Replying to @united_oz and @MarcTennant

So it is worth it for everyone, even if you weren’t going to die in the first place 😁

this thread is sobering and informative with respect to what overloading health services means in terms of individual experience...worth popping into google translate fir non-German speakers

the pathologies of science Twitter are on full display in this thread featuring a non-expert blasting an epidemiologist for "stealing" an idea (a minor statistical insight) that is part of epidemiological basic understanding

The @CovidGenomicsUK Mutation Explorer http://sars2.cvr.gla.ac.uk/cog-uk/ is now tracking the combinations of spike substitutions known to reduce binding by either casirivimab or imdevimab, the constituents of the therapeutic antibody cocktail Ronapreve

South Africa: Christmas update Hospitalizations15% week over week, 0.4% from yesterday. Gauteng Province 1.8% week over week0.1% from yesterday We are 2+ weeks from peak in cases and plateauing is not complete. Longer tail to this than usual.

NEW: @UKHSA Variant Technical Briefing Technical Briefing 34 https://gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings… Updated Omicron Risk Assessment https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1046614/12-january-2022-risk-assessment-SARS-Omicron_VOC-21NOV-01_B.1.1.529.pdf… A

South Africa Hospitalizations15% week over week0.3% from yesterday Gauteng Province2.4% week over week0.7% Long plateau: Ventilators are last to peak (17% of Delta peak) Should see meaningful declines later this week.

this exchange is unedifying in style, but the content principles play - scoring past output for accuracy- seems important to online science discourse, particularly under conditions of high uncertainty. How could we build this in a less divisive, discourse undermining way?

Attention festival goers!!! Obviously festivals have started to happen again, so here are some reminders to stay safe! #BurberryTB #foryou

Jim also traces this political sidelining of science & evidence-based assessment to the following tweet from the 17th, which presages DfE's "enough of experts" approach. 3/3

...in which he notes that the Telegraph published a piece on the 22nd by Universities Minister @michelledonelan in which she riffs on the updated HE guidance which was published on the 20th. 2/3

Googling "Risk assessments should never be used to prevent providers delivering the full programme of face-to-face teaching and learning that they were providing before the pandemic" reveals that @jim_dickinson posted a piece on this on the 22nd... 1/3

against this survey data you might set actual uptake figures in France, various Canadian provinces, and Germany after the introduction of passports

and I didn't say we *should* mandate them. I simply pointed out that when considering the impact of passports on uptake we should probably look at *actual uptake* in response to *actual mandates* in addition to survey data, which may or may not translate into action, no?

so, observational data has weaknesses- so does survey data, but it's there and we should look at it. On your second point, yes, that is important, we should study that, if we have no data we can't factor it into decision. Third is separate issue/factor to weigh.

I get that you are against mandates. I am responding to the *reasons* you give for this. Those reasons should be evidence based, right? and they should also not include the claim you are trying to justify. That's all.

pleased to share our recent work w/ @ArielKarlinsky, @ojwatson92, @LucaFerrettiEvo, & @ArisKatzourakis. tl;dr we found continued circulation of SARS-CoV-2 from late jan 2020 to sep 2021 in iran despite >100% attack rates in 11 provinces. 1/ https://medrxiv.org/content/10.1101/2021.10.04.21264540v1

2/ a particularly worrying sign that natural infection didn't do much to stop the spread in many provinces despite several waves of infection. another key finding was that the estimated IFR increased by a factor of ~2 over the course of the epidemic (from wave 1 to 5).

3/ we show that nationwide excess mortality (EM) follows the same pattern as confirmed covid deaths but is higher by a factor of ~2. As the epidemic progressed, the timing of the peak EM across different provinces were more in sync, suggesting local measures didn't stop the surge

4/ across different ages, the third wave in oct 2020 & the current wave with Delta had the largest impact on younger age-groups. Age-stratified excess mortality also shows a log-linear increase in population fatality rate with age (signature of covid IFR).

5/ more importantly, we see a significant drop in population fatality rate for >75 age-groups during the Delta wave very likely due to a good vax coverage for individuals in these age-groups (not so much for the rest of the population -- only ~3% were vaxxed before Delta)

6/ we also compared our analysis to the number of confirmed & suspected daily hospital admissions in each province. this data is in very good agreement with the pattern of province-level excess mortality. black=suspected orange=confirmed hospital admissions (look at the peaks!)

7/ in fact the agreement between hospitalisation & EM is so good that the ratio of confirmed nationwide hospital admissions to confirmed deaths matches the ratio of province-level suspected hospital admissions to excess mortality (huge under-reporting in some provinces).

end/ finally, and this is the key point, at the same time that Manaus was experiencing >75% attack rates, some provinces in Iran had equally high ARs. Since then, some provs reached >100% AR but natural immunity DID NOT stop the spread --> Everyone should get vaccinated ASAP!

