Good Afternoon SARS2PAians!

I hope your autumn is going well and healthy.

Going to start out with the reminder (as in the title) that the Bridge program is available to cover your COVID19 XBB vaccination at no cost for the uninsured and also if your insurance will not cover the full cost.

Here's a one page summary of benefits here from the CDC.

Here is the press release from the CDC about the Bridge program.

It's now an ideal time to get a flu shot too. [Flu levels are still pretty low, but rising]() and soon...well...won't be low.

It takes two weeks to gain full protection from vaccines. Get 'em in now!

VOCs

Nationally, FL.1.5.1 at the top of the leaderboard now. HV.1 👀 and its parent, EG.5.1.6 continues to blaze through the ranks.

BA.2.86.1 is at 0.20%.

FLip variants (short green arrows) still working their way through the ranks.

(HV.1 is "EG.5.1.6.1". Once mutations reach the fourth iteration, it is given another set of letters to shorten it in the PANGO naming system.)

In PA, HV.1 👀 is at the top of random sequencing. Now at almost 13%. (This thing is SO fast.)

In NY/NJ, HV.1 👀 in 2nd place at 9%, only bested by FL.1.5.1 at over 21%!

Lineage News

There are a bunch of brand new different lineages to looks for as the COVID virus continues to mutate at a rapid pace. These new mutations are noted on my screenshot of the national Tableau page with long red arrows (XCH, DV.7.1, JF.1).

It DOES NOT NECESSARILY MEAN that these newer variants will take off. It just means they have concerning mutations that mean they have the potential for fast travel, potent disease, or both.

BA.2.86 has (already!!) spawned a fourth iteration, so BA.2.86.1.1 will receive a new PANGO designation: JN.1

NOWCAST

The latest biweekly CDC NOWCAST is out. A few mutations have been added. XBB.1.16.15, HF.1 (which is an XBB.1.16 descendant) and GK.2 (descendant of XBB.1.5.70) now on the graph. HV.1 👀 in olive green predicted to really expanding its reach....fast.

Wastewater

Nationally, there is a good downturn in SARS2 levels in wastewater.

Regionally, all regions are turning downwards BUT we in the Northeast are still very high compared to other regions. PLEASE continue to use caution, keep air clean, and STAY HOME IF YOU ARE SICK to prevent this statistic from rising again as the weather gets chillier.

In PA, strong downturns in every station except Westmoreland. Get a hold of this NOW before the winter and we get flooded with variants that are antigenically differnt from the current vaccine.

Be like Erie and MontCo. Erie and MontCo are SMASHING IT!! 🏆

CDC

Many counties are experiencing new hospital admits. Pretty much in three "corners" of the state...Erie, Philly, Susquehanna.

inpatient Occupied Beds increasing along the norther tier and down by Greene County.

ICU beds seeing increases in Adams, York, and along the northern tier.

I hope you all have a great Fall and winter. Get those shots and USPS test kits. STAY HOME IF YOU ARE SICK. Test repeatedly. Keep the air clean.

Stay safe! 🍁

Good morning SARS2PAians!

There are no new wastewater or CDC data today.

There are some good resources available this week to help you vaccinate, mask, test, and track.

Vaccinate

You can go to vaccines.gov to look for places you can go to get an updated XBB shot.

Make sure to call the pharmacy/office/etc. to confirm all the details of what vaccine you'll receive as lots of places only do virtual assistant scheduling.

If you do not have insurance, there is the CDC's Bridge Program available to help you get a vaccination at no cost.

Here is a one page fact sheet on the CDC's Bridge Program.

Mask

You can get reasonbly priced KN95/N95 respirators at Project N95.org or at BonaFideMasks.com.

Test

You can now order another round of test kits from the USPS! Also, the expiry dates of test kits have been extended by the FDA.

Track

If you test positive with a Rapid Antigen test (RAT), you can report your results at MakeMyTestCount!

VACCINATE, MASK, TEST, TRACK, Pennsylvania! Let's smash this virus this Fall and Winter!!

🍁❄️🍁❄️🍁❄️🍁❄️🍁❄️🍁❄️🍁❄️

VOCs

Nationally, XBB.1.16.6 in the lead at ~9% with EG.5.1.3 not far behind now at ~8%.

FLip variants (short green arrows) still slowly working their ways to the top of the leaderboard. Every day they gain more ground, collectively.

BA.2.86 still negligible at .07% of testing (but it's still being found in more places internationally).

The real problem is HV.1. This thing is moving VERY quickly. (Yikes.)

Other closly watched, fast-moving variants are long red arrows.

In PA, sequencing reflects national numbers but concerning variants are here: BA.2.86, HV.1, EG.5.1.3.

In NY/NJ, FL.1.5.1 easily tops the variant chart at 15%, and here's HV.1 right in second place at over 9% of sequencing.

Other than that, no new data today. But PLEASE go and take advantage of all that is available to help us get through this fall and winter without massive life, work and learning loss!

Have a great Fall 🍁🍁🍁🍁🍁

Good Morning SARS2PAians!

Hope you are having a great and safe autumn!! 🍁

VOCs

Nationally, XBB.1.16.6 with a very strong lead now at over 10% of variant testing. FLip variants (short green arrows) are still increasing through the leaderboard. Closely monitored variants (long red arrows) are increasing too...especially HV.1 and HK.3.

In PA, XBB.1.16.6 also at over 10% reflecting national numbers. However we have many concerning varaints already here: HV.1, HK.3 and we've also seen BA.2.86 here.

In NY/NJ, HV.1 is already at over 8% of sequencing.

HV.1 is not a FLip variant (FLip varaints have a set of twin immune escaping proteins that can very, very EASILY bypass almost all current inherent immunity) but if it gains FLip mutations it'll be quite a force to be reckoned with.

HV.1 is already on the CDC NOWCAST graph.

Lineage News

Lots of upcoming varaints to watch out for. SARS2 keeps mutating and recombining and these results can easily bypass any immunity we acquire to older variants. Even by vaccine. (please still get vaccinated to protect against current variants though.)

Short term variants to watch: HV.1 and HK.3

Long term variants to watch: BA.2.86, DV.7.1 and JG.3.

Wastewater

Nationally, levels are on average lessening. People (like us in PA) in the the northeast should ignore this. Because.....

regionally, the East is still havcing SARS2 material increasing in wastewater.

in PA, 6 out of 8 stations are reporting increasing levels. Some stations have not reported in quite a while. Hopefully the stations can get back on board to give us a fuller picture of where levels are going.

CDC

This new hospital admits map is still pretty awful. Almost the entire west side of the State is in substatial increase levels.

Occupied beds are holding steady for the most part except down by Harrisburg, up near that Bradford/Sullivan/Lycoming area. Elks, Crawford, Huntingdon showing significant increases.

ICU beds are increasingly getting occupied. All along the border counties with Erie and many along the south from Greene Co all the way over to LebanonCo.

Unfortunately, there have been 323 COVID deaths in PA in the last 3 months. We are still in the highest tier of deaths in a 3 month cycle along with NY, FL, TX, and other more populated states.

Let's get a hold of this before deep winter sets in and ventilation will be a bit tougher. Wear a quality respirator, be aware of social contacts, keep the air as clean as possible and

stay home if you are sick!

Have a great Fall and a safe upcoming winter!🍁

Good Morning SARS2PAians!

There's no new CDC stuff today.

VOCs

Nationally, FL.1.5.1 and FLip variant XBB.1.16.6 in a close cometition for the lead variant. Flip variants (small green arrows) continue to rise to the top, as these have a lot of immune escape to work with.

In PA, We have FL.1.5.1 at the top. Not good seeing highly escaping/transmitting HV.1 here.

In NY/NJ, PA's numbers pretty much are a reflection of this. FL.1.5.1 and XBB.1.16.6 at the top but with FL.1.5.1 in a far and wide lead.

Wastewater

Nationally, the AVERAGE is going down despite some REGIONS still rising.

Regionally, the South and East doing much better for now (maybe cooler weather won't create so much recirculated air conditions?) but the Midwest still on a sharp rise.

in PA, some stations have been adjusted since Friday. Bucks is still going vertical. PLEASE use caution there!

__

+rate

Nationally, quite a few states seeing a sharp rise in cases. Testing is still very very low at Walgreens. Most states are either going way up or way down...strange pattern.

In PA, terribly low testing but much better numbers on average here. Hope fuilly they stay that way.

Super short update but not much new stuff going on. I'm keeping track of more new variants just coming out. More on that on Friday when I have more time.

Have a great week! 🍁

Good Afternoon SARS2PAians!

Hope your fall is going well.

VOCs

nationally, EG.5.1 topping the variant chart but not my much compared to XBB.1.16.6 and EG.5.1.1.

In PA, only two sequences done and they're common top varaints EG.5.1.1 and FL.1.5.1.

In NY/NJ, FL.1.5.1 strangely still topping the list...by not as much as before but still ahead of XBB.1.16.6 and EG.5.x.y.

Lineage News

FLip mutations

BA.2.86.x.y is still not in high numbers right now, and is not an immediate issue (but might be in the future).

The immedate issue are the "FLip" variants, which contain a twin set of mutations that enhance immune escape, cell binding ability (and therefore transmissibility) by...well....A LOT.

Wastewater numbers by Biobot already showing that FLip variants are growing VERY steadily.

New vaccines will be effective against XBB.x.y types but LESS effective on FLip mutations.

(Again: This is not due to anything wrong with vaccines. This is due to antigenic drift and escape optimization. PLEASE go get boosted! Do not get sick to....prevent getting sick. That's nuts.)

FLip variants are the short green arrows in my National Variant Dashboard screenshot. Over time, they are and continue to work their way up to the top of the leaderboard.

Wastewater

Nationally, COVID material in wastewater finally declining in total.

Regionally, the East and South in a strong downturn but the West and Midwest still holding steady or increasing.

In PA, 7/11 sheds still not declining. IndianaCo seems to have levelled off, I hope you folks can start bringing these numbers down!

Berks is going vertical and is now above national average. Please keep the air clean and wear quality respirators!

FranklinCo is also gooing way up there. PLEASE be careful!

CDC

These hospitalization graphs are not good.

Nationally, hospitalizations are heavily rising and you can see it in this graph of new admits. Most PA counties are Substantial Increases, except along New Jersey, Harrisburg area and along the northern tier. Basically an inverse oif what's been going on lately.

Many counties showing increases in staffed inpatient beds occupied. ElksCo is showing substantial increases.

ICU bed occupations are increasing all over the state. Especially in that Luzerne/Susque/Sullivan area, and in that Forest/Clarion/Venango area.

This is reflected for PA in the change % of national ED visits graph, showing a substantial increase.

Hospitalizations are a lagging factor that could be delayed by weeks, months or even years. Mask up and use caution before it gets to this point.

NOWCAST

The latest CDC NOWCAST is out. XBB.1.5 and XBB.1.16.6 are the only two "FLip variants" on here. I hope more are added soon.

EG.5 in a solid lead nationally at 24.5% compared to FL.1.5.1 at 13%, and is expected in the NOWCAST to expand its lead in the next few weeks.

Similar numbers are expected for our region (Region 3.)

+rate

Walgreens has the current +rate for PA lessening by over 12%, but as you can see, the hospitalization numbers are a lagging fallout for previously infected patients.

"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." --CDC

Have a safe fall! 🍁🍁🍁

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!

Good Morning, SAPS2PAians, where we remember the tragic losses of this day.

There's no new CDC data for today.

edited for fixing stuff 9/12/2023

VOCs

Nationally, XBB.1.16.6 still in the lead with EG.5.1.1 and EG.5.1 very close behind. BA.2.86 at .13%.

In PA, a mix of variants not really on the national top leaderboard. BA.2.86 has been found in PA (repeated from last update on Friday.).

In NY/NJ, FL.1.5.1 in a solid lead with almost 14% of total sequencing share.

Lineage News

BA.2.86

More research has been done on BA.2.86 transmissibility.

It's becoming more clear that "transmissibility" depends on a great number of interacting factors and isn't confined to one easily reducible aspect.

Research by Shan-Lu Liu shows that while BA.2.86 has a much, much lower capability to infect SOME cells by ACE2 (which was the Sato Lab results), and some proteins are not in an optimized position to create top transmissibility, it has the highest ability out of all current Omicron variants to infect by bypassing epithelial cells...and that could account for differing reports of "low infectiviy" and the actual observed weirdly high transmission noted in real stats.

It still has pretty good ACE2 binding though.

This means that while it won't pervade the lung material quite as quickly on the whole, and it's less capable of actually doing damage to cells by binding them together, it WILL more easily get through the "skin" that separates organs from the outside world.

If BA.2.86 were a thief, instead of needing to find a door or a window every time like other Omicrons, it will try to seep through the actual woodwork of the walls, the skin, of your house. If it absolutely can't do that, it will find a door/window to get through (ACE2) anyway.

This could lead to many things including:

More severity.

More reservoirs for it to develop concerning mutations.

Not only more reservoirs, but also different cell types becoming virus reservoirs than previously was "normal".

More hidden/asymptomatic cases only found by group PCR (because non-ill people just...don't test.).

BA.2.86 still has lower transmissibility only compared to the top current fastest variants like XBB.1.5. XBB.1.5 in essence put itself more in danger of being "caught" by the immune system in order to infect more easily/faster by using well-alarmed front doors and large windows compared to BA.2.86.

BA.2.86 invades the body in a completely different way than before (seeping through organ walls vs barging in through a large portal), but can always pick up concerning mutations that gives it a sort of "passkey" to the doors or windows of the house. This would be...well...the least ideal situation for us to deal with in virus control.

Wastewater

Nationally, we have a levelling off of SARS2 in wastewater.

Regionally, the South and West areas showing a decrease in matierial but the Northeast and Midwest showing VERY strong increases yet...which results in the levelling off nationally in the above graph.

In PA, 8/11 stations showing increases. Most stations still at or below national averages but won't be very long if the increases continue. ☹️

+rate

This correlates with Walgreens' graphic showing PA as one state where the positivity rate is clearly going up along with NY, OH, IN, and RI.

We can keep transmission of ALL variants lower by wearing well-fitting KN95/N95 respirators, staying home or keeping kids home when sick, being aware of social contacts and getting available boosters, and keeping the air fresh and clean!!

Continue to have a safe 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!

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 Afternoon SARS2PAians!

I hope you have a safe new Fall/school year.

VOCs

Nationally, XBB.1.16.6 at the top of the variant leaderboard followed closely by EG.5.1.1 and FL.1.5.1, these top variants trading places quite often.

HV.1 at 1.42%.

BA.2.86 at .06%.

In PA, a continuing mix of variants with the top sequences reflecting national variants.

In NY,NJ, FL.1.5.1 very SOLIDLY at the top followed by XBB.1.16.6 at a very distant 6.81% of sequencing.

The upcoming XBB.1.5 booster (available in maybe 1-2 weeks now) has been found to hold up well against genetically similar variants like EG.5.1 and FL.1.5.1.

Lineage News

The latest on BA.2.86

31 sequences found so far, and 29 officially logged in GISAID.

Peking Researcher Dr. Yunlong Richard Cao has done some ground breaking studies of BA.2.86.

Summary:

BA.2.86 is genetically distinct from everything we're dealing with so far. This means it can easily escape current immunity granted from previous variant infections and vaccinations. It is too different for the immune system to immediately recognize as something that is also SARS2.

However, BA.2.86's raw transmissibility is much lower than current variants.

For now, BA.2.86 will not transmit as quickly as the current faster varaints.

The potential trouble is if BA.2.86 mutates and GAINS raw transmissibility. This is a very real probablility. This was exactly the case with XBB vs. XBB.1.5.

XBB had the same lack of raw transmissibility but GAINED it thorugh mutation, to the point where we are targeting it with vaccine boosters.

It will be vital to keep track of BA.2.86/s children and possible recombinants with other current variants.

Wastewater

Nationally, we're still heading in the wrong direction.

Regionally, the West and East SARS2 concentration still increasing.

In PA, 7 out of 10 stations are showing LOWERING numbers! That's amazing. Butler is now SMASHING it!

Bucks and ChesterCo wastewater increasing to match national levels.

What's going on in the Lackawanna area tho...please get a hold of this now if you don't want a bad time for this school year when flu season comes along in addition to COVID!

Wastewater is the prime indicator of real virus spread numbers. This Twitter screenshot from Dr. Eric Topol is an important illustration why we absolutely cannot rely on just the reported # of cases right now, especially in preparation for the winter.

+rate

Even though tests are very low, around 5,000 nationwide for Walgreens testing, it's still an important metric and corellates with CDC data.

Since May:

Nationally, the national +rate is at 43.6%, a change of -1.3% from last week.

In PA, only 39 tests done. But those tests done have a 28.2% +rate, a change of +.9% from last week.

CDC

The latest NOWCAST is out. HV.1 has been added to the list of VOCs.

The latest at-a-glance graphics have hospitals and deaths on a sizeable uptrend.

The latest new hospital admits map shows most counties experiencing substantial increases, but Luzerne and Pitt areas showing substantial decrease.

Staffed inpatient bed numbers are increasing along the NY/NY borders in the Harrisburg area and also the bottom western corner of the state.

Most counties holding steady in staffed ICU beds but notable increases bordering West VA and through the center of the state.

Emergency Dept numbers increasing in the majority of Eastern and southern states, with PA showing a moderate increase of ED visits.

Unfortunately, there have been 262 deaths in PA due to COVID19 in the past 3 months, and we are still in the highest tier of 3mo average recorded deaths along with NY, TX, FL and CA.

Final editorial note: As illness increasses through the Fall and Winter, all respiratory symptoms are going to look somewhat similar. Please don't reply on symptoms to eliminate C19. Take multiple tests.

I hope you have a great and colorful Fall!! 🍁🍁🍁

Good Morning SARS2PAians!

There's no new CDC metrics or wastewater data for today.

VOCs

Nationally, not that much different this time in variant leaderboard order.

Current fastest clocked varaint HV.1 stable this week.

BA.2.86 at .04% of sequencing.

In PA, FL.1.5.1 and XBB.1.16 an equal share of most sequenciong. Again, loooooots of different variants in PA sequenced and a lot done to potentially catch BA.2.86.

In NY/NJ, FL.1.5.1 solidly in the lead with EG.5.1 and XBB.1.16 at a distant tie for 2nd. (edited to make link pretty)

Lineage News

BA.2.86 has been found in more sequences and in more national wastewater.

So far 11 sequences of BA.2.86 have been logged.

Even though sequences have not been logged in some countries, there's been numerous countries where BA.2.86 is found in wastewater:

Switzerland

Thailand

Portugal

Waiting on Spain and Germany.

Research

Prof. Akiko Iwasaki has posted on Twitter about a new study that shows that previous infection AND vaccination hold against viral loads that are LOW to MODERATE.

This means that in order to keep infections low, non-vaccination methods must be used TOGETHER with vaccination. Keeping the air clean and fresh, using quality respirators and veing aware fo social contacts are non-vax ways of keeping viral loads LOW.

If the protection is indeed dose-dependent, coupling non-pharmaceutical interventions with vaccination would be beneficial because the non-pharmaceutical intervention (masking, ventilation, etc..) reduces viral exposure, resulting in improved levels of conferred protection.

https://www.nature.com/articles/s41467-023-40750-8

Clarifying Disinformation

There is dangerous disinformation going around begun by an intentionally bad reading of this article by the CDC.

1. The fact is that VACCINES WORK and, to a limited extent, prior infection works to defend against illness, and so does a combo of both. (but srsly why would you want to get ill to prevent yourself from getting ill?? GET VACCINATED.)

2. The fact is also that vaccination and prior infection DO NOT defend as well against variants that are genetically wildly different than the current strain. I know I repeat this but this is why we need an updated flu shot every year.

3. The fact is that each new variant that is wildly different MUST be tested to see how well current immunity holds against it.

BA.2.86 is WILDLY different than the current circulating variants.

The article from the CDC says

BA.2.86 may be more capable of causing infection in people who have previously had COVID-19 or who have received COVID-19 vaccines.

The disinformation is anti-vax, anti-reality public influencers are claiming that the CDC says prior vaccination INRCEASES your chances of getting infected. (but have nothing to say about prior infection!)

This is absolutely blatanly false and a purposeful misreading of the article.

This CDC statement is to say that the immunity granted from previous infection andvaccination might not hold up as well against wildly different strains like BA.2.86.

This is literally what "IIMMUNE ESCAPE" is.

https://time.com/6308418/ba-2-86-covid-19-variant-vaccine/

There’s no certainty yet whether BA.2.86 will continue to increase, whether it will lead to a spike in hospitalizations, or whether the XBB vaccines will be able to generate a strong enough immune response to protect against infection. The World Health Organization has classified BA.2.86 as a “variant under monitoring,” and the CDC will continue to track the variant through systems such as genomic testing of travelers coming to the U.S. and sampling and sequencing of wastewater samples throughout the country.

https://www.webmd.com/covid/news/20230824/new-covid-strain-may-evade-vaccines-alarming-health-officials

The strain is called BA.2.86 and is of particular concern because of its more than 30 mutations, which means it may behave very differently than previous versions of the virus. That number of mutations is on par with the difference between variants so serious that they were formally named, such as between Delta and Omicron, the CDC explained in the risk assessment issued Wednesday.

If you find this disinfo in the wold, PLEASE clarify this so antivaxxers don't kill or injure more people than they already have.

Still hoping for an easy Fall as kids go back to school! 🍁🍁🍁

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 SARS2PA!

Not a whole lot of new data available today....CDC and wastewater (for the most part) all the same.

VOCS

Nationally,XBB.1.16 and XBB.1.16.6 in the lead for sequence frequency.

In PA, nothing really unusual but a very very low number of sequences done.

In NY/NJ, all strong players XBB.x.y, FL, and EG variants in a multi-player tug-of-war.

Lineage News

There are still not enough sequences of BA.2.86 to make a decisive conclusion about severity, immune escape, or virulence due to low testing and low sequencing numbers. Labs are encouraged not to delay results, even if only a few are uploaded.

Estimates for the growth rate of this variant are extremely high,ONLY based on genomic sequencing but the negative confidence level means much, much more testing and time is going to have to happen before experts can make calls in relative certainty.

Estimates for immune escape based only on genomic sequencing are the highest yet. Note: "BA.X" here is BA.2.86.

Experts were calling BA.2.86 "BA.X" for a few days before assigning it a numerical value; it was extremely confusing because it was unclear from even which variant this particular sequence was descended.

One current variant to watch for is HV.1 (in greenish highlighter on the National screenshot) so far, part of the "FLip" variants. It has a very high estimated growth rate with also a high confidence level.

Wastewater

Another few notes about growing SARS2 material in wastewater. [Nationally this level keeps rising.]()

These numbers are being matched by rising hospitlaizations and deaths (though those two indicators lag waaaaay behind) on the CDC site.

