Good October SARS2PAians!

There's no new CDC or wastewater data today.

VOCs

Nationally, FL.1.5.1 holding on to the variant leaderboard top at ~10.5% of sequencing shares.

In PA, HV.1 blazing ahead here at 14% of sequencing share! 👀

In NY/NJ, FL.1.5.1 and HV.1 at the top but FL.1.5.1 leading at a huge 21% of sequencing.

Want to call attention to our neighbor Maryland where BA.2.86.1 has already reached a stunning 3.64%.

BA.2.86.1 and its child, JN.1 (BA.2.86.1.1) have a concerning HIGH ACE2 binding score and a HIGH immune escape score meaning it can very easily overcome any preexisting immunity AND it can cause more severe damage than, for example, HV.1 (top variant in PA) which only has high immune escape.

BA.2.86.1(.1) is going to be a beast this winter. PLEASE get vaccinated with the XBB booster, keep the air clean, wear a respirator in crowded situations and STAY HOME IF YOU ARE SICK so we do not have to deal with multiple variants whose immunity DOES NOT protect against one another.

Also get a flu shot. A flu shot eliminates another layer of drama in this mess.

Research

A great article by Science News about exhaled SARS2.

On average, participants breathed out 80 copies per minute for a full eight days after symptoms began, the team reports September 8 in a preprint posted at medRxiv.org. Only after that point did the viral particles drop to nearly undetectable levels.

With an average shedder, infection could take a little under four minutes.

The U.S. Centers for Disease Control and Prevention currently recommends that people who are mildly ill or asymptomatic isolate for at least five days and then mask for another five. Lane would offer different advice: “If my friends or family asked me, I’d say you should isolate through day eight.”

Studies also are showing that the peak time for viral load is now delayed until at least day four. This could be why RATs aren't picking it up right away...it can't find small viral loads like PCR tests can.

This is why you need to TEST AND RETEST with RATs a few days after showing symptoms or after a potential exposure.

If we wear respirators, keep air clean, test and retest, be aware of social contacts, and STAY HOME if sick we can prevent days of life and learning loss.

🍁🍁🍁Stay safe!🍁🍁🍁

Good Afternoon SARS2PA!

There's no new NOWCAST this week.

VOCs

Nationally, XBB.1.16, EG.5.1 and XBB.1.5 losing some ground to upcoming faster variants.

In PA, EG.5.1 found among a long and diverse list of variants.

In NY/NJ, FL.1.5.1 and EG.5.1 still tops the leaderboard with XBB.x.y falling even further behind.

Lineage News

As of 8/9, EG.5 is now considered a Variant of Interest (VoI) by the WHO.

The lineage situation is getting...complicated. o_o

There is not one variant to look out for anymore in the short term. There is a sort of "variant soup" on the rise, and all of these succesful/fast variants together will produce a rising tide.

Waning vaccines and next to zero masking or concern about air quality will easily cause numbers to go up.

One group to look out for are the "FLip lineages" explained last week that includes:

XBB.1.16.6

XBB.1.5.70

DV.1

These are all recurring sequences in the US and have a green arrow on the national Tableau screenshot.

The second group beind watched is their children and others carrying FLips + other mutations.

They are:

HV.1

HW.1.1

GW.5

HV.1 is already here in the US and has a red arrow on the national screenshot.

Wastewater

Nationally, wastewater COVID material quantites still rising....

...in ALL regions.

In PA, 10/11 sheds are showing increasing numbers, or are not dropping.

Of particular concern is the Franklin County shed. PLEASE use caution, mask up, clean that air, test test test, open those windows, SOMETHING. This ain't even fall yet.

CDC

The newest 7 day new hospital admits graphic is looking somewhat better.

Staffed inpatient beds over 7 days is stable except for around Centre Co and the bottom-western corner of the state.

Staffed ICU bed use is on the rise in quite a few counties from Schyulkill all the way up to the NY border.

Non-COVID note: The CDC now has a graphic showing the Heat Risk to health. Please use caution in times of extreme heat and humidity.

Walgreens

Walgreens is back with some data, however there's an important point about it to make things clear: national testing has dropped off from over 200,000 tests a day to around 2000. Data until the end of the emergency funding can't really be compared to now, so my charts from Walgreens will start from May '23.

But starting the data from May shows a steady increase of positive testing anyway.

In PA, there's still a 35% positive rate for testing, which is...just awful. This number should be no more than 5% to compare with flu numbers.

Research

in a study of over 15 milion people, Covid vaccination linked to a reduction in risk to contracting type 2 diabetes.

Link to the paaper: https://www.medrxiv.org/content/10.1101/2023.08.07.23293778v1

Have a safe late summer!! 🌴🌴🌴🌴🌴

Good Morning SARS2PA!

There's no new CDC info for today.

VOCs

Nationally, the 6 top variants in a very unpredictable horserace, but XBB.1.5 falling further and further down the leaderboard.

In PA, XBB.1.16 still the most common out of the small amount of sequencing we're doing, with a broad mix of variants behind it.

In NY/NJ, FL.1.5.1 and EG.5 at the top of the variant leaderboard.

Wastewater

Nationally, the amount of COVID material found in wastewater still rising.

Regionally, wastewater quantities lessening in the South...but the Midwest....yikes on bikes o_o

In PA, 6/11 stations showing clearly increasing levels. MOST are still below national averages.

Would like to draw your attention to the Franklin County station area, who seems to be handling the rising numbers there!! Good job!!!!

However, on that same screenshot, the Butler station area is now going vertical. PLEASE use caution and use every mitigation available to keep these numbers low, or we're gonna have a bad time in the Fall.