"reveal myself"? really? this is the account of http://SciBeh.org, the human being typing this right now is Ulrike Hahn. What is the relevance of that to the very specific piece of information I sought to inject in your thread for the benefit of readers?

How could my identity possibly affect the evidence I provided and gave sources for? Does knowing my name make those articles more or less relevant in any way? and, if yes, by what mechanism?

I literally only responded to *one* point in your overall argument/set of tweets. You somehow seem to assume that it is not possible to try to accumulate facts in order to come to a decision,

I *literally* came to respond to your subtweet because I *retweeted* your thread with this information account, which also means it gets indexed in the http://SciBeh.org database. Along with high quality pro arguments- because this is what that account is for.

NBA player says he doesn’t need vaccine… 40-thousand likes and 1.4 million views. Scientist/doctor corrects NBA player… 4-thousand likes. We’re so screwed…

depending on interpretation, and interpretation of current UK Covid policy, Singapore is not "the first country" to be trying this 7/7

t's lizard-people-level crazy to think the JCVI meant this: https://twitter.com/BallouxFrancois/status/1454980187976871941?s=20… 6/7

this is a reasonable thing to consider: https://twitter.com/apsmunro/status/1454792162000916481?s=20… 5/7

https://twitter.com/dgurdasani1/status/1454383106555842563?s=20… 4/7

t can't possibly be what the JCVI meant with the respective bullet points in their minutes. Here a selection of that debate: 3/7

The JCVI seems to have at least considered the value of childhood infections as providing boosters for adults, sparking intense debate about the ethics of this, whether this makes epidemiological sense, or whether, in fact, it would be so crazy and nonsensical that ...2/71

interestingly the Singapore Health Minister also mentions "boosting through mild infections" - a concept that is currently generating much furore in the UK in the wake of the release of the JCVI minutes on child vaxx decisions 1/n

Lots of useful international examples in the comments to this post And more from @cmmid_lshtm here: https://github.com/cmmid

I am not American either, but I would imagine that it is decision relevant when the costs of policies not only hit some citizens more than others, but particularly when they hit groups likely to be under-represented or even excluded from making those very decisions

Where is the money for ventilation in schools? Well said @GeorgeMonbiot

The first episode of the @thejabgab http://thejabgab.com is LIVE!! Join me and the fabulous comedians @nazeem_hussain and @calbo as they chat about the Delta variant, vaccines …. and cows? with experts @DrKGregorevic and @BedouiSammy! Search your fav platform or...

Dear Europe, couldn't find this graph anywhere so I plotted it myself in case anyone would like to know.#Europe #vaccinated #COVID19 @VaccinationEu

We can also include the number of cases for the same period.

BEST. VIDEO. ALL. YEAR. Please share with friends how the mRNA vaccine works to fight the coronavirus. NOTA BENE—The mRNA never interacts with your DNA . #vaccinate (Special thanks to the Vaccine Makers Project @vaccinemakers of @ChildrensPhila). #COVID19

Finally, both days will feature breakout discussions to focus on case studies and contribute to manifesto drafting. 6/6 Full schedule here:

Deepti Gurdasani will share insights from her experience as a science communicator on Twitter in the pandemic. And the panel will discuss how we can build and sustain systems---particularly online spaces---that can support the role of collective intelligence in Sci Comm 5/6

Day 2 with keynote Deepti Gurdasani followed by a panel with * Dr Joshua Becker, UCL * Dr Niccolo Pescetelli, New Jersey Inst. of Techn. * Dr Aleks Berditchevskaia, NESTA * Dr Philipp Lorenz-Spreen, Max Planck Institute Human Development * Prof Sune Lehmann, Uni. of Copenhagen

Kai Spiekermann will speak the need for science communication and how it supports the pivotal role of knowledge in a functioning democracy. The panel will focus on what collective intelligence has to offer. 3/6

Day 1 with key note Kai Spiekermann followed by a panel with * Arend Kuester, Springer Nature * Dr Geoffrey Supran, Harvard University * Prof Timothy Caulfield, University of Alberta * Dr Kai Kupferschmidt, Science Magazine * Prof Cecília Tomori, John Hopkins University 2/6

Join us this week at our 2021 SciBeh Workshop on the topic of "Science Communication as Collective Intelligence"! Nov. 18/19 with a schedule that allows any time zone to take part in at least some of the workshop. Includes: keynotes, panels, and breakout manifesto writing 1/6

Charting the COVID-19 spread in Australia

Opening of the WHO Global Evidence to Policy Summit with @DrTedros. #E2PSummit2021

The state of the UK’s statistical system 2020/21 by @StatsRegulation Thank you! See the report: https://osr.statisticsauthority.gov.uk/publication/the-state-of-the-uks-statistical-system-2020-21/pages/8/

Big Thread coming on ‘returning to on-site teaching’. Intended mainly for universities (because I work in one), but may also be useful for schools. Mute thread if not interested. I’ll base it around real questions I’ve been asked. 1/

transparent public discourse is *not* easy, nor automatic. We need better tools, better community norms, and, generally, a better understanding of online discourse

and that any attempt to bring to the table a fact that runs counter to a particular conclusion is some kind of lobbying. That really -to me- is not how science should work, nor is it how science-based policy should work.

Growth advantage and extrapolation of AY.4.2 based on Sanger Institute data in the UK (multilevel multinomial model). Based on this data AY.4.2 seems to have a ~20% growth advantage/week over AY.4 and will become dominant in the UK in December.

The number of people dying after both vaccines is rising, says Boris Johnson The number of people dying after both vaccines is bound to be high because so many are vaccinated says Vallence Seriously?

Finally, both days will feature breakout discussions to focus on case studies and contribute to manifesto drafting. 6/6 Full schedule here:

Deepti Gurdasani will share insights from her experience as a science communicator on Twitter in the pandemic. And the panel will discuss how we can build and sustain systems---particularly online spaces---that can support the role of collective intelligence in Sci Comm 5/612

Day 2 with keynote Deepti Gurdasani followed by a panel with * Dr Joshua Becker, UCL * Dr Niccolo Pescetelli, New Jersey Inst. of Techn. * Dr Aleks Berditchevskaia, NESTA * Dr Philipp Lorenz-Spreen, Max Planck Institute Human Development * Prof Sune Lehmann, Uni. of Copenhagen

Kai Spiekermann will speak the need for science communication and how it supports the pivotal role of knowledge in a functioning democracy. The panel will focus on what collective intelligence has to offer. 3/6

Day 1 with key note Kai Spiekermann followed by a panel with * Arend Kuester, Springer Nature * Dr Geoffrey Supran, Harvard University * Prof Timothy Caulfield, University of Alberta * Dr Kai Kupferschmidt, Science Magazine * Prof Cecília Tomori, John Hopkins University 2/6

Join us this week at our 2021 SciBeh Workshop on the topic of "Science Communication as Collective Intelligence"! Nov. 18/19 with a schedule that allows any time zone to take part in at least some of the workshop. Includes: keynotes, panels, and breakout manifesto writing 1/6

A kit that enables users to disable misinformation: The #DigitalEnquirerKit empowers #journalists, civil society #activists and human rights defenders at the #COVID19 information front-line. Find out more: http://sdf.d4dhub.eu #smartdevelopmentfund #innovation #Infopowered

This one is worrying and I’ve not said that since delta. Please get vaccinated and boosted and mask up in public as the mutations in this virus likely result in high level escape from neutralising antibodies

Some of the docs who stepped up and got vaccinated early when we didn't have the data we do now. What we all knew: protecting moms protects babies! All have had their babies by now!

I would love to start a thread of photos of all of the #medtwitter Doctor Moms who have been vaccinated while pregnant to show that they AND their babies are healthy! Can we do it? The public is asking!

An illustration of communicating risk with 'less severe' variants: [thread] Assume Omicron is 4x more transmissible than Delta. [1] Assume Omicron leads to 1/3 less admissions than Delta. [figure below] Assume 1 in 100 cases of Delta are admitted to hospital.

Stolen from Reddit. May be of some use.

The UK published all cause death data from 1/2/21-9/24/21 split out by vaccination status/age group: https://ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/datasets/deathsbyvaccinationstatusengland… In young (10-59yr), all cause deaths in 2 dose group are ~2x higher than unvaccinated. Does this mean the vaccines are "killing more than they save?"

As I will show in this thread, this conclusion is erroneous, an artifact of Simpson's paradox, since the 10-59yr is far too wide an age range, and vaccination rate and death risk vary substantially from the younger to older end of the age range.

To investigate this, I pulled some public data to try to adjust for the hidden age effects within the 10-59yr age group First, note how widely the annual death rate per 1000 varies significantly from the young end to older end of the 10yr-59yr age group https://ourworldindata.org/grapher/death-rate-by-age-group-in-england-and-wales?time=latest&country=~England+and+Wales

Here we put it in a table we will use to do the relevant calculations.

Next, consider the variability in vaccination proportion over time across the various age groups, with the younger end of the 10yr-59yr age group having far lower vaccination rates than the older: https://coronavirus.data.gov.uk/details/vaccinations?areaType=nation&areaName=England…

Here, I will focus on August 1, which is the end of week 30 with the annotated 1.82x ratio. Note the extreme variability in vaccination rate, with those in their 40's and 50's much higher vaccination rates than 20's and 30's, and with few teens vaccinated as of 8/1/21.

Also, note the population size of each semi-decade group is not the same, so we also consider the proportion of total UK population within each age group, here for UK from 2019: https://populationpyramid.net/united-kingdom/2019/

Here we add it to our spreadsheet with the other data.

Since we are only looking at the 10-59yr population, I normalize the proportions of each semi-decade age group, to yield the age distribution within the 10-59yr cohort.

If we multiply the % vaccinated by % in that age group, we can get the proportion of the 10-59yr population the are (1) vaccinated and (2) in that age group.

By subtracting from 1, we get the proportion of the 10-59yr population that are (1) unvaccinated (haven't gotten 2 doses) within each age group. (This is sufficient for our purposes -- later I will include more nuanced analysis incorporating single-dose vaccinated)

Next, we will normalize each of those two columns by dividing by the respective sums (62.2% and 37.8%) to get the age distribution within the vaccinated and unvaccinated cohorts in the 10-59yr cohort.

To make easier to see, I plot these age distributions. Note that the vaccinated in the combined 10-59yr cohort are MUCH older than the unvaccinated.

As well as Tom's new one (B.1.1.529), C.1.2 seems to be spreading in S Africa - C.1.2 was the one with lots of worrying mutations first reported in August... plus cases in S Africa suddenly increasing again in the middle of their summer.

Some info about B.1.1.529 from the South African research community. Thanks so much for sharing.youtube.comHealth Department briefs media about a new so-called super-variantThe Health Department is this hour hosting a briefing about a new so-called super-variant of the coronavirus. South African

so no cases of B.1.1.529 cases in UK as of Mon 22nd Nov? do you know when the S-gene drop out PCR results for 23-25th Nov will be available?

Could they go one better and actually produce a Ritter Sport chocolate with the theme of Germany's longstanding vaccination booklets? That would be amazing.... https://twitter.com/AllerbesteWelt/status/1467921713535070213?s=20…Quote TweetStephan Lewandowsky@STWorg · 7 Dec 2021Very cool ... but this should have happened in early 2021. @CorneliaBetsch @PhilippMSchmid @philipplenz6 @stefanmherzog @SciBeh twitter.com/UnimogCommunit…

agreed- BUT, one of the real things I'm noticing trying to engage with anti-vaxxers in Germany is that they seem to think they are a huge group ("we the people"). So public campaigns that bring together all of Germany's most visible companies actually seem useful to me. We'll see

The boosters aren't stalling though. The problem is refusal of even the first dose. Unfortunately rejection has time to become solidified because there was never a proactive campaign--until now, about 10 months too late.

indeed... but it is still very welcome now, with German vaccination campaign stalling!

Very cool ... but this should have happened in early 2021. @CorneliaBetsch @PhilippMSchmid @philipplenz6 @stefanmherzog @SciBehQuote TweetUnimog Community@UnimogCommunity · 7 Dec 2021A very impressive campaign in Germany: within a few days, 150 companies and organizations have agreed to support the efforts pro vaccination. We support the #vaccination campaign and wishes everybody - vaccinated or not - the best health. Take care! #zusammengegencorona

and every now and then we have to watch a clip like this to be reminded what all of this is really about. This pain and suffering is happening in one of the richest countries in the world at a time in the pandemic when we *know* exactly what to do to avoid it

... and she was on her way to the cemetery and she was angry that nothing was done during the summer in anticipation of this. Populism kills. It's pretty much as simple as that.

because I'm worried they will bring something from school and now I'm on my way to the cemetery. It's outrageous what things are like here, it shouldn't be like this, and if they had just done something about it in the summer it would all be half as bad."

This is horrible indeed. For context: AfD vote share 31% (plurality) https://en.wikipedia.org/wiki/Erzgebirgskreis_I…, double vax uptake 44.8%, worst in Saxony https://coronavirus.sachsen.de/ueberblick-coronaschutzimpfungen-in-sachsen-9874.html… @PhilippMSchmid @CorneliaBetsch @SciBehQuote TweetFlorian Krammer@florian_krammer · 27 Nov 2021Das hat mich jetzt grad zum Weinen gebracht. Es tut mir so leid. twitter.com/SvenMobrep/sta…

this clip got me too- for non-German speakers. She is asked whether she is "concerned". Her response: of course I'm concerned, I'm double vexed, I'm waiting for my booster vaccination, my husband died of Covid, I was in hospital, now I'm avoiding my grand children

Agree. But there is a reason for the distrust (AfD first and foremost). And this was knowable and a concerted campaign from Day 1 about vaccines would have made a difference. When I was in Berlin for 3 months this year I never say anything about vaccines being available.

But the German East-West divide in vaccination rates also shows how difficult it is to do something about it because the real issue is not wealth or knowledge but trust23

and every now and then we have to watch a clip like this to be reminded what all of this is really about. This pain and suffering is happening in one of the richest countries in the world at a time in the pandemic when we *know* exactly what to do to avoid it

... and she was on her way to the cemetery and she was angry that nothing was done during the summer in anticipation of this. Populism kills. It's pretty much as simple as that.

this clip got me too- for non-German speakers. She is asked whether she is "concerned". Her response: of course I'm concerned, I'm double vexed, I'm waiting for my booster vaccination, my husband died of Covid, I was in hospital, now I'm avoiding my grand children

This is horrible indeed. For context: AfD vote share 31% (plurality) https://en.wikipedia.org/wiki/Erzgebirgskreis_I…, double vax uptake 44.8%, worst in Saxony https://coronavirus.sachsen.de/ueberblick-coronaschutzimpfungen-in-sachsen-9874.html… @PhilippMSchmid @CorneliaBetsch @SciBehQuote TweetFlorian Krammer@florian_krammer · 27 Nov 2021Das hat mich jetzt grad zum Weinen gebracht. Es tut mir so leid. twitter.com/SvenMobrep/sta…

I do not understand the continued narrative that makes it sound as if *extant legal systems* don't already provide the framework for assessing whether rights are unduly infringed by vaxx passports and mandates. This is exactly what constitutions are for.Quote TweetAllyson Pollock@AllysonPollock · 5 Dec 2021Thread below worth a read. Some points and more I raised in my talk at TromsoUniversity this week Re covid passes and mandates. We Need the the human rights specialists to engage with public health science and to work together to show stupidity and folly of vaccine mandates twitter.com/JobbingLeftieH…

Servicetweet für Labore: #Omicron wird auch von 3 PCR Systemen in den angegebenen Genen detektiert.

There is nothing new about this idea at all In fact, this is one of the reasons we don’t vaccinate children against chicken pox in the UK It is a totally reasonable thing to include as a point of discussion

It must be so frustrating to work on an expert committee and have non-experts totally misunderstand and misrepresent your work for their agenda The comment in the JCVI minutes about circulating virus in children providing immunity boosting to adults is a great example

Some tips on interpreting models (from an @SMC_London talk I gave a few months ago):

B.1.1.529 seems to have gone from 0.1% to 50% in just a couple of weeks, when it took Delta several months to achieve that..!! Brace up folks..!! #NuVariant

Many thanks ⁦@AymanM⁩ ⁦@AymanMSNBC⁩ for hosting me on ⁦@DeadlineWH⁩ I’m concerned about the steep acceleration of omicron in US especially in NY NJ as announced by ⁦@CDCDirector⁩ this is not good news, here’s why:

1. Paxlovid from Pfizer won’t be available in quantity for several weeks to Rx patients with breakthrough infections or the unvaccinated

2. Vaccine protection even with 3 doses is not as good vs omicron, around 70-75% range and this means unprecedented number of breakthrough symptomatic covid infections. This situation may even be worse for those who got their 3rd dose a couple of months ago due to waning immunity

3. Therefore we should expect breakthrough symptomatic covid among our vaccinated health care work force, this will place stress hospitals ICUs and health systems. I hope it doesn’t break. I’ve suggested consideration of 4th dose for health care workers but no one listening

4. Finally we should expect lots of kids hospitalized based on what we’ve seen in Africa, UK. Worried about our nation’s children’s hospital.

6. I was really hoping we would get the holidays in before the omicron wall hit. Doesn’t look like it

I should state I catagorically did not 'discover' B.1.1.529 - the first seqs were uploaded by teams from Botswana and HK, followed shortly by SA. Several other people had independently spotted this (including SA health authorities). I just posted the public Pango request first...

We have completed our first experiments on neutralization of Omicron by Pfizer BNT162b2 vaccination elicited immunity Manuscript available at https://sigallab.net and should be available on medRxiv in the coming days

We now have B.1.1.529 sequences (designed at @nextstrain clade 21K) up in our Africa build. You can check them out below. These are from South Africa & Botswana - you can see the high number of mutations. CoVariants focal build & updates will come ASAP.

Hi Journalists! Are you interested in covering the new B.1.1.529 #B11529 variant? Here's a link to a TABLE with the names & institutions of THE PEOPLE WHO DISCOVERED THIS VARIANT & SHARED THEIR DATA via the @GISAID community. PLEASE REACH OUT! https://dropbox.com/s/vb6k9l6ekl24k0g/gisaid_hcov-19_acknowledgement_table_2021_11_26_00.pdf?dl=0

because I'm worried they will bring something from school and now I'm on my way to the cemetery. It's outrageous what things are like here, it shouldn't be like this, and if they had just done something about it in the summer it would all be half as bad."

This is horrible indeed. For context: AfD vote share 31% (plurality) https://en.wikipedia.org/wiki/Erzgebirgskreis_I…, double vax uptake 44.8%, worst in Saxony https://coronavirus.sachsen.de/ueberblick-coronaschutzimpfungen-in-sachsen-9874.html…

Interested in #causalinference? Learn from top experts in the field. Summer courses offered at the Harvard T.H. Chan School of Public Health in June, 2022. Key Topics in Causal Inference Target Trial Emulation Stay tuned for more details. https://causalab.sph.harvard.edu/courses

Not a thread, but key point: 6/6

In populations with high vaccine coverage, wouldn't we actually *expect* many infections to be breakthroughs? What would this mean for the impact of unvaccinated-only testing programs as vacc. rates increase? These questions frame our new preprint. 1/ https://medrxiv.org/content/10.1101/2021.10.19.21265231v2

