Replying to @united_oz and @MarcTennant

As part of the July 21, 2021 FeedbackASAP meeting, Ludo Waltman (CWTS, Leiden University), James Fraser (UCSF), Cooper Smout (Free Our Knowledge) organized a breakout session entitled “Posting journal reviews on preprints” to identity an evolutionary bridge between a system based around journal-organized peer review and referred preprints.

Considering campaigns to post journal reviews on preprints

In the last decade Open Science principles have been successfully advocated for and are being slowly adopted in different research communities. In response to the COVID-19 pandemic many publishers and researchers have sped up their adoption of Open Science practices, sometimes embracing them fully and sometimes partially or in a sub-optimal manner. In this article, we express concerns about the violation of some of the Open Science principles and its potential impact on the quality of research output. We provide evidence of the misuses of these principles at different stages of the scientific process. We call for a wider adoption of Open Science practices in the hope that this work will encourage a broader endorsement of Open Science principles and serve as a reminder that science should always be a rigorous process, reliable and transparent, especially in the context of a pandemic where research findings are being translated into practice even more rapidly. We provide all data and scripts at https://osf.io/renxy/.

10.1186/s12874-021-01304-y

Open science saves lives: lessons from the COVID-19 pandemic

This article reviews the current state of knowledge and promising new directions concerning the psychology of pandemics. Pandemics are disease outbreaks that spread globally. Historically, psychological factors have been neglected by researchers and health authorities despite evidence that pandemics are, to a large extent, psychological phenomena whereby beliefs and behaviors influence the spreading versus containment of infection. Psychological factors are important in determining (a) adherence to pandemic mitigation methods (e.g., adherence to social distancing), (b) pandemic-related social disruption (e.g., panic buying, racism, antilockdown protests), and (c) pandemic-related distress and related problems (e.g., anxiety, depression, posttraumatic stress disorder, prolonged grief disorder). The psychology of pandemics has emerged as an important field of research and practice during the coronavirus 2019 (COVID-19) pandemic. As a scholarly discipline, the psychology of pandemics is fragmented and diverse, encompassing various psychological subspecialties and allied disciplines, but is vital for shaping clinical practice and public health guidelines for COVID-19 and future pandemics. Expected final online publication date for the Annual Review of Clinical Psychology, Volume 18 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

10.1146/annurev-clinpsy-072720-020131

The Psychology of Pandemics

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

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!

Now that the FDA has authorized the shots for a broad range of Americans, many people want to know if they need a booster dose. Here’s what we have learned so far

Who Needs a COVID Booster Shot? Experts Answer Common Questions

This week, YouTube joined Twitter and Facebook in banning misinformation about vaccines from social media. But many myths about the COVID-19 vaccines still persist.The Covid-19 vaccines are overwhelmingly effective, reducing the risk of hospitalization and death by 95%. They are also incredibly safe—severe side effects are exceptionally rare, occurring in just 0.002% of the 390 million doses that have been delivered. Compare that to the 1.6% mortality rate of Covid-19, which has resulted in the deaths of more than 700,000 Americans.

Five biggest myths about the COVID-19 vaccines, debunked

Advisory Committee on Immunization Practices- ACIP

Extension of the interval between vaccine doses for the BNT162b2 mRNA vaccine was introduced in the United Kingdom to accelerate population coverage with a single dose. At this time, trial data were lacking, and we addressed this in a study of United Kingdom healthcare workers. The first vaccine dose induced protection from infection from the circulating alpha (B.1.1.7) variant over several weeks. In a substudy of 589 individuals, we show that this single dose induces severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibody (NAb) responses and a sustained B and T cell response to the spike protein. NAb levels were higher after the extended dosing interval (6–14 weeks) compared with the conventional 3- to 4-week regimen, accompanied by enrichment of CD4+ T cells expressing interleukin-2 (IL-2). Prior SARS-CoV-2 infection amplified and accelerated the response. These data on dynamic cellular and humoral responses indicate that extension of the dosing interval is an effective immunogenic protocol.