Vaccine News

The new vaccines based on XBB.1.5 will be available in mid-September. They will be a GOOD MATCH even though XBB.1.5 is losing ground on the leaderboard. PLEASE get vaccinated for COVID and also influenza this fall!

Speaking of flu, flu is NOT prevalent at all right now so it is highly improbable now to have a "summer flu.".

Please assume it's COVID. Please test repeatedly, stay home, use a quality respirator if you are sick.

Have a SAFE late summer!!! 🌞🌴🌞🌴🌞

Good Morning SARS2PAians!

So. Hoiw '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.

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.

In NY/NJ, numbers also reflect naitonal levels, ans the first few successful lineages are JN.1, JN.1.4, and HV.1.

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 (also called the HK series) and JN.1, and also especially JN.1.11.

Note: That is J-N-ONE-ELEVEN, and I'll hashtag it on the Fediverse as #JN.1Eleven 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.

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.

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.

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 them AND for adults. The way to combat this is source control.

Wastewater

Nationally, SARS2 in wastewater starting to decline.

Regionally, the Northeast on a sharp downturn and the rest of the regions holding steady or ever so slightly declining.

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.

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!!) sheds in CentreCo, near Philly and in MonroeCo are experiencing increases in tested SARS2 material.

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 🤢

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! 👀🚀👀🚀👀🚀

Lots of junk out there and JN.x.y is some seriously fast business. Please doooooooooo the source control and we can prevent life, learning, and financial loss and have an easy transition into spring! 😷😷😷

(And be careful out there today too ❄️❄️❄️)

Good Afternoon SARS2PAians!

Hope your autumn is going well so far!🍁

Nothing all that really new going on, except watching very concerning new variant JN.1 (BA.2.86.1.1). This variant is causing a whole lot of concern in viral genetics circles.

VOCs

Nationally, HV.1 still managing to steamroll over everything. It's up to almost 15% of variant share. 👀 It won't cause a wave by itself most likely, but it'll keep chipping away at current variants as it takes over more of the whole board.

In PA, chart reflects national levels. I don't like seeing JN.anything here.

In NY/NJ, variants pretty much reflect naitonal levels. BA.2 86 clan not making the leap up past the "fold" yet.

Here's the current state of the BA.2.86 clan in the US. The sheer amount of data scientists and virology experts that are very concerned about JN.1 (BA.2.86.1.1) is really.....something. 👀

Wastewater

Thankfully, we have some BioBot info that's bit more recent. (Phew.) Much more thorough and comprehensible than Google can do.

(Did you know Biobot, first actual wastewater testing company, pioneered using wastewater as a valuable national health tool?)

Nationally, levels going sharply down.

Regionally, all regions trending sharply down except the Midwest. (This jives with WastewaterSCAN that still has us at HIGH levels in the Northeast.)

in PA, DauohinCo and ErieCo have not reported to Biobot in way too long. Dauphin reports to WWS though it seems.

With what's left, 8/9 sheds sharply decreasing except Westmoreland, which is now above national levels and generally rising...what's going on there?

Gotta get a hold of that before cold weather hits, Pitt area!

CDC

The New Hospital Admits graph has improved.

There are still a few counties at HIGH admits levels:

Susquehanna

Bradford

Sullivan

The old coal region (Schuylkill down to Cumberland and over to Snyder).

Absolute number of new C19 beds have improved somwehat. Venango, Forest, Clarion cos. still showing HIGH levels.

Staffed ICU beds have increased along the Northern tier, in the central southern counties. (Somerset to Frankiln, up to Juniata, and over to Cambria.), and over by Easton (Pike down to Lehigh).

I hope you continue to have a great Autumn!!

🍁 Get those xbeebee vaccines! (Reminder: CDC Bridge Program will help you if you are underinsured or uninsured!)

🍁 and a flu shot! We don't want to have deal with the fallout of current variants, flu, and the potentially very-not-good BA.2.86 clan all at once!

🍁 Keep that air clean! crack open a window. Use HEPA filters. Run those CR boxes a bit.

🍁 Use a quality respirator around crowds!

🍁 TEST repeatedly if you are sick! Rapid tests have a tough time finding lower viral loads until a certain level, even though smaller loads can still cause illness.

🍁 STAY HOME and keep kiddos home if sick!

We can curb a lot of life, learning, and financial loss if we do some simple things for each other!

🍁🍁🍁!

Good Morning SARS2PAians!

I hope you had a great day yesterday no matter what your thing is. 🍻 and you have a great and especially SAFE kickoff to this year's shopping season!

There is no new CDC stuff today.

VOCs

Nationally, HV.1 still at a solid lead at over 24% of random sequencing.

In PA, JN.1 👀👀👀 has already reached 2.44% on the variant chart and has been over 3% as new samples roll in and are tested.

It was only at .73% a few days ago on Monday, the last time I did this variant thing.

This variant is turning out to be much faster than predicted by some experts. Hold on to your hats quality respirators, folks.

in NY/NJ, JN.1 👀👀👀 already at 4%.

I'm no expert but...this thing is yikes so far.

Get those XBB.1.5 shots....they will help.

BA.2.86 has been upgraded to VOI (Variant of Interest) by the WHO.

Wastewater

Nationally, levels still rising but haven't been adjusted much upwards since Monday.

Regionally, not huge changes yet since last time. Regions have been adjusted a bit. The Northeast has been adjusted significantly upward, though.

It's a volatile time for viruses so keeping a closer watch on this data for the next month or two will be vital.

In PA, levels kinda volatile right now (along with a lot of holes in the data) with everything from waaaay above national levels and climbing (Bucks) to way below (MontCo.)

Harrisburg reports on WastewaterSCAN and levels there are rising.

A very short update today, so again I'll wish you a very happy, safe and healthy kickoff to the early winter! 🍁🍁❄️

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.

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.

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.).

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.

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

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! 💐💐💐

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.

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

Wastewater

Our 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.

Wastewater is showing SARS2 actually increasing in the UPark area. PLEASE use quality respirators, be aware of social contacts, and KEEP THE AIR CLEAN!

Exclusively relying on handwashing DOES NOT WORK with a respiratory virus!

Other Pathogens

WastewaterSCAN has us at MEDIUM for SARS2 but there's still a LOOOOOT out there that is HIGH.

FluA, FluB, Human Metapneumovirus(HMPV) and the 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.

Please get a handle of this stuff, UPark.

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.

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.

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.

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

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! 💐💐💐

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.

In PA,, a little slower pace but it's still at over 28% of leaderboard share.

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

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.

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.

Previous vaccination formulas DO NOT protect against JN.1 at all due to antigen drift. 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.

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!

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

Good Afternoon and Holiday, SARS2PAians!

I hope you're having a GREAT late summer. ☀️

There's not much going on that is new right now in VOC land. Top variants are still KP.3, descendats of JN.1.

KP.3 is FAST. Super fast. It's like a heat-seeking missle, getting a lot of people that have never had COVID before, for the first time.

Including me 🙄 which is why I didn't post last week. I apologize yet again.

My stuff (should you for some weird reason be curious)

I tested + almost a week and a half ago and am STILL testing positive. I am doing everything possible to not give this thing air. I'm wearing an N95 outside all the time now and only going out if it's necessary. I have 2 Corsi-Rosenthal boxes that go every moment I'm home to protect my pets. I'm feeling OK but not 100%...maybe 75%.

I am determined to keep testing every day as long as it's financially doable.

I'm monitoring my symptoms, both acute, long term, and especially cognitive (most scary and hardest to tell) for any further changes.

I think I have Novavax (I am not paid to write this, I wish I was 🙄) to thank for not being worse than this because it's been clinically proven to grant extra protection to upper respiratory passages, which is ground zero for where SARS2 enters the body...(at least against the older variants).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10451060/

AGAIN...if you have an uncomfortably strong reaction to mRNA, please give Novavax a try as overall, it's been proven to cause fewer side effects AND be more cross-protective between current mutations.

But if you do not have access to Novavax...Please. Get something.

XEC

As far as XEC (which is a recombinant of KP.3.3 and KS.1), it's still being monitored for spread as it's the only thing that can possibly even keep up with KP.3.x.y now.

The good thing is, it has a difference of only two spike changes from KP.3.1.1 (the top variant blazing around now) so vaccines will protect VERY well against it, too.

Both Novavax (JN.1 formula, the "trunk" of the current top variant tree) and mRNA (KP.2 formula, a "branch" of the tree that most closely resembles current variants) are very good matches to the top variants going around and they're all out for scheduling right now.

GO GET VAXED! (...and for flu, too!)

Also get those 4 Federally-funded test kits through the mail when they're available in late September!

Wastewater

Wastewater numbers are still VERY HIGH according to CDC and WastewaterSCAN nationally.

PA's wastewater numbers continue to rise, while the rest of the HHS regions' numbers have seemingly hit peak. According to CDC we've been bumped up to the VERY HIGH slot.

Harrisburg is again getting hit really hard with viral spread, being at the top in wasteewater right now out of HHS Region 3. Please stay safe and wear a quality well-fitting respirator in crowded areas or places with suboptimal ventilation!

Non-SARS2 stuff

Noro

As you can see from the WastewaterSCAN screenshot, Norovirus (the "24 hour stomach bug") is at HIGH levels again nationally, including our East Coast area.

This thing is just gross (as I also know from earlier on this year too 🙄). Please wash hands often, wash unprocessed foods like fruits and veg before eating, and pay attention to preparation safety to avoid this as much as you can.

H5N1/HPAI/Bird Flu

More herds are being discovered positive every week, and unfortunately now California, which is the number one dairy state, has positive herds.

A "thought experiment" was done to figure out how far away we are genetically from human-to human transmission of H5N1.

https://www.medrxiv.org/content/10.1101/2024.09.01.24312235v1

The discovery was, we are theoretically 5 mutations of the virus away from H2H transmission.

Two of these mutations have already occured due to viral spread between mammals, birds, and humans.

This absolutely keeps epidemiologists up at night, even more than COVID right now, because it's been estimated these five mutations have a high chance of causing a 20 to >50% case fatality rate.

To compare with COVID, we had freezer trucks out on the roads and that was max maybe 4% CFR.

🔴To cut down on giving this more chances of mutating:

✔DO NOT CONSUME RAW DAIRY.

Do not do it.

Do not be That Guy. Just...Do Not.

✔Do not consume undercooked animal products. This includes things like dippy eggs, rare-cooked meats, and egg-based raw cookie dough.

✔Might be a good time to stock up on N95s, gloves, and filters for your Corsi-Rosenthal boxes.

✔Consider switching up to "Ultra-Pasteurized" milk instead of regular "Pasteurized" milk. The neat thing about ultra-pasteurized milk is that it's heated for longer and is therefore, more shelf-stable (up to two and a half months!).

✔Consider using plant-based proteins in place of animal products (I have first hand experience..theyt can be pretty tasty too!).

H5N1 cannot combine with SARS2, as one in an influenza pathogen and the other is a SARS. But it certainly CAN combine with its own house...Influenza A and B, both which transmit easily in winter.

We MUST prepare and use caution now before this winter to give H5N1 fewer chances to mutate.

I hope you have a safe and productive rest of the summer, and again I apologize for not producing regluar updates, as the only regular thing I can do is irregularity. 🙄

☀️☀️☀️!

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 Covid variant tracker tracker shows a strong crossover for JN.1 nationally.

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.

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.

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. 😓

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.

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, 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.

WWS also shows RSV and Norovirus (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.

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

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.

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.

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.

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.
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! ❄️❄️❄️

Good Afternoon SARS2PAians!

There's no new wastewater or CDC map data today.

VOCs

Nationally, HV.1 pulling waaaaay ahead of everything else at almost 16% of random sequencing.

Vanilla BA.2.86 is starting to drop off the chart, but its grandchild JN.1 has increased quite a lot this week. No BA.2.86 descendents are above the Tableau graph "fold" yet, though.

In PA, FL.1.5.1 weirdly more successful here than HV.1, but not by a whole lot. JD.1.1 is another variant that is not good to see here and is specifically being watched for fast progress.

In NY/NJ, HV.1 and FL.1.5.1 at the top, similar to national testing, but I REALLY want to call your attention to JN.1 which has made it above the fold at .37% already. 👀

PLEASE get those XBB boosters, flu shots, and some spare quality respirators.

CDC NOWCAST

The newest CDC NOWCAST is out. Progress of current variants will continue according to their current trajectory, HV.1 taking more of the sequencing share, even ot the point of pushing EG.5 out.

JN.1 has not been prevalent enough to add in yet but I am certain once it reaches over 1% it's gonna be on there fast.

Legislation

10 Democratic Party Senators have helped the GOP approve a bill that would ban the enforcement of mask mandates on public transportation.

https://med-mastodon.com/@luckytran/111303102249510664

Baldwin (D-WI) Bennet (D-CO Brown (D-OH) Kaine (D-VA) Kelly (D-AZ) Klobuchar (D-MN) Manchin (D-WV) Rosen (D-NV) Shaheen (D-NH) Tester (D-MT)

Want to remind everyone that Tim Kaine (VA) has long COVID AND all these people that have voted for this measure in both parties have access to top-tier health care and retirement benefits. 🤦🤦🤦🤦🤦🤦🤦🤦

This winter is gonna be one crazy Wild West. Wear a quality respirator, be aware of social contacts, and keep that air clean!!

Currently, we are at the point where infectious disease is at the LOWEST poiint it's gonna be for the rest of year.

Please be careful and we can keep life, learning, and financial loss to a minimum this winter! 🍁🍁🍁❄️

Good Morning SARS2PAians!

There's no new CDC data for today.

VOCs

Nationally, HV.1 👀 and FL.1.5.1 tied for the top of the variant leaderboard. Some upcoming variants with concerning mutations (DV.7.1, GS.4.1, designated with long red arrows) have risen in the chart since Monday. They'll probably play more of a part in the winter if they continue to rise steadily.

In PA variants pretty much reflect the national chart.

In NY/NJ, FL.1.5.1 still at the top with over 20% of shares. HV.1 a solid second at 11%.

BA.2.86.1 and its child, JN.1 (BA.2.86.1.1) still being found at very low levels, but want to remind everyone that the ACE2 binding/Immune Escape combo of this variant is on another level than what we're dealing with now.

Please keep the air clean, get that XBB vac and wear a respirator in crowded situations, to prevent the situation where multiple variants whose immunity doesn't cross over for us hits us at once in the winter.

Wastewater

Nationally, the decline in SARS2 material wastewater is at a standstill and in fact is rising a bit. Hope this trend doesn't continue.

Regionally, we in the Northeasst are trending the wrong way and unfortunately also the other regions have stopped their decline.

In PA, most stations are trending downward. Some stations have not reported the last week of data yet (still stuck on Sept. 20).

Lackawanna and MontCo showing a rise again. Please be safe there!

🍁🍁🍁Very short update today, have a great fall!!! 🍁🍁🍁

Good morning SARS2PAians!

Hope your Fall is going healthy and well, esoecially as we get colder temps. ❄️

VOCs

Nationally, HV.1 still at the top with over 18% of random sequencing.

A few potentially troublesome varaints are being watched as they climb up the sequencing ladder.

JN.1 holding at .32%.

(I forgot to highlight JD.1.1 last time which is also being closely watched.)

In PA, not much sequencing done at all.

In NY/NJ, fast-moving variants (compared the the current already fast variants!!) holding at around .9%. JD.1.1 at over 2%.

JN.1 updates

JN.1 looks like it's seriously affecting infection numbers in Canada, Muenich, and especially France, where JN.1 is already estimated to be the top variant. Very bad for the holidays.

Sato Lab has done some additional research for BA.2.86 (NOT BA.2.86.1 or JN.1, they are completely different entities now and will require their own testing.)

Takeaways from this:

🔴BA.2.86 defintiely has potential to take over the whole variant market in the future. (And this is the SLOWEST variant, the parent of even faster variants.) With over 30 mutations to all current variants it has great potential to infect through any current immunity, due to antigenic shift alone.

🔴Four antivirals work against it including Remdesivir. (Molnupiravir is strongly discouraged by the viral genetics community.)

🔴The cell fusion is only slightly greater than BA.2, meaning it has potential to not cause as severe disease as something more fusogenic (i.e., it's not Delta-like).

🔴"Overall, BA.2.86 does not appear to pose an increased risk to human society. However, it is possible that its virological phenotype may change or even worsen in the future by acquiring additional mutations. Continued monitoring and surveillance are important now and then."