By definition: when no one is vaccinated, 0% of infections are breakthroughs. When everyone is vaccinated, 100% of infections are breakthroughs. So what happens in between? Our study examines this question using a modeled population with mixed vax & prior infection status. 2/

Two things happen as vaccination rates increase: 1. Total infections decline—even imperfect vaccines reduce transmission. 2. The % of those infections that are breakthroughs increases, hitting 50/50 at 68% vax coverage in this scenario (35% prior inf. rate, VE≈2x mRNA). 3/

This 50/50 tipping point was surprisingly insensitive to prior infection rates, ranging from 63-75% vax coverage. This means we should stop being surprised when breakthroughs constitute a large % of infections… …particularly in places (e.g. universities) w/ 80%+ vax rates. 4/

The @nextstrain http://CoVariants.org focal build for 21K (B.1.1.529) is now live. http://nextstrain.org/groups/neherlab/ncov/21K… As previously, the long branch leading to 21K is clearly visible, making it hard with current sequences to tell much about the evolutionary history.

I was @scoilidepps today looking at ventilation. Built in 60’s with dual aspect classrooms for cross ventilation. Handy outdoor ‘corridors’ too. All designed to prevent the spread of TB. School has also bought HEPA filters for classes. Re Covid it has managed pretty well so far.

Clearly we haven't "kept borders closed forever" - most borders have been open for many months now. The question is whether we urgently close a particular border now. "kept borders closed forever" = straw man (and I say this as a researcher on fallacies of argumentation)

True, but what’s the rationale? Early on it was to ensure more ppl are vaccinated. But now the majority is vaccinated & high risk groups have received boosters. There will always be new variants as long as sars-cov-2 is circulating. We cannot keep borders closed forever.

How it started 3 months ago— How it’s going. #COVID19

Bingo. The numbers appear contradictory but they’re not if you do the maths on it. Looks like this pic will need to be spread a bit in the near future again.

A snapshot of the top of the vaccination table - highlighting a few countries of interest

Reminder that reactive travel bans typically slow but don’t stop importations. If new B.1.1.529 variant genuinely more transmissible/can evade immunity to some extent, reasonable to assume already undetected cases in other regions... 1/

In December, many countries reactively banned travel from the UK (https://theguardian.com/uk-news/2020/dec/20/europe-bans-travel-from-the-uk-over-new-covid-strain-what-we-know-so-far…), but this didn’t stop the rise of B.1.1.7 across the continent (https://nytimes.com/interactive/2021/04/09/world/europe/europe-coronavirus-variants.html…). 2/

"Let's aim to be like Denmark in 2022."

I thank researchers from and for sharing information with @WHO & the world about B.1.1.529 variant that has been recently detected. We will convene our TAG-VE again today to discuss Everyone out there: do not discriminate against countries that share their findings openly

and this still sounds needlessly aggressive in 2021.... I doubt this is the best way to build accuracy promoting science discourse online...

This may have sounded somewhat naïve in early 2020, but by now, I would have expected that anyone with an interest in covid-19 might have acquired some basic notions in infectious disease epidemiology. 1/

The new covid sceptic All Party Parliamentary Group on Pandemic Response and Recovery is backed by Gupta and Heneghan's Collateral Global to the tune of over £30,000. £5,000 in financial benefits plus £25,501 - £27,000 benefits in kind (CG is acting as their secretariat).

"Herd immunity may not even be possible to reach with this virus". 'By the time you get enough people vaccinated, you get a new variant that arises that escapes previous immunity', says clinical epidemiologist Dr Deepti Gurdasani.

If you re-encounter the threat again, memory cells allow you to skip a bunch of time and effort in finding the right B and T cells and produce a larger and more rapid immune response to protect you than if you didn't have them.

When those B and T cells are identified, they get signals to divide and differentiate into highly active cells that can go on to clear the threat and a portion of them get left behind as memory cells that can recirculate, live in the bone marrow, lymph nodes, or in our tissues.2224

You already have a bunch of B and T cells specific to a bunch of things that you have never seen and probably never will see. The task of the immune system is to select the correct B and T cells to deal with the infectious threat.

This occurs in the precursors to B and T cells in the bone marrow and thymus respectively. There they undergo quality control checkpoints to prevent autoimmune disease in case the random combination of genes that they used specifies a receptor that reacts to self too strongly.

There are a few genes encoding specific segments of the antibody and TCR called the variable, diversity, and joining regions (VDJ). B cell precursors and T cell precursors splice these segments together randomly to give rise to an antibody or T cell receptor.

It takes time and energy to replicate our genome, so making it encode for each individual antibody and TCR all in one would be kind of insane. Instead, we evolved a smarter way: we encode them in pieces and splice them together in a process called V(D)J recombination.

There's a similarly ridiculous number of T cell receptors. The issue is: all that information has to be packed into a genome and our genome only has about 3 billion base pairs. We need a massive and diverse repertoire of antibodies and T cell receptors to address infections.

The human genome encodes about 23,000 proteins. This number will vary a bit with the source you check but it's around there. Both T cell receptors (TCR) and antibodies are proteins. However, it's estimated that you can make about 1 quintillion antibodies: https://scripps.edu/news-and-events/press-room/2019/20190123-burton-antibodies.html

I think this was probably well-intentioned but in the end, I think it's creating confusion and is leading to some poor messaging so let's discuss how your immune system deals with some difficult genetic challenges for a minute

So, no, vaccines do not change your DNA. Your immune system has already done that part long before you got the vaccine (it's always doing it). It's more like your immune system is a key factory and the vaccines are bringing them a lock they can test keys against.

This is also not limited to the vaccine- any infection we encounter will do the same thing. It's how we evolved to get around a massive genetic and bioenergetic challenge and it's brilliant and it's happening all the time regardless of any vaccines we get.

From today's Ontario Science Table's COVID update slide deck:

A reduction in rates of severe disease and death relative to cases is not a new pattern! Remember first chart in this thread? Here’s the exact same pattern, but in UK. Did we say "Delta appears to be milder"? Nope. What changed was levels of immunity, here mostly via vaccines.

1. Evidence that while admissions are growing fast, they are growing less fast than cases, which suggests weakening severity 2.Evidence that the % of admissions that require ventilation or ICU is far lower in the omicron wave, than in earlier waves

But is this believable? If we remove the booster effects, LSHTM are still suggesting the omicron wave would be more severe. And that seems increasingly at odds with the emerging evidence from South Africa. I don’t have time and space to do justice to it here, but it includes:

Severity of Omicron Wave = Current Delta Severity + Impact of Shift to Omicron - Impact of More Boosters And in the low-escape scenarios at least, those latter two terms are roughly netting out, leaving the severity of the omicron wave similar to the recent history, with delta.

While the recent experience includes some booster effects, it won’t include much from boosters in the first half of December, nor in the second half, or in January – all of which are included in the LSHTM model. So in summary we have the following equation:

…be similar in severity to the recent experience of delta. But hang on, didn’t we say that LSHTM were implying that omicron increased severity, not left it the same? We must be missing something, and we are: the impact of more boosters going into arms.

We can estimate that the current UK ratio of admissions to infections is around 0.9% (assuming that we detect around 50% of cases, and noting that the ratio of admissions to cases is around 1.8%). So for the “low escape” scenarios, LSHTM are estimating that the omicron wave will

So the LSHTM model is in a similar place to my made-up numbers above – their estimate is that omicron will result in higher severity overall. We can confirm this by looking at the ratio of hospitalisation to infections in their output scenarios. (note: my table, not theirs)

If we do the same calculations, looking at (1-VE) and how this changes, we can estimate that in the “low escape” scenarios, severity will go UP by a factor of ~1.6, and by a factor of ~2.2 in the “high escape” scenarios (note this varies a bit by vaccine status, but not by much)

With all this in mind, we’re ready to look at what LSHTM assumed for their VE under different scenarios and vaccine statuses (and note they have modelled prior infection as having similar protection to 2 doses of vaccine).

Now these were all just made-up numbers to show that an escape variant doesn’t necessarily drive less severe outcomes… it all depends on what happens to VE vs. severe, or rather to (1 - VE vs. severe) in relation to the movements in (1 - VE vs. infection)

…that aren’t prevented – from 5% of the pre-vaccine total up to 20%. Meanwhile the number of infections not prevented is only increasing by a factor of 3 – from 30% up to 90%. Hence the severity ratio increases by a factor of 4/3 (from 1.7% to 2.2%).

And what’s happening here is that while VE vs. severe disease dropping from 95% to 80% might not seem that bad – it’s only 15%, compared to the 60% fall in VE vs. infection (from 70% to 10%). But that drop from 95% to 80% is really a fourfold increase in the severe infections

What happened here? Well, mostly what happened is that we were focused on VE when we should have been focusing on (1 - VE). As has been explained by @BristOliver and others several times, that’s often the number that really matters, and which drives outcomes.118159

Infections are now reduced by 10%, to 900, and severe cases are reduced by 80%, to 20. So the severity ratio is now 20/900 = 2.2%. So that’s…. oh. It’s gone up, not down. Check the figures: that’s right. Our new variant with a lot of breakthroughs made severity worse??

So this is maybe a bit like omicron – it permits a lot more infections, but still has a (we hope) a decently strong effect against severe disease. Given that it’s permitting a lot more (typically mild) infections, the severity ratio should have fallen, right? Let’s check:

But now let’s see what happens when we introduce a new variant, with significant immune escape. Let’s assume our VE vs. infection is nearly wiped out, dropping to only 10%. The VE vs. severe disease is better preserved, but still drops to 80%.

Here the severity ratio has been reduced to 5 / 300 = 1.7%. So far, so good – the vaccines have substantially reduced the severity of the disease, as well as the number of infections.

