outbreak! (ebola, sars, coronavirus, etc)

a more even-handed summary: https://www.nature.com/articles/d41586-021-03552-w

Friendly reminder that new variants are just that: new. We can’t know if they will be bad or just meh based on sequence alone, nor guess at their provenance. Lots of mutations ≠ very bad.

This Thanksgiving, I remain grateful for genomic surveillance & safe, effective vaccines. https://t.co/Zx0jKoyNh0

— Dr. Angela Rasmussen (@angie_rasmussen) November 25, 2021

Virologists—including myself—are concerned. But I don’t think anyone can conclude based on the data we have so far that we are screwed. There are actions we need to take, starting with providing lots of support to South Africa to enable public health measures and vaccination.

— Dr. Angela Rasmussen (@angie_rasmussen) November 25, 2021

UK have just added 6 southern African countries to the travel red list.

another challenge is that prevalence of Delta is low in South Africa because up until recently, cases themselves were low, so it's hard to tell whether it would actually overtake in a Delta in a country that has a high rate of Delta.

Correct. The low incidence of Delta in SA kinda means that Nu becoming dominant is weaker evidence of it “outcompeting” it when there really wasn’t much to outcompete so to speak. https://t.co/gHzNyLmQOg

— Chise 🧬🧫🦠💉🔜 MFF (@sailorrooscout) November 25, 2021

xpost it's probably the right move, being precautious. just not a fan of how twitter has already moved into "we're back to square one, the vaccines are obsolete" territory. Eric Feigl-Ding is cumming in his sock right now

Some key words in that tweet I cited: "suggests", "might have", "not yet known". otoh, if we panic now, we can avoid the coming holiday rush.

(also, sadly it's occurring in a country that is only 24% vaccinated, which is another confounder)

and one more.

which isn't to say this won't be the Big Bad Wolf, but let's remain calm because it's far from a certainty

Important thing to keep in mind:
- We don't know what other factors may be helping spread, for example, an event or recent behaviour change
- SA has a low vax rate - 28% 1dose, 24% 2dose. Immune evasion may not be needed to spread. Fitness could differ in higher-vax countries.

— Dr Emma Hodcroft (@firefoxx66) November 25, 2021

Lol Christina Pagel is an indie sage doomer who doesn’t work in immunology, vaccinology or anything relevant. I’d go so far as to say her opinion is worth less than Eric Feigl-Ding’s.

is that it is going to take a lot to fully evade these and again, looking at an area of low vaccination and this variant is not a reflection of an area of high vaccination and this variant.

— Chise 🧬🧫🦠💉🔜 MFF (@sailorrooscout) November 25, 2021

Also want to point out for double lolz that she has been a total lockdown doomer and yet was posting about going shopping with covid symptoms the other day “I was convinced we didn’t have it bEcAuSe WeD bEeN sO cArEfUl”

Also

There we go: it's a backlog of antigen tests added to the cumulative total. Importantly, "The estimated number of new cases for 23 Nov 2021 is 868" https://t.co/1v2IAuYTq3

— Edouard Mathieu (@redouad) November 25, 2021

just not a fan of how twitter has already moved into "we're back to square one, the vaccines are obsolete" territory

twitter is talking about cat pictures and missing Doctor Who episodes now, it’s safe to go back :)

🐦[Virologists—including myself—are concerned. But I don’t think anyone can conclude based on the data we have so far that we are screwed. There are actions we need to take, starting with providing lots of support to South Africa to enable public health measures and vaccination.
— Dr. Angela Rasmussen (@angie_rasmussen) November 25, 2021🕸]🐦

⚠️“DOMINANT”… a new variant is worrying epidemiologists—called #B11529–it has just “becoming dominant” in South Africa, displacing even #DeltaVariant (HT @MoshabelaMosa). And our other variant #C12 also growing. B11529 has an “awful spike profile” says @PeacockFlu. 🧵 #COVID19 pic.twitter.com/3c9VXXp1q6

— Eric Feigl-Ding (@DrEricDing) November 25, 2021

Nu's growing fast, probably not quite that fast.

South Africa's whole genome sequencing efforts in November focused on one cluster, initially seen at one the unis in Tshwane, conveniently near much of the nation's biomed expertise. It's not a nationally representative sample.

https://i.imgur.com/uFsq5L2.jpg

Better data will be forthcoming soon, as Nu shares the same signature Alpha had on one of the most common PCR kits (TaqPath), detecting N & ORF genes but false negatives for the S gene.

scariants

lol

“DOMINANT”… this fall on Peacock

sanpaku real quick please never post itt or any others where you feel the urge to play scientist cosplay.

thx, management

Move to extend to all posters and include general "public health expert" in the occupational field

If a success move to politics thread next

lol this approach would kill 70% of football chat stone dead

not that i disagree

I too hate hipster analysis

Dave2398126395 from Wigan amirite

Broke his leg in the cup final so he did

lol

Katelyn Jetelina has typically thorough and nuanced take on what we know and don't about b.1.1.529: https://yourlocalepidemiologist.substack.com/p/new-concerning-variant-b11529

My own gut instinct is that it's going to be bad, but that's only based on what we already know about Nu Metal.

The Bizkit Variant

of course Feigl-Ding is bonering over this

so, i've been following this since it was initially reported, and one thing that stands out to me is that some countries are still doing and saying the "found one case" language. if the pandemic has taught us anything, it's that it's never just a single case, so we're back to square one.

it's just a matter of waiting to see how bad the community spread is, at this point

i've also read a couple reports saying that south africa's vaccination rate is one of the lowest at 28% and that it has one of the worst HIV rates, which they think may have played a part. in fact, one report said they believe "patient zero" probably has HIV. but who knows. usual disclaimer, i'm no expert! just repeating what i've read

also, if it matters, i just saw a video on CNN where fauci says they're trying to get the "precise molecular make up of it" to test it against antibodies to see if it works. so, short of not doing that, what else can you really say about this?

https://www.cnn.com/2021/11/26/health/covid-variant-b11529-us-fauci-wellness/index.html

the other concerning thing is some airlines not being able to withstand another lockdown, which i think could disrupt our world a lot more

uk shutting flights from 6 countries on sunday, so if you've got nu-variant covid be sure to rush back to avoid quarantine. (never understood why they do this)

also lol at travel minister on radio this morning saying that the one thing they've learnt is to act quickly. not the mask thing or the distance thing or the kids in school thing.

good thread

This pandemic has been all about communicating uncertainty and it doesn’t get more uncertain than early data on new variants.
So a few things to keep in mind the next few days and weeks as the picture around B.1.1.529 becomes clearer and why it’s right to be concerned

— Kai Kupferschmidt (@kakape) November 26, 2021

OMICRON

the 1999 video game starring David Bowie?

did they skip Nu and Xi so it wouldn't look weird when they only skip Xi? hmm

I’ve been calling it nu all day, thanks WHO now I look a right prick

I think they should name the variant viruses after fraternities and sororities.

ERMAHGERD

i mean you were saying "the new variant"? you're not wrong

it's pronounced neu!

Fred Durst lobbied WHO, he saw what happened to Corona beer.

OMICRON

― Alba, Friday, November 26, 2021 10:27 AM

Under-rated Mike Oldfield bootlegs I have owned.

want to see a bunch of depressing charts??

https://www.kff.org/coronavirus-covid-19/poll-finding/kff-covid-19-vaccine-monitor-october-2021/

moderna is working on a vaccine that targets omicron:

https://investors.modernatx.com/news-releases/news-release-details/moderna-announces-strategy-address-omicron-b11529-sars-cov-2

Second, Moderna is already studying two multi-valent booster candidates in the clinic that were designed to anticipate mutations such as those that have emerged in the Omicron variant. The first candidate (mRNA-1273.211) includes several mutations present in the Omicron variant that were also present in the Beta variant of concern1. The Company has completed dosing in a potentially pivotal safety and immunogenicity study of mRNA-1273.211 at the 50 µg (N=300) and 100 µg (N=584) dose levels. A second multi-valent candidate (mRNA-1273.213) includes many of the mutations present in the Omicron variant that were also present in the Beta and Delta variants2. The Company has completed dosing at the 100 µg (N=584) dose level and also plans to explore the 50 µg dose level in approximately 584 participants. Moderna will rapidly expand testing of sera from completed and ongoing multi-valent booster studies to determine if these multi-valent candidates are able to provide superior neutralizing protection against Omicron.

novavax has, as well

moderna just doin a little heat check on omicron

yep, still got it

a bunch of depressing charts

true, but they merely confirm once more what was already fairly well known. the newer numbers about vaccinating 5-11 year olds merely reflect their parents' entrenched views, as could have been predicted, since the kids aren't making those decisions.

in the united states we have this guy who has been trying to prevent people from dying, this entire time. as a result, the entire right wing has demonized him, and a sizable portion believe he is actually connected to the antichrist, in a literal way. here is what the man who is trying to save lives is saying, these days, after 2 years of it:

“I’m trying to save lives and the people who weaponize lies are killing people. … So the only question I have is that when you show Tucker Carlson and Peter Navarro criticizing me, I consider that a badge of honor."

“They always throw up those people that make those ridiculous statements, you know, they’re telling people to do things that they’re going to die from and they’re telling me I should go to jail. As they say in my old neighborhood in Brooklyn, ‘Give me a break will you?’”

Last week, Fauci was interviewed as part of a COVID event discussion put on by the Bipartisan Policy Center where he directly addressed the partisan divide over vaccinations, fueled by Republican politicians. He was being interviewed by Dr. Bill Frist, the former Republican Senate majority leader. Fauci told the former GOP leader that he would likely have “heartburn” if he was still in the Senate today, addressing reports that show vaccination rates are substantially higher in U.S. counties where President Biden won versus areas where voters overwhelmingly supported President Trump in 2020.

“You should never have, looking at a map, and seeing that people who are vaccinated fall heavily into one group and people who are unvaccinated fall heavily into another group,” Fauci said. “That is so antithetical with what public health should be, which should be a concerted effort on the part of the entire population.”

And earlier this month, Fauci told CBS that he’s not planning to leave his position until he feels he’s done his job, again going after pundits who have painted him as some sort of COVID-19 boogeyman.

“I’m going to keep doing that until this COVID-19 outbreak is in the rearview mirror, regardless of what anybody says about me, or wants to lie and create crazy fabrications because of political motivations,” he said, pouring cold water on any speculation he might soon retire.

america to the guy who is trying to prevent them from dying: burn in hell you surrogate antichrist!!!

Things must be serious, Johnson seems to have stayed sober for the Omicron briefing :-/

the people who believe in the literal existence of the antichrist think the sanctity of those beliefs far outweigh their own death. in other situations that sort of fixity of belief can be a source of great strength, but in this case it's been imprinted onto a situation where it does nothing but evil. its kind of like when ducklings hatch and instead of imprinting on their mother, they imprint on a human -- who will later chop off their heads and eat them.