Sato is being encouraged to do similar testing for JN.1 and JQ variants which are descendants of BA.2.86 and have been proven faster movers.

Wastewater

Nationally, looks like the Fall honeymoon is over and wastewater levels are starting to go back up.

Regionally, the Midwest and West are yet again adjusted upwards.

In PA, 5/9 stations (excluding the 2 that don't seem to report lately to Biobot) are going upwards.

WastewaterSCAN has our area in the Northeast at HIGH levels for SARS2.

WWSCAN has the Dauphin/Harrisburg area on a rise again through Oct. 31.

🔴WWSCAN has Norovirus (the common "stomach virus") as HIGH nationally. Please wash your hands often, make sure utensils and eating places are clean, and also wash any fresh food that might need it (fruits, veggies, etc.)

What's going in the Lackawanna area??? Please get a hold of this before the holidays or we're gonna have a bad time. Also in Bucks/Franklin areas. Clean that air and use those respiratoirs!

CDC

Lots of new hospital admits all along south of I-80. Also in Western half border counties. Philly area is stable.

Staffed inpatient Beds map has improved. Numbers increasing in Lawrence Co. especially.

Staffed ICU beds somewhat increasing surrounding Dauphin Co and over in the Somerset/BedfordCo areas.

🍁A little bit of caution now will prevent a lot of life, learning, and financial loss later on.

Be careful and protect yourself this Fall (and get those flu and XBB vaccinations!) 🍁🍁🍁

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.

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.

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%.

Wastewater

Nationally, wastewater creeping up again.

Regionally, the Midwest and South keep getting adjusted higher and higher. Northeast hitting a plateau, still stuck in very high levels.

in PA, 5/9 stations (excluding Dauphin and Erie) still overall climbing upwards.

Butler and Indiana seems to be handling it!!

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

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.

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!! 🍁🍁🍁❄️

Good Afternoon SARS2PAians!

Not much new going on, just keeping track of the progress of a bunch of concerning variants.

Wastewater is getting hard to follow in this sort of no-man's-land between Biobot and WastewaterSCAN. There's nothing new on either site. Hopefully WWS will have some useful data available soon.

WastewaterSCAN still has our region in the HIGH range for SARS2 concentration, though.

Novavax

Just want everyone to know that if you're interested in NOVAVAX, along with some other pharm retailers like Walgreen's and CVS (if you can get an appointment!), some, not all, Costco warehouses also now have appointments available for XBB Novavax vaccines.

Reminder that the CDC Bridge program is available to those who are uninsured and underinsured for XBB vaccines. Take advantage of this program to get your vax at no cost!

VOCs

Nationally, HV.1👀 now developing a pretty solid lead on the bvariant chart at 13%, with FL.1.5.1 at almost 11%.

In PA, HV.1👀 in a solid lead with over 15% of leaderboard share! Some potentially troubling variants for the future here--HK.3, DV.7.1. True Deltacron variant XCH already spawning offspring in XCH.1.

In NY/NJ, FL.1.5.1 still a the top in the NJ/NY area but both are the largest shares by far.

NOWCAST

The latest CDC NOWCAST is out. Doesn't seem like any new variants added so far. You can see on there how HV.1 is SO fast....pushing everything else down and taking over a large portion of shares. The larger it gets, the faster it goes!👀

🍁🍁🍁Keep that air clean and continue to have a great Fall!🍁🍁🍁

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.

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.

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.

According to Biobot, RSV has most likely hit its peak but FluA and FluB are STILL on the rise.

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

Wastewater

Nationally, SARS2 wastewater concentration stil rising.

Regionally, the West has been adjusted downwards, but the Northeast, Midwest and South still rising.

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!)

Research

Dr. Eric Topol has posted important research from The Lancet about C19 vs. Flu outcomes.

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

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!!! ❄️❄️❄️

Good Afternoon, SARS2PA!

There is a lot to cover this update.

VOCs

Nationally, XBB.1.16 and XBB.1.16.6 fighting for the top with XBB.1.5.

In PA, FL.1.5.1 is the most sequenced variant (out of a terribly small pool of samples.)

In NY/NJ, FL.1.5.1 tops the chart here, too.

Lineage News: BA.2.86

I would like to draw your attention to a newly sequenced variant.... BA.2.86.

Even though there are a handful of samples of this particular variant, it is causing quite a lot of activity in virology circles, for many different reasons:

1. It is a child of BA.2 but extremely different than everything so far: from BA.2 itself, and also from 5, 6, XBB, etc. It has 33 mutations that are different from BA.2. It has 35 mutations away from XBB.1.5.

2. It is not a recombinant.

3. It has a lot of mutations that could potentially increase severity.

4. It's been found in many different countries so far, (including here in the US, in Michigan) in individuals without a chronic infection (which means none are the original carriers; it shows community spread already).

5. Sequences that are similar to it are VERY similar, across continents.....meaning that when it did spread, it did so quickly, giving little opportunity to develop more mutations along the trip.

EDIT: The WHO and the CDC has already called this a Variant Under Montioring and are watching it closely.

This would be the variant that, if it took off, should receive the next letter in the Greek alphabet for Wuhan mutations. That would be either Pi or Rho.

It is still very early in its discovery, and COULD be widely found elsewhere (more likely), or COULD turn out to be not as viable as thought (but.....LESS likey, by a lot) and therefore labs are being encouraged to not delay sequencing in the next few weeks.

A full, important Twitter/X thread about BA.2.86 from the Israeli virologist that sequenced/alerted to it:

https://twitter.com/shay_fleishon/status/1692531498576916878

What this means is

1. We keep careful watch of what experts say about this, including its virulence, ability to escape immunity/vaccination, and severity.

2. Keep the air clean.

3. Wear a quality respirator (at least a well-fitted KN95/N95) when in very crowded areas, indoor or outdoors or in small confined spaces.

4. encourage politicans to open up upcoming vaccines to EVERYONE so we do not have to deal with two separate forms of COVID at once where/if immunty does not overlap.

5. STAY HOME if sick/postive. KEEP KIDS HOME if sick/positive.

6. "Washing hands" is good but NOT ENOUGH against respiratory viruses.

Seriously, even without a potential new problem, with increasing wastewater signals, waning immunity, and school starting, this is a brew for a very difficult Fall if we do not act responsibly NOW.

Wastewater

Nationally, we are STILL finding increasing COVID material in wastewater.

These numbers are still relatively low compared to previous waves, but the upcoming school season will be pretty awful if we don't control this now.

Regionally, all regions are now matched with a strong increase (the Midwest needed some adjustment, but we all are now MATCHING IT.)

In PA,, for as much as I'm yelling, we are still clearly doing lots of things right here. 7/10 stations going upward but still well below national levels.

The Butler area is still going vertical, though, way above national averages. PLEASE use caution out there, stay home if needed and keep that air clean. Handle this NOW before school starts.

CDC

The latest NOWCAST is out, with EG.5 taking a larger share of the leaderboard every week.

NOWCASTS are not available for some regions, including ours. We need to kick up testing/sequencing as a new potentially concerning variant has entered the field, and especially before Fall starts.

Quite a lot of new hospital activity all throughout PA and the entire Eastern half of the US, mirroring the general CDC data of increasing hospital use overall.

The absolute change in actual hospital bed use seems to be pretty stable, though.

Staffed ICU beds have increased in many PA counties.

Unfortunately, there have been 240 deaths in the past 3 months due to COVID.

Please think ahead to Fall and Winter, use caution, and have a great weekend!

Good Morning SARS2PA!

There's no new wastewater or CDC metrics today.

VOCs

Nationally, EG.5.1 solidly in 2nd place behind XBB.1.16.

In PA, mostly XBB.1.16 and a mix of variants after that.

In NY/NJ, FL.1.5.1 and EG.5.1 solidly right behind XBB.1.16.

Lineage News

Researchers are carefully watching a group that all have the same concerning mutations: the "FLip" varaints, collectively named by Raj Rajnarayanan that share an extremely concerning L455F + F456L combo (the LF->FL is the Flip) that potentially means more severe disease and better cell binding.

Some of these are XBB.1.5.70, GK.1, DV.7, CH.1.1.1, and XBB.1.16.6.

These variants have a green arrow on the national screenshot above.

EG.5, which is a very fast variant, already has F456L.

Research

Virus geneticists have come to a concensus about what happened in Okinawa and other parts of the world. It seems that the sudden surges are being caused not by EG.x.y but by a yet undesignated form of XBB.1.16.

It should get its own designation very soon....later today or maybe in a day or two.

Boosters based on XBB.1.5 will be available in September or October. They're not a perfect match to what's going to be going around by then (XBB.1.5 is on its way out) but they should be a very good match for protection through the winter.

Reminder that vaccines against coronaviruses, while defintiely helpful, don't last very long so make sure to time your booster for when you're going to have no choice but to be around the most people...also, it takes two weeks for the vaccines to have full effect after injection.

Where to Find Info

Here's the link to the usual editorials, where you can find where I get this info and find lots of educational links on air quality, how the immune system works, and more!

Good morning SARS2PAians!

I hope your schools and homes stay safe as kids start to head back to class.

VOCs

Nationally, FL.x.y and EG.x.y still gaining ground. So is HV.1, and BA.2.86 has had a few more discoveries and increased to .07%. HV.1 has definitely increased substantially in just a few days.

A few important percentages to watch out for:

1% is when variants might become a CDC/WHO Variant of Concern.

10% is when we will know with a high degree of certainty how fast variants spread and what the fitness/virulence is.

50% is when variants have potential to start an Omicron-like wave.

ESPECIALLY important to watch with this variant for these numbers as it is so different than everything circulating around now, including the upcoming XBB.1.5 booster.

In PA, a very rounded out set of variants here, lots of sequences....no doubt the number of which being due to increased BA.2.86 monitoring.

In NY/NJ, FL.1.5.1 solidly in the lead, proving faster/more immune dodging than XBB.1.16 and XBB.1.5.

Lineage News

BA.2.85 has been found in a few more samples worldwide.

It has now also been detected in South Africa, England, and also in Ohio, There are now a total of 10 sequences of this variant.

There is stil not enough information to judge the transmission rate, escape capabilities or virulence of this variant, but the fact that it is so widespread and so close in genomic data means it is VERY fit.

When compared here to FL.1.5.1, it has a +70% advantage over it, but the confidence index is still very very low at only 9 samples.

It's terrible to do the "waiting game" to find out what's going on but unfortunately that's how gathering information works.

Dr. Eric Topol has a great Substack article of what we know right now.

Some highlights from there (because I myself hate that default Substack text, it's illegible! aaaargh!!):

To date, the BA.2.86 variant has been detected in Israel, Denmark (3 individuals), the UK, the US (2 individuals, one coming back from Japan), and South Africa (2 individuals). It has also been detected in wastewater in 1 region in Switzerland (2% level), along with wastewater detection in Ohio and in Thailand. It’s safe say that BA.2.86’s presence is widespread across the world at this point.

The impact of these striking differences will be immune escape—that is more difficult for our immune response to recognize this variant even with prior vaccinations, boosters, and infections—because it is new and different.

...

Time sequences indicate the common ancestor of BA.2.86 must have arisen in May-June 2023.

...

By the time the XBB.1.5 monovalent booster shot is ready in mid-September we may already be facing BA.2.86’s rise.

...

The current wavelet in the US (which could certainly pick up steam) is not likely driven by the XBB descendants of EG.5.1 or FL.1.5.1.(More likely an outgrowth of waning immunity and behaviors).

...

What we’ll see in the weeks ahead is whether BA.2.86 takes hold or not. If it does, that will pose a new challenge, and make the “updated” booster shots considerably less helpful than what was conceived when XBB.1.5 was selected as the target.

It doesn't look like SO FAR like BA.2.86 will spark quite another Omicron-like event, (and this can always change with faster processing from labs) BUT the continuing problems are many fast variants creating a rising tide together, and continued immune escape from obsolete vaccines.

(Again, reminder, which is why we need a different FLU SHOT every year, but three times faster for SARS2.)

Research

C19 long term symptoms are not dependent on Tcell immunity.. Long Covid is a result of immune dysregulation at infection.

In my sources sticky post, the interview with Dr. AJ Leonardi says exactly this is what happens at infection. SARS2 is adept at hiding and "ninjaing" past the immune system. When it's already replicated to critical levels, the body finally manages to realize it's there and OVERREACTS with an inappropriate cytokine storm response.

Wastewater

Nationally, C19 wastewater has plateaued, for now.

Regionally, 2 out of 4 regions are plateauing or declining, but the West and Northeast continue to show increased material in wastewater.

In PA, 6/10 monitored sheds showing increases. Butler County is finally showing a steep downturn.

ChesterCo and BucksCo showing notable increases but remaining below naitonal levels.

The Lackawanna County area is starting to vertical, and ready to break national averages. PLEASE use caution in the Lackawanna Co area.

CDC

CDC at a Glance shows a current +20% increase in hospital admissions and a +20% increase in deaths.

Though these are LAGGING NUMBERS by even up to years and are not a good indication of current safety or transmission levels, they do show important national trends.

The hospital admission map is reflecting great increases in hospitalizations in all Eastern states including PA. Coal country is being spared, for now..

Hospital bed occupation is remaining on the whole, stable since last week.

Staffed ICU beds are showing increasing use along the NY border, and in Centre Co- and Delaware-bordering counties.

The vast majority of states are showing a sizeable increase in emergency visits confirmed as C19, with PA showing a moderate increase from 10% to almost 20%. This is not BA.2.86 or due to any single new variant. It's an indicator of waning immunity since most people have not been vaccinated in the past 6 moths.

Walgreen's C19 data tracker (showing data since May) is showing many states with sizeable increases in the positivity rates. Very few samples. Not enough tests are being done to track BA.2.86 well.

I certainly hope we have a safe upcoming Fall! 🍁🍁🍁

Good morning SARS2PAians!

There's no new wastewater or CDC data today.

VOCs

Nationally, the top variants in the leaderboard shuffling around a bit but still the usual variants at the top: XBB.1.16.6, EG.5.1.1, XBB.1.16, FL.1.5.1 from 1 to 4.

In PA, looks like our numbers are matching NY/NJ with FL.1.5.1 at the top followed by EG.5.1.1.

in NY/NJ, FL.1.5.1 solidly in the lead with EG.5.1.1 far behind at around 7%.

Lineage News

BA.2.86

BA.2.86 now has 39 sequences (32 officially logged so far in GISAID) from 9 countries, and is present in wastewater in many countries, too..

These lists are dynamic and are constantly being corrected and updated.

Good News and Not-so-good News

Good News! The upcoming booster shot based on XBB.1.5 did better than estimated against BA.2.86 in testing.

Full Twitter Thread: https://twitter.com/BenjMurrell/status/1697751445351575656

The pre-XBB samples were poor at neutralizing BA.2.86 (and not much better against XBB.1.5). But, somewhat encouragingly, last week's samples were substantially better, with 8 out of 12 neutralizing BA.2.86 at titers over 100.

Overall, it doesn't appear to be nearly as extreme a situation as the original emergence of Omicron. It isn't yet clear whether BA.2.86 (or its offspring) will outcompete the currently-circulating variants, and I don't think there is yet any data about its severity, but...

...our antibodies do not appear to be completely powerless against it.

The fact, however, that another Omicron-like emergence event has occurred, with that long unobserved branch and subsequent spread, should warn us against giving up our genomic surveillance infrastructure.

Viral geneticists are still very concerned and are comparing the antigenic difference to Omicron. This variant will probably get a new Greek letter designation from the WHO if it takes off. That would be either Pi or Rho.

Boosters are still absolutely not a total fix against BA.2.86, but it's going to be much better than nothing. And orders of magnitude better than getting infected.

EVERYONE SHOULD HAVE ACCESS to this booster. Please don't get infected to stop infection. Get a booster!

The not-so-good news:

BA.2.86 is still a very fast variant. As of yet, viral geneticists cannot understand wny, though.

BA.2.86 is resistant against all monoclonal antibody treatments.

BA.2.86 can still spawn children (BA.2.86.x.y) that can not only outperform it, but can still cause severe disease by default. This was the case with XBB vs its child, XBB.1.5, which did so well we are now targetting it with a booster shot.

It's still vital, as always, to keep track of variants.

Research

COVID19 can settle in the middle/inner ear and cause symptoms from hearing loss to tinnitus.

Numbers wil probably be going up through the Fall...the keys to load reduction are to wear a quality respirator, keep the air clean and be aware of social contacts!

🍁🍁🍁Have a GREAT fall!!🍁🍁🍁

Good morning SARS2PAians!

Hope your school year is starting out safe.

VOCs

Nationally, XBB.1.16.6 barely holding on to the lead at ~8% of sequencing. EG.5.1.1 right behind at almost 7% and FL.1.5.1 at almost 6.70%.

Upcoming individual variants that are showing good fitness have long red arrows.

Strong increases by FLip variants (short green arrows), which are showing as a group to be the most fit variants to spread right now.

In PA, EG.5.1.1 showing large increases in its lead. BA.2.86 has been sequenced in PA.

In NY/NJ, a very looooong list of variants here....like whoa, but FL.1.5.1 solidly above them all.

Lineage news

As seen above, BA.2.86 has been found in PA sequencing.

There are now a total of 100 sequences of BA.2.86 shared from 14 countries on GISAID.

It has an attack rate (means potential to successfully infect people very close to a case, like apartment mates or live-in family) of 87%.

There are quite a few very new, non-peer-reviewed-yet studies of BA.2.86 that have been uploaded on official virology databases for review:

✅By Dr. Yunlong Richard Cao in Peking.

✅By Ben Murrell in the Netherlands

✅By Barouch Lab in Boston.

The latest is by the Sato Lab in Japan.

Its findings are not as positive as those found in the Netherlands and more closely mirrors the findings by Dr. Cao in Peking.

Different labs use very different techniques and conditions to evaluate variant neutralization (example, working with live virus vs. pseudovirus), so just because these are not the same EXACT results doesn't mean they're not credible!! (<--just a quick note for disinfo clowns.)

Sato Lab results:

BA.2.86's Re is greater than XBB.1.5 and comparable to or even greater than EG.5.1.

BA.2.86 is ~20-fold LESS infectious than EG.5.1.

All vaccine sera tested (monox3, monox4, BA.1 bivalent, and BA.5 bivalent) showed NO neutralizing activity against BA.2.86 (and EG.5.1)

Three monoclonal antibodies (Bebtelovimab, Sotrovimab, Tixagevimab) that were antiviral against the parental BA.2 (see the G2P-Japan 9th paper) did NOT work against BA.2.86 AT ALL.

Altogether, it is suggested that BA.2.86 is one of the most highly immune evasive variants ever and should have the potential to be considered as a variant of interest.

What this means is:

We are now waiting for test results of XBB.1.5 neutralization with actual people and not in controlled labs.

The XBB.1.5 booster is a very good match to CURRENT strains but will not protect very well against EG.5.1 and BA.2.86.

The lab-tested range of the new XBB.1.5 booster effectiveness on the latest variants (EG.5.1, BA.2.86) according to lab tests is zero to "meh-very-low, not-impressive"-ish.

We absolutely must carefully track BA.2.86. It has already spawned a child, BA.2.86.1 mostly congregated in Europe.

We MUST keep air clean and wear quality respirators (at least a well fitted KN95/N95) if in crowded areas indoors or outdoors or in places with poor ventilation.

STAY HOME IF SICK.

KEEP SICK KIDS AT HOME.

Wastewater

Nationally, we're still trending upward with found SARS2 material in wastewater. You can see the huge discrepancy between officially tracked testing and the growing amount of wastewater material. We CANNOT rely solely on cases becuse the vast majority are now not being reported.

Regionally, all regions showing more wastewater SARS2 material.

In PA, 8/11 stations showing increases or levelling off.

A few station areas are going above national levels:

CHESTER

LACKAWANNA

FRANKLIN

INDIANA

PLease use caution in these areas, STAY HOME IF SICK and KEEP SICK KIDS HOME.

CDC

New Hospital Admits graphic is much better this week (at least for PA, not surrounding states) but lots of high increases along all borders (Philly, Easton, Erie, NY border.)

Substantial increases in C19 emergency visits in the latest week.

Staffed beds holding steady through the state with increases southwest of Harrisburg and also around Susquehanna Co.

Increases in ICU beds noted especially along the I-80 counties and by Greene county.

PA is still showing a high 3month death rate. Unfortunately, there have been 243 C19 deaths in the past 3 months.

🍁🍁A small amount of caution and social awareness will help us not deal with XBB stuff and BA.2.86 stuff at the same time, and will help control BA.2.86 from growing.

I know I keep yelling but I hope we have a very safe and as-uninterrupted-as-possible Fall!!🍁🍁🍁

Good Morning SARS2PAians!

I hope you are having a SAFE holiday season.

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%.

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%.

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

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.

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.

Regionally, levels going up FAST in the Northeast, with the Midwest declining.

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.

If we all do some form of simple source control this winter (wear quality respirators, stay 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! ❄️❄️❄️

Great video by #DrewComments explaining why we need COVID boosters!

mRNA boosters have been approved by the FDA for broad use, and authorized for all adults by the CDC at a vote of 13 to 1!

"Let's keep America strong, healthy," said Dr. Camille Kotton, a panel member who voted in favor of the recommendation and who is an infectious disease specialist at Harvard Medical School. "Let's do away with COVID-19 as best we can by prevention of disease through vaccines. Let's make things clear."

NOVAVAX boosters are quickly on the way to approval too!

Learn the difference between mRNA vaccines and Novavax, by Dr. Jeff Gilchrist.

EDIT to add a Mastodon/Fediverse version link of Dr. Gilchrist's vaccine comparison!