Experiment: Surface Best COVID19 threads from @ThreadReaderApp

Good Morning!

Here Is All You NEED TO KNOW About The New COVID-19 Booster Shots Planned for This Month.

Thank You For Reading! 🧵⬇️

@LaurieADen As in they can get up to three updated vaccines. They don’t go back to the older ones.

@LiteraryMouse And it hasn’t been approved by the FDA yet and is still being reviewed so frankly I’m not sure how long approval will take. I’m going to take the chance to protect myself now at the moment.

1/ What are the factors driving the mysterious slowdown in Medicare cost growth?

It's been a longstanding dinner conversation among health policy folks, and I have one idea to add to the mix that I haven't seen discussed yet..

2/ There were lots of theories batted around in the article and the followup from @sangerkatz

My fav: "Talk Therapy Actually Works" (@ZekeEmanuel)

Policymakers setting expectations of cost control inhibit investments and behaviors that drive cost growth
nytimes.com/2023/09/09/ups…

We saw similar unexplained slowdown in healthcare costs during the *ultimately unsuccessful* Clinton health reform efforts.

The slowdown happened almost immediately in 1992, even though nothing had happened yet, other than campaign talk

(@jrovner can prob give history on that)

Veel heisa over “mijn bewuste acties om zaken onder de pet te houden”, volgens @mauricedehond. Bronnen: mails, een dia, en een shot uit een interview. Voor hem HET bewijs dat ik me het recht toe eigende om de wereld voor te liegen. Dat is nogal wat. Laten we ff echt kijken.

Voorafgaand aan de meeting met Dr Fauci was er een publicatie die concludeerde: komt uit vleermuizen, kijk maar naar de fylogenie. Daarvan zei Kristian A: dat kun je met fylogenie niet bewijzen (wat klopt). Is makkelijker om daar even overleg over te hebben (mail 1 februari 2020)

De mogelijkheid van lablek was door bronnen uit de Amerikaanse overheid (intelligence) gesuggereerd. Die hadden gevraagd om eens naar het genoom te kijken vanuit die optiek. Aangezien ik vind dat politiek en wetenschap niet gecombineerd moeten worden, maakt mij dat extra scherp

The @FDA is expected to authorize updated COVID-19 vaccines any day, & @CDC’s ACIP will then vote on 9/12. Once recommended, COVID vaccines will enter the commercial market for the first time. Will you have to pay for them? 🧵

Generally, if you have insurance (private or public ), you are in good shape. COVID vaccines — and any ACIP recommended vaccine (for flu, etc.) — should cost you nothing.

If you are uninsured? You once again may face costs to access recommended, life-saving interventions.

Until now, the federal government has purchased all COVID vaccines and provided them for free, regardless of insurance coverage or ability to pay.

This ensured what amounted to universal coverage of COVID-19 vaccines during the pandemic emergency.

I'm excited to announce a new paper with @MLReichmuth and @C_Althaus, out now in @PLOSPathogens!

We used phylogenetics & modelling to investigate the introduction & expansion of #SARSCoV2 Alpha & Delta variants into #Switzerland & to simulate different interventions.

1/17

First, we wanted to estimate the number of times Alpha & Delta were introduced into Switzerland before they were dominant.
For this we used sequences: we looked for where Swiss Alpha/Delta seqs descend from non-Swiss sequences - coming to Switzerland from elsewhere.

2/17

We looked at two ways of counting these introductions:

Liberal: every Swiss sequence coming from non-Swiss sequences is an introduction
Conservative: only the first Swiss sequence in a subtree of mixed-Swiss-non-Swiss sequences is an introduction

3/17

A balance between procoagulants and anticoagulants underpins hemostasis.

Science behind the Study: 1/10

#hematology nej.md/3QZxlfQ

Hemophilia, a form of disrupted hemostasis, is caused by dysfunctional variants in genes encoding the procoagulant factors VIII (causing hemophilia A) and IX (causing hemophilia B). 2/10

In NEJM, Matsushita et al. report the results of a trial in which a first-in-class drug restored hemostasis in persons with hemophilia with inhibitors. Read the full results: 3/10nej.md/3L0y9wW

We can’t keep neglecting the intersection of human, animal, and environmental health. This article underscores the increasing health threats we’re facing. It reminds me of a RMSF cluster we faced years back in AZ…(1/n) washingtonpost.com/health/interac…

A few years back we began seeing very sick pediatric patients admitted with RMSF (like multiple children in families, etc.) and many from tribal lands. To be blunt, RMSF is a really nasty disease - it hits hard and fast, despite being quite treatable. (2/n)

The number of patients we saw led to a close working relationship with local public health colleagues (shoutout to those relationships!) who took the reigns in identifying why we were seeing an influx of this tickborne disease (3/n)

HOW LONG DOES IMMUNITY LAST? To COVID vaccines or infection? We do not really know but there have been some really nice papers lately that give us more information. Please remember immunity divided into antibodies (which can come down & not work as well against variants)

IgA is one in the nose & mouth ("mucosa") that is raised by shots (vaccines) to certain extent but rise higher after natural infection; IgG is the one that is "humoral" or in the bloodstream. Many threads on here about cellular-mediated immunity: B & T cells cover all variants

This recent preprint is really important and summarized by @florian_krammer below in depth. Main take-aways: Breakthrough infections induce IgA (we knew) but protection from vaccine long-lasting even against former variants to severe disease/mortality

https://twitter.com/florian_krammer/status/1696249545854775705

Here are data from new XBB.1.5 spike deep mutational scanning by @bdadonaite in our group

Go to see how mutations affect:

1⃣ Neutralization by human XBB breakthrough sera

2⃣ Spike-mediated pseudovirus entry in 293T-ACE2 cells

3⃣ Spike affinity for ACE2dms-vep.github.io/SARS-CoV-2_XBB…

It will be a few weeks before we finish & post pre-print for study, but we wanted to share data now for those interested in interpreting current SARS2 evolution.

Measurements were made using lentiviral deep mutational scanning () with XBB.1.5 spike.sciencedirect.com/science/articl…

Experiments map sites in XBB spike where mutations escape neutralization by sera of humans w recent XBB infection

(Antibody response depends on exposure history, so escape may differ for other exposures not studied here)

Greatest escape is at sites 473, 357, 455/456, 420

1) Our preprint describing 3 years of our PARIS study is live. There are a few interesting observations I wanted to highlight. This was the work of a large team but the lead is really @VivianaSimonLab medrxiv.org/content/10.110…

2) First, here is an overview of the spike titers of all the study time points. We had 501 individuals in the study and measure their anti-spike binding antibodies on a regular basis.

3) The first take home message is: Antibody decay after mRNA vaccination is biphasic. First a steep drop, then a stabilization phase. The graph here shows titers after the primary immunization series. Blue is previously naive individuals, orange is hybrid immune.

A short 🧵on a recent study by @MaggieLind2 with @MHitchingsEpi @datcummings Albert Ko et al. Data show that immunity induced by vaccines, prior infection or both (hybrid) protects against SARS-CoV-2 infection when viral exposure is low to moderate (1/)

nature.com/articles/s4146…

Question being asked: What is the risk of becoming *infected* with SARS-CoV-2 after developing immunity following a vaccine, prior infection, or both if exposure to the virus is very high, moderate, or low? They did not study the severity of symptoms. (2/)

How? The authors used the existing database of the Connecticut Department of Correction, where infection data based on high frequency of testing for SARS-CoV-2 on ~9300 residents across 13 facilities were available. (3/)

evidence review "Stay-at-home orders, physical distancing measures, and restrictions on gathering sizes were repeatedly found to be associated with significant community-wide reductions in SARS-CoV-2 transmission" royalsociety.org/-/media/policy…

"Within care home settings, strict cohorting of staff alongside residents and restrictions on visitors were frequently found
to be associated with reduced SARS-CoV-2 transmission among residents and reduced outbreaks within care homes".

"Similar for school closures and other school-based measures but effectiveness was more varied, time-dependent, and often contingent on
the adherence to the measure or measures implemented (for example, mask wearing) and the targeted age group of school children".

This is HUGE news! The FDA has officially approved Abrysvo, the first RSV vaccine designed for use in pregnant individuals to prevent lower respiratory tract disease (LRTD) AND severe LRTD caused by RSV in infants from birth through 6 months of age. Let’s talk about that! 🧵⬇️

On August 21st, the U.S. Food and Drug Administration approved Abrysvo (Respiratory Syncytial Virus Vaccine), the first vaccine approved for use in pregnant individuals to prevent lower respiratory tract disease (LRTD) and severe LRTD caused by respiratory syncytial virus (RSV)

in infants from birth through 6 months of age. Abrysvo is approved for use at 32 through 36 weeks gestational age of pregnancy and is administered as a single dose injection into the muscle.

Two new papers @NatureMedicine and @JAMAInternalMed shed light on #LongCovid at 2-years. But there's no shortage of known unknowns.
Reviewed in a new Ground Truths (link in my profile, because that would be it X-suppressed)

Links to the new reports
@NatureMedicine by @zalaly and colleagues
@JAMAInternalMed nature.com/articles/s4159…
jamanetwork.com/journals/jamai…

@NatureMedicine @zalaly @JAMAInternalMed Summary of previous 2-year Covid follow-up studies

For Science! 🥼🧬🦠🧫⚗️🔬💉

🎨: @Sepiapaws

IN CASE YOU MISSED IT BEFORE.

IT IS TIME FOR AN UPDATE THREAD. Many of you have had questions in regards to COVID-19 booster schedules and updated boosters. I have some news for you!

Here is all you NEED TO KNOW! 🧵⬇️

On April 18th, the FDA amended the emergency use authorizations (EUAs) of the Moderna and Pfizer-BioNTech COVID-19 bivalent mRNA vaccines to simplify the vaccination schedule for most individuals. This action includes authorizing the current bivalent vaccines to be used for all

Covid (@UCSF) Chronicles, Day 1249
While good data are far harder to come by than in the past, it’s clear that we’re experiencing another Covid uptick. Today: what that means and how you might choose to alter your behavior in response. (1/25)

First, the evidence for the uptick (I don’t say “surge” since I associate that with the massive surges of the past):
This curve of hospitalizations (a reasonable proxy for the amount of Covid in the community) shows a definite, but relatively mild, upward trend. (2/25)

Alas, one can't look at any single measure to quantify an uptick anymore. But all arrows now point in the same direction: up (⬆ wastewater,⬆ hospitalizations,⬆ deaths,⬆test positivity). Even my fave measure, @UCSFHospitals’ asymptomatic test positivity rate, is no… (3/25)

For the AJ Leonardi fans recent quote posts of me (he blocked me, so it took others to point them out🙏; I've returned the favour now), I'll add that the definition of "immune" or "immunity" does not imply never getting infected. It's a term scientists use & it can differ from..

..that used by you in the wider community.
To us, if I can speak for all scientists (!I can't🙂), it means your body has mounted an immune *response*. That response - such as the one _most humans_ mount to SARS-CoV-2 after infection (whole virus) or vaccination (mainly Spike...

..protein) generally make future infection by the same thing, less severe. Having immunity (producing or 'mounting' an immune response) protects you from serious disease (hospital-level stuff) & death. It may protect you from less severe disease too. Not all vaccines are as..

I wanted to provide assessment of spike amino-acid mutations in new highly mutated 2nd generation BA.2 SARS-CoV-2 variant

This is analysis for those (like me) scientifically interested in SARS2 evolution

(Anyone else is completely within reason to ignore this variant right now)

https://twitter.com/LongDesertTrain/status/1690989522035617792

Full analysis of the mutations is in these slides:

Analysis is based mostly on deep mutational scanning experiments

TLDR: lots of antigenic change, and some interesting RBD mutations (addition of N-linked glycan & deletion in receptor-binding motif)slides.com/jbloom/new_2nd…

First, to emphasize, only THREE sequences of variant identified so far. There is not currently evidence of wide transmission.

As this thread outlines, people who study SARS2 evolution may want to pay attention to features of this variant. Everyone else can ignore if they wish.

1) I feel this paper by Mattias Forsell's group is often overlooked but shows something very important: Binding antibody to SARS-CoV-2 spike - in the absence of strong neutralizing antibodies to a new variant - predict protection from mortality. .thelancet.com/journals/lanep…

2) Individuals with the lowest antibody titer have the highest risk, individuals with higher titers are protected. Of course, we are not talking about protection from infection or protection from symptomatic disease by binding, non-neutralizing antibodies here, but protection....

3) ...from severe outcomes. Why is this important? Neutralizing antibodies (which likely are the main protective factor when it comes to protection from infection or symptomatic disease) often drop steeply against new variants while binding antibodies are in most cases.....

Them: The COVID-19 vaccines don’t work. The majority of hospitalizations are fully vaccinated.

Me: Base Rate Fallacy would like a word with you.

I’m seeing some bad takes circulating about this AGAIN so let’s talk about it. ⬇️ 🧵

Let’s try something. Most people get this question wrong. Can you solve it? A town has only two colours of car: 85% are blue and 15% are green. A person witnesses a hit-and-run and says they saw a green car. If witnesses identify the colour of cars correctly 80% of the time, what

are the chances the car is actually green? You might have said 80%. A lot of people do. The correct answer is 41%. The reason so many struggle with this question is due to the Base Rate Fallacy. Our brains tend to ignore statistical information (aka base rates) and focus on

Good Morning. ☀️

🎨: @PrismPaws

Speaking of making it EVERY pathogen’s problem…

IN CASE YOU MISSED IT BEFORE.

IT IS TIME FOR AN UPDATE THREAD. Many of you have had questions in regards to COVID-19 booster schedules. I have some news for you!

Here is all you NEED TO KNOW! 🧵⬇️

On April 18th, the FDA amended the emergency use authorizations (EUAs) of the Moderna and Pfizer-BioNTech COVID-19 bivalent mRNA vaccines to simplify the vaccination schedule for most individuals. This action includes authorizing the current bivalent vaccines to be used for all

How should we be thinking about COVID at this moment?

Last week, I had an op-ed in @BostonGlobe to lay out what I think is a pretty reasonable way to think about it

But first, here's the state of COVID

Thread

bostonglobe.com/2023/07/31/opi…

Infections are rising in every part of the US based on wastewater data

This is exactly what many of us expected this summer

How bad is it?

Well, its up about 3X from lows of mid-June

But still only a third of last summer's peak

So its up. But not a lot.

So what to do?

The most important thing you can do is ensure your immunity is up to date

Getting an annual vaccine (for most folks) and 2X/year for vulnerable folks makes a lot of sense

But also: SUPER important to consider getting treated if you get infected

Treatments are still free!

1) In a recent study with @gabagagan, Anass Abbad, Juan Manuel Carreño and @VivianaSimonLab we wanted to see how much crossreactivity exists in the post-COVID era to spikes beyond SARS-CoV-2. We expressed all the spikes shown in the tree below and got going.

2) We ran ELISAs with longitudinal samples from people who had received the primary vaccination series of COVID-19 mRNA vaccines including naive individuals (grey) and people who previously had SARS-CoV-2 infections (black).

3) Titers actually went up for all sarbecoviruses and even for most other betacoronaviruses (with the exception of nobecoviruses where there was no increase in reactivity for one of the two spikes tested).

The EG.5 variant continues to show a growth advantage in the latest US genomics surveillance, from 11->17% in past 2 weeks
FL.1.5.1 also on the rise. The XBBs are on the wane. https://t.co/50Eq338zXLcovid.cdc.gov/covid-data-tra…

EG.5.1 rise seen in many other places, nicely summarized in @kallmemeg 's thread about the new @UKHSA report
https://t.co/Ba3GZmwVWF

https://twitter.com/kallmemeg/status/1686785744508010501

Highlighting the evolution of these variants from XBB in @dfocosi's convergence map. The added F456L mutation may reflect impact of monoclonal antibody treatment escape mutation (see ) https://t.co/bZtWCt1oMH

https://twitter.com/LongDesertTrain/status/1543610358753099777