Going to say this again because it's important. Case-control studies to determine prevalence of long COVID are completely flawed science, but are often presented as being scientifically robust. This is not how we can define clinical syndromes or their prevalence! A thread.

More than seventy peer-reviewed #COVID-19, #SARS, and #MERS @J_Immunol articles are #FreeToRead http://ow.ly/lwTr50Hyu5F #immunology #ReadTheJI

Another 13 people in Queensland have died from COVID and 8,580 new cases have been recorded, Premier Annastacia Palaszczuk says.

Queensland records another 13 COVID-19 deaths, schools to resume with mask mandate

The US federal government will no longer require hospitals to report the number of people who die from COVID-19 every day, according to new guidelines from the US Department of Health and Human Services (HHS).

US government moves to end daily COVID-19 death reporting by hospitals

Novavax says it’s officially filed for EUA of its #covid19 vaccine in the US

Cases will increase today. The way that cases are counted is changing. A short thread. https://coronavirus.data.gov.uk/details/whats-new/record/af008739-ffa3-47b8-8efc-ef109f2cfbdd

Have tried to now visually illustrate an earlier thread I wrote about why prevalence estimates based on comparisons of 'any symptom' between infected cases, and matched controls will yield underestimates for long COVID. I've done a toy example below here, to show this

The ever-evolving landscape of Covid-19 vaccines shifted again on Monday, with Moderna winning full approval for its jab from the Food and Drug Administration, and Novavax submitting a long-awaited application to the agency for an emergency use authorization for its vaccine.

Moderna wins full approval for its Covid-19 vaccine, as Novavax seeks authorization for its version

UK Deaths following a reinfection! Tell me what you see here

10.1038/d41586-022-00210-7

The variant’s rapid spread, different vaccine strategies and varying levels of immunity worldwide make the pandemic’s future difficult to model.

Will Omicron end the pandemic? Here’s what experts say

Got Omicron? You are not alone! See our thread on what we know so far [1/11] #ScienceUpFirst

Majority (54%) now say they want all restrictions to end – increase of 15-points since early January

Incidence of Omicron: One-in-five Canadians report COVID-19 infection in their household since Dec. 1

10.1136/bmj.o89

Patients with the omicron variant of covid-19 shed virus for longer after symptoms emerge, show data from Japan, potentially jeopardising hopes that the period of isolation for people testing positive could be shortened.Preliminary data from the National Institute of Infectious Diseases—which conducts disease surveillance in Japan—suggest that the amount of viral RNA is highest three to six days after diagnosis or symptom onset.1

Covid-19: Peak of viral shedding is later with omicron variant, Japanese data suggest

“We are really working day and night” to figure out long Covid, one researcher said.

What causes long Covid? Scientists are zeroing in on the answer.

How Do You Respond When an #AntiVaxxer Dies of Covid? https://nytimes.com/2022/01/30/opinion/culture/covid-death-mental-health.html?smid=tw-share… by @JamesMartinSJ "Indulged in regularly, #schadenfreude ends up warping the soul." "Don’t find another person’s misery the subject of mirth, glee or satisfaction." Good reminder. One I needed.

Thank goodness we didn’t hold off on opening up to see what Omicron was capable of. We had to have Christmas. And there were national cabinet agreements. Anyway, how could we have known? Or this is what we expected? I forget.

Thank goodness we did all the work

Experts said the recent omicron variant surge will happen again

A new COVID-19 variant surge ‘will happen again,’ experts say

As the first vehicles from the trucker convoy started appearing on Ottawa streets, some Twitter users shared a particular photo: a pickup truck with a confederate flag flying from the bed. Now, as the convoy descends on Ottawa with the stated aim of opposing all COVID-19 mandates, anti-hate experts allege those with white nationalist and Islamophobic views don’t just represent the fringes of the movement but are among the organizers of the convoy.

Some trucker convoy organizers have history of white nationalism, racism

Wait two years before we can tell who took the correct approach. OK, we'll check back in March.

10.1038/s41591-021-01591-4

There is now a rich body of knowledge on acute COVID-19, but much less is known about the risk factors, clinical presentation, duration and management of persistent or new symptoms following recovery from initial infection, often termed long COVID1. Post-infection follow-up data show that a significant proportion of hospitalized and non-hospitalized patients experience persistent symptoms and organ dysfunction2,3,4.

Understanding and tracking the impact of long COVID in the United Kingdom

While the U.K. official figures and ⁦@BBCNews⁩ say cases in U.K. have plateaued- the reality is that they have been increasing for the last two weeks based on the Zoe data . Now at 176000 cases per day - thanks for logging !

PORTUGAL 90% of the Country is double dosed. This is what a good job looks like

One U.S. child loses a parent or caregiver for every four COVID-19-associated deaths I’m not discounting mental health effects of the pandemic on children. That is real. But the risks associated with #COVID19 for children and its affects on them aren’t always obvious

For those with underlying medical conditions, the latest pandemic wave has still posed a threat.