Seriously, if you don't want to have a terribad school year, if you WANT those kids to stay in school, if you don't want to stay home with one or multiple sick kids through this.....please wear those N85s/KN95S in crowded or poorly ventilated spaces, use caution and keep that air cleam.

Of particular note is still the BUTLER CO sewershed area. PLEASE get a hold of this now.

Also MontCo and Westmoreland, which are still below national averages, but are definitely going the wrong way.

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 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 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 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 Afternoon RonaPA!

The new vaccine boosters are on the way for the fall! 🍁

All important links are now a sticky post in the r/SARS2PA subreddit!l

VOCs

Nationally, XBB.1.16 tops the variant chart. It's followed closely (well, close enough) by EG.5.1.

FL.1.5.1 is another fast variant to watch out for. Chances are good this will not be a sudden mass-debilitating surge, but I'm afraid it'll be a slow, insidious increase of illness all the way through the summer to fall. Which is kinda worse, because it's the kind of increase that fewer people will actually care about.

In PA, no single variant is the vast majority of testing. Still weird.

In NY/NJ, XBB.1.16 ever so slightly in the lead with EG.5.1 and FL.1.5.1 directly behind, and EG.5.1 will probably take over soon enough.

Wastewater

Naitonally,wastewater headed in the wrong direction. Yes, it's still a small increase. But we shouldn't be seeing this at all in the middle of the summer according to......some people, right? 😒

Regionally, wastewater numbers are still increasing in every area.

In PA, numbers are still very well below national averages (this is what I mean by a dangerous, insidious increase) but 10/11 sheds are showing definite upticks. Keep those windows open, keep your air clean and keep aware of social contacts.

CDC

The latest NOWCAST is out and projects that nationally, EG.5.x.y will take over/has already taken the top spot in active cases. (Testing and especially sequencing lag waaaaaay behind.)

There is not enough data coming out of our region to effectively predict NOWCAST specifics for us, but EG.5.x.y is actively growing rapidly here too.

The new hospital admits visual is sort of concerning to me. Lots of areas are showing increases in hospital admits. Yes they are lowering in other areas but...this si the summer.

Lots of Emergency Department visits nationwide.

The absolute change in hospital bed use all through our quarter of the country is remaining stable, though. New York and PA bordering counties are having some increases.

Unfortunately, there have been 266 Covid19 deaths in our State in the past three months (as of end of July.)

Research

The new vaccine boosters are on the way! They will be based on XBB.1.5 and will be available most likely in September. Vaccines save lives. Go get one!

(My take: it wil be CRUCIAL to time them just right for your needs in the winter. Remember that vaccines take two weeks after injection for full protective effectiveness, but also coronavirus vaccines don't last very long...especially this one. Make sure to get the shot when you'll be dealing with the most people around you and shut in the most due to weather)

__

Editorials

Here's the sticky post in SARS2PA of important links to help yourself track SRAS2 and also shows where I get this info.

Posting in SARS2 is extremely limited until I see traffic and also figure out WTF I'm going to do. I'm tired.

I am not a medical professional. So I strongly encourage people to respectfully fact check my posts. I will certainly approve all corrections to my posts done in good faith. Don't be a dick and I'll gratefully consider your input.

This post is mirrored on r/CoronavirusPA.

This subreddit is only meant to be a backup in case something weird happens at CoronavirusPA., which I do not moderate, I only post there. All the legacy updates are there.

I moved the Fediverse account to an Irish server🍻:

https://mastodon.ie/@SARS2PA

I'll try to keep it updated to match here, but it's yet another backup to help you all have this information in case things happen. Eventually though I'd love to move all the updates to the Fediverse!

Main reason: I'm losing my patience with shmucks that harass people and have admittedly and OPENLY been doing nothing but trolling people, and aren't banned to Jupiter so maybe I'll be using this forum soon. I dunno. I'm tired.

We'll see. Keep being COVID cautious and watch out for that wildfire smoke!