Now suppose we have a strongly effective vaccine, which has a vaccine effectiveness (VE) of 70% vs infection, and 95% vs severe cases. Once this vaccine has been rolled out, for the same amount of exposure, we’d expect infections to reduce to 300, and severe cases to only 5.

Let’s start by supposing that pre-vaccine, we have 1000 infections, of which 100 are severe (requiring hospitalisation). So I’ll report this as a severity ratio of 100 / 1000 = 10%.

However, this rosy picture is not guaranteed. To explain this, I need to get pen & paper out, and go on a small mathematical diversion – but don’t worry this is all primary school maths (addition and multiplication), there’s no log scales or differential equations in sight.

The hope is these effects make the omicron wave significantly less severe on average. Omicron’s large immune escape means it has many more susceptibles to infect than delta, so can spread faster and further – but a lot of these infections will be mild.

a) Higher levels of immunity in the population (from vaccines / boosters and infections) b) Higher levels of immune escape by omicron –permitting many more reinfections and ‘breakthrough’ (post-vaccine) infections, which tend to be milder on average.524203

So the best assumption is that it is similar to delta on that count (and we should consider scenarios on both sides). But even if its intrinsic severity is similar to delta’s, the experienced severity of an omicron wave may be quite different to previous waves, due to:

So it’s really a game about severity, and that’s where things get a lot more uncertain. At the moment I don’t think we have any solid evidence that omicron is intrinsically more, or less, severe than delta – i.e. the impact it would have on an unvaxxed / uninfected population.

Still, I expect a large wave of omicron cases in the UK, even if it doesn’t stay at a constant 2-day doubling period. NPIs and voluntary behavioural adjustment may also help to flatten the wave, but that won’t stop a very large number of people getting infected.

But it wouldn’t be totally surprising if these rates of growth did change over time, as omicron works its way into different networks and localities that have different levels of immunity. We might well see some similar surges and pauses as it spreads across the UK.

There are also some hints from South Africa and Denmark that high rates of growth may be slowing after an initial surge. I’m not close enough to the data to give a confident explanation of what’s going on – please follow @lrossouw and others for that.

n the meantime, omicron has continued its path towards world dominance, and is now firmly established in the UK, with an apparent doubling time of around 2 days – although with some hints that it may have slowed very slightly in recent days.

In case you missed it, there’s a great explanatory thread here from @BarnardResearch. But in summary their scenarios are looking at 20-35 million omicron infections, and peak hospitalisations somewhere between half and double the January 2021 level.

Most of what I said in last week’s thread (see below) remains true. And I was somewhat gratified to see that the great minds at @cmmid_lshtm, using far more computer power than the back of my envelope can provide, came to very similar conclusions:

Another week, another long thread on omicron. This time, I’m still concerned, but perhaps a bit less worried than I was – mainly because I’m starting to be more confident that our experience of omicron will be significantly milder than earlier covid waves.

R2 = .49 .... 50% still unaccounted for? I'm game..

Interesting question. Not sure there is much variance left to explain once you take into account ideology. For climate change r=.7 between denial and libertarianism. Massive.

but I feel I know smart people who definitely believe their own Covid minimising nonsense, and while ideology is undoubtedly a factor, it can't be all....

Hmm. post-Brexit I'd say. Pandemic puts all that on steroids but it all ultimately comes back to the original Project Gaslight (a.k.a. Leave).

there is an interesting post-pandemic research stream on "successive detachment from reality in non-clinical populations" to be had here that could become a thing...

It's pretty stunning. The expectation that they can gaslight not just the British public (that's easy) but other governments (that don't drip feed on UK tabloids) is beyond weird.

"act like"

.@SciBeh !?

So those critiquing others for being too certain (I get subtweeted a lot for this)- Am I certain about the exact impact of omicron in the UK? Not at all Am I certain it'll be high impact? Quite Am I certain we should act now? Absolutely

Best to act early, quickly & scale back if the response was an overreaction. I can safely say that I've not seen any overreaction in UK pandemic policy though, so this is extremely unlikely. Under reaction which is far more damaging has been the mainstay, and continues to be.

Same with long COVID. The greater the uncertainty, the more the need for caution, and the more the need for early action. Even the best-case scenarios look very concerning with omicron. So please don't use uncertainty as an excuse for inaction. Inaction will kill in a pandemic.

I've seen people use 'uncertainty' around aspects of evidence to justify inaction. Uncertainty in evidence *does not* mean uncertainty in policy. As I've said, while there's a lot of uncertainty around the exact impact of omicron, there's little doubt that it'll be severe

Worth exploring I believe

Maybe this always happens in times of great instability? Or maybe it reflects misplaced values of university administrators/boards? Where building endowments is all? Where many College Presidents are no longer scholars/thinkers but selected to keep Universities off the headlines?

As a professor who trained or taught at similar great universities I’m interested in understanding how professors or even whole institutions lost their moral compass during the pandemic and were so eager to align with authoritarian leaders new outlets podcasters