When Omicron Isn’t So Mild

Seems that the second Omicron subvariant BA.2 may soon be about to cause cases to start rising again in South Africa... Or at least to stop the decline in new infections. Shows how fast immunity wanes & evolution can catch up.

10.1101/2022.01.14.22269235

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection elicits an antibody response that targets several viral proteins including spike (S) and nucleocapsid (N); S is the major target of neutralizing antibodies. Here, we assess levels of anti-N binding antibodies and anti-S neutralizing antibodies in unvaccinated children compared with unvaccinated older adults following infection. Specifically, we examine neutralization and anti-N binding by sera collected up to 52 weeks following SARS-CoV-2 infection in children and compare these to a cohort of adults, including older adults, most of whom had mild infections that did not require hospitalization. Neutralizing antibody titers were lower in children than adults early after infection, but by 6 months titers were similar between age groups. The neutralizing activity of the children’s sera decreased modestly from one to six months; a pattern that was not significantly different from that observed in adults. However, infection of children induced much lower levels of anti-N antibodies than in adults, and levels of these anti-N antibodies decreased more rapidly in children than in adults, including older adults. These results highlight age-related differences in the antibody responses to SARS-CoV-2 proteins and, as vaccines for children are introduced, may provide comparator data for the longevity of infection-elicited and vaccination-induced neutralizing antibody responses.

Dynamics of infection-elicited SARS-CoV-2 antibodies in children over time

Omicron wave and its consequences....

10.1056/NEJMc2119912

The highly transmissible omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of mounting concern globally. The omicron variant carries a large number of spike mutations, including at least 15 mutations in the receptor-binding domain, which is a major target of neutralizing antibodies.1 To assess the potential susceptibility of this variant to the mRNA-1273 vaccine, neutralization of the omicron variant by serum samples obtained from vaccinated recipients was compared with neutralization of the prototypical D614G variant and the beta (B.1.351) and delta (B.1.617.2) variants. In a pilot study, neutralization of the omicron variant after the primary two-dose regimen of the mRNA-1273 vaccine was lower than that of the D614G and beta variants but increased substantially after a booster dose of the mRNA-1273 vaccine (Figs. S1 through S3 in the Supplementary Appendix, available with the full text of this letter at NEJM.org).

SARS-CoV-2 Omicron Variant Neutralization after mRNA-1273 Booster Vaccination

it's a bit like criticising the person trying to drive from Cardiff to London that they haven't got to Birmingham yet

of course you can criticise the target function (maintaining hospital capacity) * itself* and argue that we should be focussing largely on cases, but arguing that a policy doesn't fulfil a *different* goal than it is designed for is either dense or bad faith

we've had at least 4 months of European governments tailoring policy to *hospital capacity*, not cases per se - so why are we still seeing arguments against the effectiveness of those policies based solely on cases, and not the actual target function? @AllysonPollock

New data show that vaccines still protect against a spinoff of the Omicron variant, a welcome sign as the world keeps a close eye on the latest coronavirus iteration.

Early data indicate vaccines still protect against Omicron’s sister variant, BA.2

Here is a relatively simple way of giving people important context about the number of deaths and ICU hospitalisations with Covid between vaccinated and unvaccinated people

The simple numbers every government should use to fight anti-vaccine misinformation

10.1136/bmj.o210

A booster dose of a covid-19 jab other than CoronaVac significantly increased antibodies in those who had received two doses of the Chinese vaccine, a study funded by Brazil's Ministry of Health has found

Covid-19: CoronaVac immunity is strongest after boosting with a different vaccine

10.1073/pnas.2121644119

Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ∼75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive “One Health” approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2.

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

I'm not sure what to say anymore

10.1136/bmj.o142

Latest evidence is limited but reassuring

Menstruation and covid-19 vaccination

10.1140/epjds/s13688-021-00314-6

Citizen-generated counter speech is a promising way to fight hate speech and promote peaceful, non-polarized discourse. However, there is a lack of large-scale longitudinal studies of its effectiveness for reducing hate speech. To this end, we perform an exploratory analysis of the effectiveness of counter speech using several different macro- and micro-level measures to analyze 180,000 political conversations that took place on German Twitter over four years. We report on the dynamic interactions of hate and counter speech over time and provide insights into whether, as in ‘classic’ bullying situations, organized efforts are more effective than independent individuals in steering online discourse. Taken together, our results build a multifaceted picture of the dynamics of hate and counter speech online. While we make no causal claims due to the complexity of discourse dynamics, our findings suggest that organized hate speech is associated with changes in public discourse and that counter speech—especially when organized—may help curb hateful rhetoric in online discourse.

Impact and dynamics of hate and counter speech online

Since last summer, the conservative campaign against vaccination has claimed thousands of lives for no ethically justifiable purpose.

