.: https://ibb.co/jgsnv72

The newest mutation to watch seems to be KP.4.1 which is in very low numbers, currently under 1%, for now.

There are no specifics on the Tableau site so for for PA as far as mutations are concerned.

In NY/NJ, LB.1.7 in the lead, and again KP.3.1.1 is shown to move fast over there at 10% of leaderboard share.: https://ibb.co/vCFVRmN

__________
+rate

Nationally, according to Walgreens, the +rate is going almost stright up. No doubt the East being shut inside for extreme hot/humid weather is NOT helping this, as is waning vaccination effectiveness due to mutational drift.: https://ibb.co/8M4ZFMb

🔴PLEASE get vaccinated when JN.1/KP.2 versions come out in the next few months.

Out of about 5,000 PCR tests done, over a third (39.6%) are positive.

This is a STRONG swing upward that started in April.

The swing upward is mirrored in PA, but only 52 tests have been done. If you aren't feeling well, PLASE use a home test and stay home if you are sick!: https://ibb.co/WnymxfP

__________
Wastewater

WastewaterSCAN has numbers considered HIGH nationally even though the CDC site is considering them LOW. (🙄): https://ibb.co/C7z96yy

Wastewater levels are LOW compared to the first Omicron wave but HIGH considering that we should not be experiencing this increased sickness in July at all.

In our HHS region, Region 3, we have quite a few stations reporting quickly rising numbers. Harrisburg and Chester rising steadily and now surpasses the highest stations in Maryland, which has been consistently high.: https://ibb.co/R7JXkND

Our region average has been going vertical in wastewater concentration in late June.: https://ibb.co/fSTXbPB

In Region 2 (NY/NJ), the Oakhurst Station has been going vertical and other stations steadily and slowly rising.: https://ibb.co/FzJL7BV

Again, extra caution by using quality air filteration (either by CR box or by a KN95, N95 or better respirator) will keep these numbers down for the summer.

Keep cool and have a GREAT WEEK! 🔥🔥🔥

#COVID19 #COVID #COVIDisNotOver #SARS2PA
#Pennsylvania #PA
#KP3 #LB1 #DeFLiRT #S31Del #KP41

#WearAMask #CleanTheAir #WashHands
#VaccinesSaveLives #StayHomeIfSick !

☣️ Las cepas FLiRT KP2 y JN1 son las que tienen este reguero de #COVID19 en Puerto Rico en estos momentos, pero en otras partes del mundo las autoridades sanitarias ya rastrean otras dos variantes, #FLuQE y #deFLiRT.

¿De verdad cree que nuestro sistema inmune aguantará este continuo desmadre sin que se adopten medidas de prevención en capas?

New Covid-19 variants emerge, sparking global health concerns as cases surge
https://www.mirror.co.uk/news/health/new-covid-19-variants-emerge-33174705

Good Afternoon SARS2PAians!

I hope you're enjoying the beautiful weather today!! ☀️☀️☀️

__________
VOCs

Nationally, nothing really new as far as VOCs go, we still have KP.2.3 in the lead, with a very tight race for the top 5 slots on the leaderboard in random sequencing.: https://ibb.co/gjbxpV0

According to Sato Lab in Japan, KP.2.3 is blazingly fast (along with LB.1) and bears a mutation (S:S31del) that makes it immune resistant and more infectious.: https://x.com/SystemsVirology/status/1806464518270369889

Numbers rising already worldwide and in the US from these S-deletion mutations.

In PA, the LB.x.y set seems to be more successful than the KP.2.3 set. This doesn't mean we don't have both out there, but LB.1.7 is showing up more often in recent random sequencing.: https://ibb.co/s3VTsy4

KP.3.1 is also very fast, and the extremely tight race shows that this is a result of mutations that are ALL very fast and infectious.

In NY/NJ, LB.1.7 is at the top of the chart just like in PA. KP.2.3 is right behind it and other fast mutations are gaining, like LP.1.: https://ibb.co/HGDhcjm

Walgreens still has a huge portion of the lower 48 states in the highest positivity growth bracket.: https://ibb.co/1b64Kns

In PA, we're stable right now but numbers are comparable to a mid-winter illness level, and these are only the reported cases.: https://ibb.co/k8VV8Cv

__________
Wastewater

The PAWSS has a lot of increases across the board. Moderate increases in Allegheny, Indiana, Centre, Cumberland, MontCo and around Philly, and Delaware Cos. Some HIGH increases in Monroe Co.: https://ibb.co/JkWTcfh

🔴Vaccines with newer mutation formulas should be available in mid-July for Novavax and earliest Fall for mRNA (Moderna/Pfizer etc.). Moderna has announced they're interested in a JN.1 formula along with Novavax and is looking to start getting in arms in August. Pfizer is still leaning toward KP.2.

The FDA needs to be pushed to get these to kids BEFORE THE SCHOOL YEAR STARTS.

Please get you and your kid(s) vaccinated. Don't be That Guy.

Get whatever is available, as they'll definitely be more effective than year-old XBB shots.

If you have a strong reaction to the mRNA shots though you might want to switch to Novavax (I did!!) but it's usually harder to find.

That's all I have this week as not much has changed even though numbers are still going up. Consider wearing a quality respirator in crowds and in places with poor ventilation.

I hope you have a BEAUTIFUL day and a healthy early summer! ☀️☀️☀️

#COVID19 #COVID #COVIDisNotOver #SARS2PA
#Pennsylvania #PA
#KP3 #LB1 #DeFLiRT #S31Del

#WearAMask #CleanTheAir #WashHands
#VaccinesSaveLives #StayHomeIfSick !

update for 5/31/2024!!

Good Morning SARS2PAians!

I hope you are enjoying your Spring! 💐💐💐

I just have an update on VOCs as I have to run out the door, and also not much has changed in terms of numbers yet. I'm so sorry this is all I have time for right now.

Nationally, for VOCs, we have a lot of fast movers that might bump up numbers for the summer as they have elsewhere globally already. Looks like the fastest are going to be KP.3 and especially LB.1.: https://ibb.co/wzcJ05J

While we don't have any immensely increased numbers so far, nationally they are starting to slowly rise, and source control will be needed as these immune evasive and FAST variants catch on.

In PA, we have quite a few of the FLiRT variants (in pink) and upcoming immune evasive variants (in teal) coming up. Numbers for these new variants are low but might rise steadily as the spring goes on.: https://ibb.co/h1XS2hP

IN NY/NJ, LB.1 is already at the top of the chart 👀 and the speed of its rise is incredible considering how fast current variants are already!: https://ibb.co/dpRDrPd

Watching these new mutations will give a big clue on when to tighten up source control.

In the meantime, keep that air clean and just for future safety, keep a stock of N95s handy for H5N1 as it spreads through more and more domesticated animal species, the lastest which is alpacas. This is starting to make epidemiologists and viral geneticists kinda nervous.

Insist on full disclosure of animal health/testing/sequencing from farms. You might consider non-dairy milk, or maybe ultra-pasteurized milk. Another option is UHT, shelf-stable milk in sterile packaging (like Parmalat).

 DO NOT CONSUME RAW MILK OR UNDERCOOKED MEAT. 

Hope to have more time to do this on Moday (but not sure) so have a great weekend and be safe! 💐💐💐

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

#DeFLiRT #S531del

#FLuQE #SQ493E

#KP3 #LB1 #JNOne50

#IFYouAreDrinkingRawMilk__STOP__DOING__IT

#WearAMask #CleanTheAir #WashHands #StayHomeIfSick !

The new SARS-CoV-2 "FLiRT" lineage LB.1 (descended from JN.1.9.2) has acquired the Spike S31del mutation so becoming a "DeFLiRT". That deletion appears to be quite efficient, with strong growth in the US (14%) and now Canada (10%). New Zealand and Singapore have not updated any data since last week.

At present this seems the most likely successor to the currently-dominant "FLiRT" KP.2 and "FLuQE" KP.3.

#COVID19 #LB_1 #Spike_R31del #DeFLiRT
🧵

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. 💐💐💐

_____
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

__________
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

__________
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

__________
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.

__________
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

__________

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 !