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
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/
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: #TuesdayisBluesday
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.
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.
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? 1/ cdc.gov/mmwr/volumes/7…
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 2/
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
🦠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
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.
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
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
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/
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..."
2/ "...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."
"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"
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)
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
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