The Anti-vaccine Right Brought Human Sacrifice to America

In France, a recent rise in hospitalizations raises the concern that BA.2 may not just be the harmless wake of BA.1's powerboat Yellow line - hospital admission Black line - death in hospital Red line - ICU admission

10.1136/bmj.o222

Coronavirus infections in England were at their highest ever rate in early January this year, with an estimated one in 23 people infected, the ongoing REACT-1 monitoring study has reported.1Findings from Imperial College London and Ipsos Mori covering 5-20 January show that the prevalence in England was 4.41%. This is more than three times the prevalence in the previous round of the survey in December, when one in 70 had the virus.Infections reached a peak around 5 January before levelling off from mid-January, but they were still at extremely high levels. Schoolchildren have shown a rise in prevalence after returning to school this month.The study authors said that they observed “unprecedented” levels of infection with SARS-CoV-2 in England in January 2022, with almost complete replacement of the delta variant by omicron. They warned that the increase in the prevalence of infection in children could pose a risk to adults despite the current decline among adults.

Covid-19: One in 23 people in England had infection in early January

Populist parties and actors now govern various countries around the world. Often elected by the public in times of crises and over the perceived failure of ‘the elites’, the question stands as to how populist governments actually perform once elected, especially in times of crisis. Using the pandemic shock in the form of the COVID-19 crises, our paper poses the question of how populist governments handle the pandemic. We answer this question by introducing a theoretical framework according to which populist governments (1) enact less far-reaching policy measures to counter the pandemic and (2) lower the effort of citizens to counter the pandemic, so that populist governed countries are (3) hit worse by the pandemic. We test these propositions in a sample of 42 countries with weekly data from 2020. Employing econometric models, we find empirical support for our propositions and ultimately conclude that excess mortality in populist governed countries exceeds the excess mortality of non-populist countries by 8 percentage points (i.e., 98%). Our findings have important implications for the assessment of populist government performance in general, as well as counter-pandemic measures in particular, by providing evidence that opportunistic and inadequate policy responses, spreading misinformation and downplaying the pandemic are strongly related to increases in COVID-19 mortality.

10.1561/113.00000043

Populism and COVID-19: How Populist Governments (Mis)Handle the Pandemic

Background: Rapid transmission of the SARS-CoV-2 Omicron variant has led to the highestever recorded case incidence levels in many countries around the world.Methods: The REal-time Assessment of Community Transmission-1 (REACT-1) study hasbeen characterising the transmission of the SARS-CoV-2 virus using RT-PCR test results fromself-administered throat and nose swabs from randomly-selected participants in England atages 5 years and over, approximately monthly since May 2020. Round 17 data were collectedbetween 5 and 20 January 2022 and provide data on the temporal, socio-demographic andgeographical spread of the virus, viral loads and viral genome sequence data for positiveswabs.Results: From 100,607 valid tests in round 17, weighted prevalence of swab positivity was4.41% (95% credible interval [CrI], 4.25% to 4.56%), which is over three-fold higher than inDecember 2021 in England. Of 1,406 sequenced positive swabs to 16 January 2022, 1392(99.0%) were Omicron including 6 (0.43%) cases of BA.2 sub-lineage and only 14 (1.0%) wereDelta. Within round 17, prevalence was decreasing overall (R=0.95, 95% CrI, 0.92, 0.97) butincreasing in children aged 5 to 17 years (R=1.13, 95% CrI, 1.09, 1.18). Those 75 years andolder had a swab-positivity prevalence of 2.43% (95% CI, 2.13%, 2.77%) reflecting a highlevel of infection among a highly vulnerable group. Among the 3,582 swab-positiveindividuals reporting whether or not they had had previous infection, 2,315 (64.6%)reported confirmed previous COVID-19. Risks of infection were increased amongessential/key workers (other than healthcare or care home workers) with mutually adjustedOdds Ratio (OR) of 1.14 (95% CI, 1.04, 1.25), people living in large compared to single-personhouseholds (6+ household size OR 1.66; 95% CI, 1.38, 2.01), those living in urban vs ruralareas (OR 1.24, 95% CI, 1.13, 1.35) and those living in the most vs least deprived areas (OR1.33, 95% CI, 1.19, 1.48).Conclusions: We observed unprecedented levels of infection with SARS-CoV-2 in England inJanuary 2022 and almost complete replacement of Delta by Omicron. The increase in theprevalence of infection with Omicron among children (aged 5 to 17 years) during January

Post-peak dynamics of a national Omicron SARS-CoV-2 epidemic duringJanuary 2022

Covid cases in schools have doubled in a fortnight, meaning infections are no longer falling across the country.

Record school infections mean national Covid cases no longer falling

Police told to detain activists trivialising the Holocaust in acts to be classified as ‘secondary antisemitism’

Germany to crack down on Covid protesters in yellow star badges

10.1038/s41557-021-00707-0

SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression and replication that depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate 0.1 seconds of the viral proteome. Our adaptive sampling simulations predict dramatic opening of the apo spike complex, far beyond that seen experimentally, explaining and predicting the existence of ‘cryptic’ epitopes. Different spike variants modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also discover dramatic conformational changes across the proteome, which reveal over 50 ‘cryptic’ pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas.