Thread by @toba

BA.4 and BA.5 are making their appearance in the US on CDC nowcast. Not sure when to expect them to comprise a majority of cases yet. /647

BA.4 & BA.5 as expected are progressing, approximately at the speed at which Delta took over from Alpha (as I've seen in the data for Massachusetts and the UK) in Illinois, here in the US. They'll likely be the majority of cases in just weeks.
/648
outbreak.info/situation-repo…

The Moderna mRNA-1273.214 booster shot sounds very promising. I'm very curious how the neutralizing titers difference that their press release indicates will stack up against the BA.4/BA.5 variants that will be dominant in the US. /649
investors.modernatx.com/news/news-deta…

WT, D614G, B.1.1.7, B.1.617.2, B.1.1.529/BA.1, BA.1.1, BA.2, BA.2.12.1, BA.5 & BA.4.

Tired of this? The virus is a lot dumber than we are, but it's got power in numbers.

We need to use our engineers. Engineered indoor air quality is our move.

ashrae.org/technical-reso…

/650

The evidence is building that the childhood hepatitis and sometimes liver failure (remember that?) is caused by COVID, in a somewhat delayed reaction.
/651

BA.4/BA.5 are really just a week or 2 from dominance in some areas of the US already based on Walgreens SGTF PCR data. This is about where I thought things were. /652

Large indoor events are dangerous right now. To mitigate, use the EPA Clean Air in Buildings Challenge to make it safer. Your event should be hybrid to ensure people don't have to choose between the benefits of participation and their health. /653

If you get the ear of anyone setting public policy, tell them we need more of this and not just for education - for all public accessible indoor spaces. /654

I wholeheartedly agree with @costrike on his latest article. The costs to us all of pretending the pandemic is over are far above what it would take to actually get it under control.

It's very much a raging fire now, but they turned the alarm off.
/655
worldhealthnetwork.global/blog/pandemici…

Action, as Chris so eloquently pointed out in that article, is how we can end this. Saying it's over didn't work.

I'm not a Christian, but if you are, maybe you can relate to this maxim:

"Faith without works is dead."
/656

New offshoot of BA.2.12.1 dubbed BG.2 is a variant to watch. It may end up competitive with BA.4/BA.5. /657

It looks like BA.4 + S:P681R mutation found, USA. 5 sequences. Unsure if it could be bad sequence reads. Not a surprise though, given how much infection is being allowed to occur here.

P681R was linked to Delta's cell fusion (syncytia) pathogenicity.
/658
github.com/cov-lineages/p…

One of the most famous impacts of current or past COVID is a tendency towards blood clots. Here is one of the effects of that. Anyone who tells you COVID is just a respiratory illness is misinformed. /659

Actual reported IL, USA cases / by IHME's Feb 10th reported cases projection.

3/18: 2.56x
3/25: 4.70x
4/1: 8.47x
4/8: 19.9x
4/15: 28.4x
4/22: 57.8x
4/29: 110x
5/6: 167x
5/13: 205x
5/20: 123x
5/27: 157x

IHME should stop. They always underestimate. /660

As I expected about IHME, their simplistic model's decay curve turned out to be a dangerous fantasy. There are real people out there making life and business plans based on IHME modeled projections without understanding that they are complete crap. /661

Long COVID trends in the UK are very bad and the BA.5 wave will only make it worse. We can expect that US situation is similar but we don't #CountLongCOVID
here. There will lag before the whole story is seen - many sequela take months to appear. /662

BA.4 w/ S:P681R mutation has more seqs that are related and one that's not. I am not a pro at reading these charts but this may be real. 10 sequences now, probably hundreds or thousands of infections to get that many sequences. /663
@trvrb @firefoxx66
github.com/cov-lineages/p…

Nothing really that surprising here. BA.4 and BA.5 have significant reduction in neutralizing antibody binding titers when compraed to previous Omicron variants. This fits conceptually with the BA.4/BA.5 waves we are seeing across the world. /664
nejm.org/doi/full/10.10…

2 more P681R mutated lineages, this time of subvariants of BA.5. Very small number of sequences so far. Will watch. /665
github.com/cov-lineages/p…

In this "personal responsibility" time of the pandemic - which unfairly puts all the weight of protecting oneself onto anyone who wants to be safe - an n95 alone on a plane is not enough. Read Dr. Akima's 🧵 to understand why and what you should do. /666

7 day average test positivity is higher than it was at any time other than first wave and first Omicron wave. This isn't a "normal" time and there is no plausible reason it will stop getting worse any time in the next month. /667

BA.2.75 may turn out to be very important. We don't know yet how it competes with BA.5, but the mutations are concerning and it is growing. @jbloom_lab has a great thread here explaining the (quite complex) interplay of different mutations. /668

A meticulous takedown or the baseless narrative that airplane travel is safe. Air travel has a variety of highly variable and hard to predict SARS-CoV-2 infection dangers. Being in a different row won't save you. Wear the best respirator you have. /669

It seems rapid antigen tests may have a sensitivity problem with Omicron after all. /670

Remember the warnings that the CDC Community levels would warn us with a "high" level only once it was almost too late to avert healthcare system overload? Well, the alarm is finally going off and it was ignored. /671

Positivity rate in Illinois going straight up. Amazing that nobody is talking about this. /672

Yes your cats/dogs can get COVID, and potentially spread it to your family. This headline should read "First Illinois Dog actually tested positive for COVID". I don't believe most people test their pets. /673

We need more of this at a state and local level, as the US federal government isn't going to do it. We need ventilation / filtration regulations too, but a mask mandate is fast to execute and implement. /674

These graphs of air pressure and CO2 on a flight from Denver (high altitude), to cruising altitude (much higher altitude) to Chicago (low altitude) really underscore that taxiing and boarding/deplaning are the most dangerous times on a flight. Cruising's not great either. /675

BA.2.75 aka Centaurus appears to have a growth advantage over BA.5. /676

Yes, children do need to be protected from #COVID19. Clear as day. /677

The variant picture has changed again. BA.5.2 or BA.4.6 may end up dominating in the US rather than BA.2.75. /678

We're not likely to see much in the way of infections going down at least for a few months here in the US, I don't think. CDC & the WH would be foolish to not change course and help boost onshore respirator production and availability to every person. /679

I'm not sure if this neutralization drop will result in significantly reduced efficacy of the BA.5 based booster (planned for US soon) against BA.2.75, but if so it may affect BA.4.6 v.s. BA.2.75 US trajectory. Caveat: only tested with hamster sera. /680

Not testing contacts, even as break-through infection and reinfection are everywhere.

This is irresponsible and cavalierly further victimizes high risk people. Daily lives of the temporarily abled cannot be the only priority. This is a moral stain. /681
cnbc.com/amp/2022/08/11…

That the CDC needs to protect the option to mask. We are nowhere near a point where it's acceptable not to protect the ability of anyone to wear any PPE they want. COVID is airborne and out of control everywhere. Pressure to not mask is violence. /682

Think you're not at risk from COVID death because you're young? Wrong. /683

CDC finally has some online data for long COVID prevalence and it's not looking good - 8% of the country. Omicron can and does still cause long COVID. Who knows whether it is getting worse? I don't, but it could. Take precautions to avoid COVID. /684

The BA.2.75 "Centaurus" variant is likely to grow more slowly in the US than the BA.5 variant did. /685

The failure of congress to provide more COVID funding is, in many respects, Biden's failure to make such things happen by whipping votes. He has not tried, and now Jha is trying to make the medicine go down (sike- failure isn't a medicine). /686
cnn.com/2022/08/16/hea…

Uninsured people are going to get screwed again. It'll be harder than it already is to get Paxlovid. Flu is going to come back which normally stressed healthcare pre-pandemic, and now we'll have a less managed pandemic AND flu. Try not to need healthcare, I guess. /687

Because of our letting it rip abandonment of strategy, newer variants are emerging faster than information about the reasons for their growth advantages over current ones.

Say hello to BA.5.2.1.7 aka BF.7.
/688

I was wrong 2 weeks ago when I said I didn't see infections going down much in the next few months. They're going down, but still very high. Whether this continues or not w/ new variants and new boosters on the horizon, I don't know. /689

That binding affinity on BA.2.75 is really way up there. I think it's actually a bit complex how docking affinity affects the probability of cell entry, but wow. It clearly evolved this way due to a fitness advantage. /690

Everywhere in the first world the authorities know there will be a fall and/or winter wave. However, they're not all doing enough about it. Omicron vaxxes are a great step, but we all need more, not less, other interventions. /691

This is a huge mistake to make the bivalent vaccines only available as boosters. If Pfizer and Moderna won't test them in unvaccinated populations, NIH should. But if mouse data is good enough for a booster, why not primary series? /692

If the Brookings Institute is publishing research that says it's as bad as a third of unfilled US jobs being due to long covid you can bet it's worse than that for the people themselves trying to make it under this COVID minimizing capitalist system. /693

Case data is sadly less solid than it used to be, by a long way.. COVID hospitalizations are going up and have been for some time, while cases remain somewhat flat. It's odd when compared to the biobot sewage data.. but biobot is not everywhere. /694

If you're wondering when to get the BA.5 booster, this thread might be food for thought. I do agree that just about everybody should get it. Interesting timing considerations! /695

Walensky should think a bit about how her top down pushing to reduce protections and cut back guidance are why this is the case. Fix your mess, director. /696

Paxlovid EUA'd for people "[...] who are at high risk for progression to severe COVID-19, including hospitalization or death."

Biden told Americans "you" can get treated (see video @ 2:07). Who truly can be is limited.

"We have the tools" is a lie. /697

Speaking of lies Biden's told us, "the pandemic is over" is one. /698

It's absolutely a politically motivated lie that will lead people to death and debility to bald facedly tell people the pandemic is over. Many can't get paxlovid and the deaths and Long COVID are still everywhere.
"Always forget" 3000 weekly dead. /699

This BF.7 variant's rise was predicted a month ago, and it's now passed BA.2.75 a little ahead of schedule. It could be the US winter wave variant. Image from @TWenseleers modeling quoted in the article.
/700

A variety of variants that are growing in case share highly evade antibody based drugs, for example BA.4.6 evading Evusheld. /701

XBB variant (outbreak.info doesn't seem to have picked it up yet) has profoundly concerning antibody titers. I'm not ready how to express and hesitate to predict what could happen here. A lot of very bad possibilities. /702

What's coming in the next wave is different than previously. There are a lot of variants coming at once that are evolving some of the same mutations. So it's hard to say for sure which will "win" where. US/Europe may get a diverse wave not all BQ.1.1.
/703

For an in depth look at the latest variants we're concerned about and what may happen, read @TRyanGregory's great thread. 🧵/704

The variety of variants convergently evolving toward similar mutations is pretty mind-boggling right now. I'm not sure how to even track this. /705

CDC screwed up by not disaggregating BQ lineages in their variant tracker weeks ago (they did it yesterday). The progression of the group of variants dubbed "pentagon" towards dominance is clear and moving fast. /706

To be clear about this, CDC somehow failed to reveal the growth of these variants until BQ.1 and BQ.1.1 amounted to 11.4% of estimated cases in nowcast. They owe the American people an explanation as to why.

People use CDC data to make vital decisions. CDC was cavalier.
/707

🧵 by @JPWeiland is an introduction to the "pentagon" variant group. It's 5 mutations in a growing group of variants, not 5 variants.

COV-lineages.org, the lineage designation authority isn't covering "variant groups". I think they should.
/708

I agree with Lin's 🧵 here. The bivalent BA.5 boosters are likely still a bit better for current variants and the next wave than it would have been to get another original formula boost. Much better to get this booster (I recommend Moderna) than not.
/709

There's no scientific basis for this assumption that yearly boosters will suffice. It's not the flu. It's absurd to assume the same things we're used to will always work for new situations. /710

An interesting perspective from Peter Hotez on the latest papers on real world bivalent booster elicited antibodies. I'm not despairing yet either. /711

The world should follow Belgium's lead on clean air. I wish the standards were a little stronger, but it'll make a huge difference if adhered to everywhere. /712

Unfortunately, it sure looks like any use of a personal 222nm UV-C device to enable unmasking is pretty low efficacy at the power levels that are within safety limits. That's too bad. /713

I am disgusted that for all the op eds about offramps there are crickets as US hospitals overload. As expected, the community levels system has utterly failed us. /714

Immunofluorescence microscopy for detecting Long COVID microclots. This may be a future standard lab test for post COVID follow up appointments. /715

The "pentagon" variants swarm has taken the lead from BA.5. Get your bivalent booster if you didn't already. /716

Long COVID doesn't just ruin your life. It ruins your finances and career too. /717

To be clear, I think a disabled or chronically ill life is 100% worth living and everyone is an equally important person. Ruining life and career from long COVID are in large part a product of both disease and our ableist capitalist system. /718

Rapid tests don't have to "not count" anymore. How this fits into local, state, and federal case counts I currently have no idea, but if you take a rapid or other home COVID test I encourage you to use this site to report your results. /719
makemytestcount.org

A great report by @PeacockFlu, @CorneliusRoemer, @LongDesertTrain, Hitoshi Sakaguchi, Federico Gueli, and Nicholas Frohber describing the what, the how, and possibly the why of how Omicron's progeny have competed, evolved. Worth a read. /720
virological.org/t/sars-cov-2-e…