10.1016/j.cell.2021.10.011

Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine

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

he data tracking Australia’s COVID-19 developments are in the charts below, which provide a guide to how the country is faring in the fight against the coronavirus pandemic.The figures are from a national dataset of every case confirmed by state and federal health authorities since January 25, 2020, when the country’s first four cases were reported. The dataset is supplemented with additional reporting by ABC News.The charts are updated daily, so bookmark this page to stay up-to-date.

Charting the COVID-19 spread in Australia

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

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!

COVID-19, Science, and the Media: Lessons Learned Reporting on the Pandemic

In January 2020, reports began to circulate internationally of a pneumonia-like illness spreading in China. Little was known about the novel pathogen, SARS-CoV-2, at that time. As scientists and public health experts worked to understand the virus, reporters worked to communicate to the public the state of the knowledge — an ever-shifting ground. From the transmission debate, to the origins investigation, to changes in mask guidance, to vaccine safety concerns, the COVID-19 pandemic has highlighted a particularly precarious nexus of science, politics, journalism, social media, and policy. This panel discussion reflected on this tenuous situation, potential areas of improvement in pandemic reporting, and lessons learned from recent experience. Panelists Introduction: Chloe Reichel, Editor-in-Chief, Bill of Health and Communications Associate, Petrie-Flom Center for Health Law Policy, Biotechnology, and Bioethics at Harvard Law School Kai Kupferschmidt, contributing correspondent, Science magazine Apoorva Mandavilli, health and science reporter, The New York Times Amy Maxmen, senior reporter, Nature Emily Woodruff, health reporter, The Times-Picayune | New Orleans Advocate Moderator: Alexandra L. Phelan, Assistant Professor, Center for Global Health Science and Security, Georgetown University Sponsored by the Petrie-Flom Center for Health Law Policy, Biotechnology, and Bioethics at Harvard Law School. For more information, visit the website https://petrieflom.law.harvard.edu/ev....

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.

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

On 26 November 2021, WHO designated the variant B.1.1.529 a variant of concern, named Omicron, on the advice of WHO’s Technical Advisory Group on Virus Evolution (TAG-VE).  This decision was based on the evidence presented to the TAG-VE that Omicron has several mutations that may have an impact on how it behaves, for example, on how easily it spreads or the severity of illness it causes. Here is a summary of what is currently known.  

Update on Omicron

reliminary laboratory studies demonstrate that three doses of the Pfizer-BioNTech COVID-19 Vaccine neutralize the Omicron variant (B.1.1.529 lineage) while two doses show significantly reduced neutralization titers Data indicate that a third dose of BNT162b2 increases the neutralizing antibody titers by 25-fold compared to two doses against the Omicron variant; titers after the booster dose are comparable to titers observed after two doses against the wild-type virus which are associated with high levels of protectionAs 80% of epitopes in the spike protein recognized by CD8+ T cells are not affected by the mutations in the Omicron variant, two doses may still induce protection against severe diseaseThe companies continue to advance the development of a variant-specific vaccine for Omicron and expect to have it available by March in the event that an adaption is needed to further increase the level and duration of protection – with no change expected to the companies’ four billion dose capacity for 2022

Pfizer and BioNTech Provide Update on Omicron Variant

Design and analysis of COVID vaccine trials: the familiar and the strange Organized by the SnB2022 Conference (http://snb2022.paris/) powered by the french society

WEBINAR Design and analysis of COVID vaccine trials: the familiar and the strange

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

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

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

LIVE NOW: With news of a new virus strain emerging, it is crucial to consider what the pandemic will look like for us long-term, years from now. With experts @ViolaPriesemann @EmilIftekhar & Prof.Knottnerus. Plus the latest numbers from @chrischirp.

indie_SAGE 26.11.21

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/

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.

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.

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

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.

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: