Experiment: Surface Best COVID19 threads from @ThreadReaderApp

4 Aug
In 2018, CEPI partnered w/ @inovio to advance the development of a vaccine against Middle East Respiratory Syndrome (#MERS) coronavirus.

MERS is part of the same family of viruses that causes Severe Acute Respiratory Syndrome (SARS) & #Covid19

bit.ly/3A9Fna9 (1/7) 🧵
MERS-CoV and SARS-CoV-1, in particular, pose a significant recurrent pandemic threat.

The fatality rates of these viruses are 10-35%, making them 5-16 times worse than SARS-CoV-2 (the virus that causes COVID-19; 2/7)
No vaccine or specific treatment against MERS-CoV are currently available.

However, several MERS specific vaccines and treatments are in development, including 4 vaccine candidates funded by CEPI.
bit.ly/3jl7wUQ (3/7)
Read 7 tweets
4 Aug
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 ⁦@medrxivpreprint

This one going up in Florida where case transmission is highest. It has 484 and 501 like South African and P.1 and potentially partially vaccinene escape medrxiv.org/content/10.110…
Also 681 mutation at the furin cleavage site in the more transmissible UK and delta variants, although to a histidine like UK
I don't think it has a Greek letter designation yet but based on these properties and the fact that we allowed it to take hold due to low vaccination rates in the South, (and their place in the Greek alphabet), I propose ζυ
Read 5 tweets
4 Aug
Covid (@UCSF) Chronicles, Day 504

To me, the most confusing time in the pandemic was May 2020, as we exited lockdown and nobody quite knew what they should & shouldn’t do (clean the mail? touch the dog?).

But now is giving May 2020 a run for its money. (🧵1/25)
Today, a smorgasbord of some of the most confusing issues: Delta, masking, vaccine efficacy, vax mandates, boosters.

Bottom line is that my thinking has changed. Six months ago, I felt like I understood all of the key variables when it came to the virus & vaccines. And… (2/25)
…when I learned that a variable had changed w/ Delta, I assumed nothing else had.

But now I see that it’s best to assume that nearly every parameter is different – usually for the worse. That creates cognitive vertigo, but it matches the facts on the ground. (see below.)(3/25) Image
Read 25 tweets
4 Aug
COVID Update: The increasingly assertive position of requiring vaccinations has clear moral grounds.

The view of DeSantis that vaccination status isn’t anyone’s business has a lot to answer for. 1/
Earlier today @BilldeBlasio introduced a policy that to enter certain venues like restaurants & gyms, proof of vaccination would be required. 2/
People fall into 3 categories with differing interests.
Group 1- Those who are vaccinated
Group 2- Those who can’t get vaccinated or get fulsome protection from a vaccine if they do
Group 3- Those who choose not to get vaccinated 3/
Read 20 tweets
3 Aug
People often ask me what I find so fascinating about blue and what it has to do with science, so here‘s a story about one particular blue from right here in Berlin:
Around 1706 alchemists in Berlin accidentally discovered a new blue. Johann Jacob Diesbach was working in the lab of Johann Konrad Dippel trying to make a red pigment, carmine. But he used some potash contaminated with animal blood by Dippel and ended up with a blue pigment.
They quickly realized the blue was stable and easy to make and that meant it was worth a fortune. Because good blue pigments were rare. Ultramarine, for instance, was laboriously made from lapis lazuli (shipped most prominently from the Badakshan region) and incredibly expensive.
Read 12 tweets
3 Aug
There's a group of pesky unvaccinated ruffians I want to discuss

You know -- no lottery tickets will get them vaccinated

They are recalcitrant

I have one of them in my house

Yes, the under 12

How best to protect them?

Empirical data can show us the way

Short thread
Despite stark differences in vaccinations by state,

In Louisiana, 0% of kids under 12 vaccinated
In Florida, 0% of kids under 12 vaccinated

Even in high vax Massachusetts

0% of kids under 12 vaccinated

So if we're in a pandemic of the unvaccinated, are these kids in trouble?
Actually, while vaccination rates for kids under 12 are identical (0%) across states,

Infection numbers are not

In Massachusetts, about 250 kids under 10 years of age infected last week

In Florida, it was about 9,000

In Louisiana, it was about 1600

Read 6 tweets
3 Aug
VACCINATION UPDATE: 70% of all adults have now had their first shot.

Vaccines are up today 25% over last week.

Now we now need to build on the momentum to do more. 1/
What’s happening?

It may not be over-simplifying things to say that when the crisis seemed over, getting vaccinated seemed more optional. 2/
It also meant that some Republican leaders were willing to play politics or allow others to tolerate their colleagues playing politics.

A good way to take credit from Biden is to question vaccines. What’s the harm after all? Cases were declining. 3/
Read 11 tweets
2 Aug
Hello, I have news!
For 18 mos, I’ve been a part-time “Covid correspondent” for @WIRED @WIREDScience.

Extremely thrilled to say I'm now joining the @WIRED staff as senior writer for health, expanding my beat to all aspects of public health, global health, medicine and disease.
I could not imagine a better landing than working for science editor @KaraPlatoni, with the outstanding team @jetjocko, @mrMattSimon, @GregoryJBarber, under the leadership of @glichfield, @Mstreshinsky, @sarahfallon, @brbarrett, at a time of great change and promise for @WIRED.
This is a chance to *slightly* loosen the pandemic’s grip on my life and fold in all my other obsessions: AMR, polio, STDs, fungi, emerging infections; health policy, technology, politics; and the long reach of unintended consequences. I start 9 Aug, and I can’t wait to begin.
Read 10 tweets
1 Aug
Let’s talk about Provincetown. There has been a lot of discussion about a recent COVID outbreak in Barnstable County, MA which is where P-town is located. Why all the excitement? And what does it mean for you?
Provincetown was once a whaling port and Portuguese fishing town, but it morphed into a party mecca many years ago, and with mask mandates ended and everyone ready to party after a year of lockdown, I’m pretty sure this past 4th of July was a wild scene
There was a COVID outbreak centered on Provincetown. About 3/4s of the Massachusetts population has been vaccinated. About 3/4s of the people testing positive (346/469) were fully vaccinate. 5 people were hospitalized, 4 of whom were fully vaccinated
Read 18 tweets
1 Aug
🦠9 (all linked) new Delta cases in Brisbane over last 24h
🦠Not found the source of the medical student tutor who infected the ISHS schoolgirl's household
🦠Intermediary link between 2cases from overseas flight 29th June from Singapore & 1st ISHS case, not been made
🦠Genomics shows the exact same variant in all those cases
🦠Sunshine Coast is being looked at hard as a likely source.
🦠Largest single-day new Qld case tally in almost 12 months. [message to take this seriously is being pushed hard]
🦠Five schools at risk now – all have different arrangements
🦠New cluster linked to a Karate school at Ironside
🦠Only 11,468 tests yesterday-this is NOT ENOUGH for this urgent need
🦠"NSW is doing 100,000 a day – let's see how we can go" – CHO on testing numbers
Read 5 tweets
31 Jul
I am convinced that at this stage of the pandemic, misleading and irresponsible headlines from otherwise reputable news outlets are a major source of damaging misinformation.
Just one example: Yesterday that @UPI posted a story with this deeply misleading headline.

What they meant is that, conditional on becoming infected and developing bad enough symptoms to get tested, a vaccinated person transmits readily. But that's very rare.
This headline, or variants thereof, appeared everywhere, from Voice of America to local news outlets to the @nytimes.
Read 14 tweets
31 Jul
1/ Here's another quiz for budding epidemiologists

The Guandong Delta outbreak was meticulously investigated. Initial report of 1000x viral load came from there

A finding that hasn't been discussed much is the seeming shorter incubation period (panel b)

2/ In 2021 delta it was only 3.7 days (vs 5.6 days for 2020 outbreak).

This would have an impact on a key transmission dynamic factor we often look for: "serial interval periods" (time between symptom onset for index case vs subsequent case in a contact tracing investigation)
3/ What you are trying to estimate from observable symptom intervals is underlying mean generation time.

tangent: If you find negative serial intervals as in COVID, it's a sign of asymptomatic and presymptomatic spread.
Read 6 tweets
31 Jul
Without looking it up,

What is Rt in Arkansas right now?
Rt is actually 1.2 (0.98-1.5). It is taking 12 days (4 generations) to double

here's some math

If Rt (aka Reff) was 5, it would mean that it would go up 5*5*5*5 = 625 TIMES in 12 days, not 2x

3/ Now, we aren't living in an R0 world. Even though it may feel like it sometimes

People are vaccinated (despite breakthrough infections)
People are infected (despite reinfection risk)
People have changed behaviors

But "Delta variant is as transmissible as Chicken Pox"(R0~9)??
Read 8 tweets
31 Jul
Perspective: Here's the most revealing set of graphs I've seen in a long time. The UK's latest surge started about 33 days before the surge here in the US. 1/thread of 5
If the US case trend follows that of the UK, we'll have more than 200,000 cases a day by early September, possibly many more. See how the lines on the right are almost perfectly parallel. 2/5
What was somewhat reassuring is the relatively modest increase in the UK hospitalization rate. This suggests that because of the UK's very high rate of vaccination of seniors, the proportion of infections that are life-threatening is much lower. 3/5
Read 5 tweets
31 Jul
Lots of confusion about what Provincetown outbreak & CDC guidance mean

Mainly: how to think about spread among the vaccinated

And as importantly, what we know and what we don't

So a short thread
First, the P-town outbreak unusual

Many thousands of people (some unvaccinated) showed up to celebrate July 4

Leading to packed bars, clubs, and lots of mixing of vaccinated and unvaccinated folks in tight quarters

Ideal conditions for COVID spread

And COVID did spread

And there were a lot of infections, including among vaccinated folks

We've seen this before -- Singapore airport, Yankees clubhouse

Key issue is: did vaccines fail to

1. Prevent infection?
2. Prevent spread?
3. Prevent severe illness?
Read 8 tweets
31 Jul
Many thanks ⁦⁦@chrislhayes⁩ for hosting me tonight ⁦@allinwithchris⁩ as I break down what’s working and what’s working not as well with our COVID19 vaccines vs delta variant
First point: there are 2 “performance features”

1. The vaccines were released through EUA because of their high level of protection vs symptomatic + severe illness + death.

2. Later studies from Israel UK showed vaccines also halted asymptomatic infections virus shedding
Versus delta, that first performance feature mostly still holds, with the possible exception of those on immunosuppressive Rx or old age who might benefit from a 3rd immunization as now practiced in Israel 🇮🇱 for example
Read 6 tweets
30 Jul
I’ve heard concern over the past few days about the impact of Delta, and questions about new guidance from the CDC. The bottom line is the virus has adapted and we must adapt too. Delta is different, but our vaccines are still doing their job. 1/thread
Earlier this week, CDC issued new guidance that everyone—vaccinated and unvaccinated​​—should wear masks indoors in areas with high rates of Covid. And last night, information was published referencing new evidence and new challenges posed by Delta. wapo.st/3lfovuy 2/
Delta is at least 2x as transmissible as the original virus, and appears to be among the more infectious viruses, estimated to spread about as readily as chickenpox. But Delta can be controlled, just as we’ve controlled chickenpox​​—through vaccination & other measures. 3/
Read 22 tweets
30 Jul
What has hair on fire in Atlanta HQ @CDCgov ?
Excerpts (thread) cdc.gov/mmwr/volumes/7…
"In July 2021, following multiple large public events in a Barnstable County, Mass., 469 #COVID19 cases were id'ed among Massachusetts residents who had traveled to the town during..."
"...July 3–17; 346 (74%) occurred in fully vaccinated persons. Testing identified the #DeltaVariant in 90% of specimens from 133 patients. Cycle threshold values were similar among specimens from patients who were fully vaccinated and those who were not."
3/ "Vaccine prods rec'ed by persons experiencing breakthrough infections were Pfizer-BioNTech (46%), Moderna (38%), & Janssen (16%)...
"79% reported signs or symptoms, w/the most common being cough, headache, sore throat, myalgia & fever."
Read 5 tweets
30 Jul
COVID Update: An internal document from CDC shows Delta is a whole “new war.”

First real estimates of spread & breakthrough cases. And a clear sense of why CDC policies are changing.

More here soon. 1/
Point 1: Vaccines work. They dramatically reduce the risk of cases (8x) & even more so serious cases (25x). But they don’t work perfectly.

With 165 million fully vaccinated people, they estimate 7,000 breakthroughs/day. 2/
A thorough discussion of breakthrough cases & vaccine efficacy is here in this discussion with what Pfizer sees in the data. Worth listening to to understand. 3/
Read 19 tweets
30 Jul
"Almost 4 million cases were reported to who last week”, says @DrTedros at @WHO presser on #covid19. “On current trends, we expect the total number of cases to pass 200 million within the next two weeks. And we know that is an underestimate.”
@DrTedros @WHO "On average, in five of @WHO’s six regions infections have increased by 80%, or nearly doubled over the past four weeks”, says @drtedros.
“In Africa deaths have increased by 80% over the same period. Much of this increase is being driven by the highly transmissible Delta variant"
@DrTedros @WHO "So far, four variants of concern have emerged and there will be more as long as the virus continues to spread”, says @drtedros
"The rise is also driven by increased social mixing and mobility. The inconsistent use of public health and social measures and inequitable vaccine use"
Read 15 tweets
30 Jul
The CDC document that was discussed in @washingtonpost today washingtonpost.com/health/2021/07… is now on line: context-cdn.washingtonpost.com/notes/prod/def…
The WashPo shared it with me before publication for reactions, and I'm quoted. Some thoughts follow. (1/13)
My overall view: we knew much of what's in here, but there's some new information & analysis. In some cases it's brand new, in others it clarified something we knew before. In virtually all cases, the new stuff's a bit worse than I expected. Here are the key findings: (2/13)
1) Delta is much more infectious than the original: they estimate an Ro of 5-9, vs. the 2-3 for the original, which makes Delta "as transmissible as chicken pox." We've been estimating Ro of ~6 for Delta, or ~2x as infectious as original. It may be a bit worse than that.(3/13)
Read 13 tweets
30 Jul
1/ Like many others, I've been frustrated that we haven't seen the data behind the CDC's new recommendations. Parsing exact wording in transcripts is🤦

We're told there will be a release tomorrow but thanks to the @washingtonpost there's an internal CDC document to parse tonight
2/ The article by @yabutaleb7 @carolynyjohnson @JoelAchenbach is here:

TY @bijans for spotting the "full pdf" download button.
3/ what do we learn?

The mysterious "other data" for high viral load in breakthrough cases came from a 4th of July outbreak in Provincetown (Barnstable, Mass) where the “vast majority” of the new cases were among fully vaccinated individuals

cc @zeynep
Read 16 tweets
30 Jul
Leaked CDC slides on delta variant got you concerned?

I find the slides insightful & largely reassuring

Bottom line

Delta variant is a problem

Vaccines prevent vast majority of infections, transmission

And nearly all hospitalizations, deaths


So let's talk about what's in the slides about the delta variant

First, it is really, really contagious

Like more contagious than Ebola, Spanish Flu and probably chicken pox

Really contagious

Second, it appears to cause more serious disease if you get infected

I've been worried this is the case but certainly not sure

The data here is suggestive but not definitive

So reasonable to say delta probably more severe

Read 9 tweets
29 Jul
T cells were supposed to be the "on-demand" reserves to kick in after the normal decline of neutralizing antibody (nAb) levels, providing protracted protection. But several new reports point to nAbs as key.
1. @NEJM report on breakthroughs w/ low nAbs
2. @ScienceMagazine report on giving vaccine -induced nAbs to protect in animal model model
3. The Israeli data on diminished protection for age >60 several months out from vaccination, due to Delta
T cells were especially supposed to be helpful, relatively unaffected by variants, as this study and others support (pre-Delta)
cell.com/action/showPdf… @CellRepMed
Read 5 tweets