SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

With many of the last COVID-19 restrictions soon coming to an end, there are whispers that the worst of the pandemic may be over. But for those whose COVID-19 symptoms remain months after their initial infection, that hope feels much further away.

Coronavirus: Inside a long COVID clinic as patient who was 'fit and healthy' can now 'barely do anything'

Here's a great thread for more info on BA.2

Here's the data for India, broken down by state. Steep rises in Manipur and Assam, with Telengana and New Delhi on similar trajectories.

I arbitrarily excluded some countries: - Germany & USA - very low frequencies amid the huge volume of sequences they share - Philippines - shared samples don't seem representative/random - NZ - samples were trapped in quarantine

The first chart above showed the top 5 countries (by the number of samples shared. Here are the next 5, showing significant rises in South Africa, Sri Lanka and Botswana.

Note the Frequency is calculated for each country independently, comparing to all the recent samples sequenced in that country. In India and Singapore, the rise of BA.2 has a similar timing to the start of their Omicron waves, so perhaps those are just "founder effects"?

Here's the latest variant picture for BA.2 (Omicron). Globally it has been far less common than it's sibling BA.1 lineage. The frequency of BA.2 is rising rapidly in several countries, notably India, Denmark & Singapore.

10.1108/IJLMA-07-2021-0183

Purpose The purpose of this study is to examine the practical and legal complexities associated with tele-homeworking in the context of the UK Equality Law. First, the paper provides a background to the recent growth of tele-homeworking as a result of the COVID-19 pandemic, outlining the tenets of the UK Equality Act 2010 and referring to additional legislation pertinent to the ensuing discussion. Second, illustrative case law relevant to the UK Equality Law is put forward to demonstrate the potential challenges that employers and employees might encounter with continued and longer-term tele-homeworking arrangements. Third, the paper outlines implications for employers and human resource managers in terms of policies and practices that might shape the nature of the employment relationship. Design/methodology/approach This study is based on a review of the literature and an examination of UK case law applicable to tele-homeworking, taking into consideration equality, diversity and inclusion concerns in the workplace. Findings Remote working can be beneficial to both employers and employees. However, there are a number of significant concerns surrounding the management of tele-homeworkers in the aftermath of the pandemic that can act as a stimulus for legal disputes around discrimination, infringement of human rights and breach of contract claims. Several policy implications surface from the analysis that relate to equality and fair treatment associated with both current and future work arrangements. Originality/value The paper is significant in offering legal insights into how the UK Equality Law relates to the complexities associated with the management of tele-homeworkers. The study also highlights how return-to-office undertakings might need to consider wider legal issues. COVID-19 and its repercussions have demanded the reorganisation of work, which can give rise to a greater possibility of legal challenges and the study highlights the importance of employers undertaking an evaluation of their equality practices and complying with the legal framework.

Implications of the UK Equality Law for tele-homeworking: COVID-19 and beyond

10.1016/j.alter.2020.12.005

The National Association of Disabled Staff Networks (NADSN) is a super-network that connects and represents disabled staff networks at organisations across the United Kingdom. NADSN has been very concerned about the development of national policy up to this time and for moving out of the COVID-19 lockdown stage as national policy has been silent in relation to disabled staff apart from in presenting a narrow, medicalised view. We have structured this paper within a social model of disability and the sentiments expressed in the UN Convention of the Rights of People with Disabilities (CRPD) in considering the current issues and setting out our 12 recommendations. This paper discusses NADSN's observations about the lived experiences of Disabled people during COVID-19. Secondly, it moves to outline COVID-19 and the changing workplace. The paper then moves to a broad discussion concerning safe working practices and policies as we move out of lockdown and beyond.

COVID-19 Post-lockdown: Perspectives, implications and strategies for disabled staff

43% The percentage of frontline workers research shows are experiencing significant levels of anxiety

2,369 The average number of deaths per day since the first #COVID19 cases were detected in the WHO European Region two years ago. That's an average of 99 lives lost every hour

0.5 million The estimated number of lives saved thanks to #COVID19 vaccination - according to a study in late November from WHO/Europe & @ECDC_EU

52% Of 46 countries surveyed - 24 identified #COVID19 related constraints as a challenge to implementing national health & climate change plans or strategies

10-20% The percentage of people suffering from a post #COVID19 condition or #LongCOVID - experiencing symptoms for weeks to months after an acute infection

732 days of #COVID19 in the WHO European Region – in 15 figures https://bit.ly/3rHKfAB Find out more in the thread

Objectives: The immunologic profile and opportunistic viral DNA increase were monitored in Italianpatients with COVID-19 in order to identify markers of disease severity.Methods: A total of 104 patients infected with SARS-CoV-2 were evaluated in the study. Of them, 42/104(40.4%) were hospitalized in an intensive care unit (ICU) and 62/104(59.6%) in a sub-intensive care unit(SICU). Human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV), Parvovirus B19 and HumanHerpesvirus 6 virus reactivations were determined by real-time PCR, and lymphocyte subpopulationcounts were determined by flow cytometry.Results: Among opportunistic viruses, only EBV was consistently detected. EBV DNA was observed in 40/42 (95.2%) of the ICU patients and in 51/61 (83.6%) of the SICU patients. Comparing the two groups ofpatients, the EBV DNA median level among ICU patients was significantly higher than that observed inSICU patients. In parallel, a significant reduction of CD8 T cell and NK count in ICU patients as comparedwith SICU patients was observed (p < 0.05). In contrast, B cell count was significantly increased in ICUpatients (p = 0.0172).Conclusions: A correlation between reduced CD8+ T cells and NK counts, EBV DNA levels and COVID-19severity was observed. Other opportunistic viral infections were not observed. The relationship betweenEBV load and COVID-19 severity should be further evaluated in longitudinal studies.

EBV DNA increase in COVID-19 patients with impairedlymphocyte subpopulation count

10.31234/osf.io/3e2ux

In this paper, the fourth in a series of white papers, we provide a summary of the discussions and future directions that came from the topical meeting that focused on model construction with social media data. A particularly interesting aspect of this meeting was, in our view, discussion of the different disciplines’ requirements and approaches to modeling and the different considerations that are used to assess model fit.

Modeling Considerations for Quantitative Social Science Research Using Social Media Data

10.1038/d41586-022-00129-z

Data on viral levels point to immune evasion as a cause of the variant’s transmissibility.

How does Omicron spread so fast? A high viral load isn’t the answer

Senior Government advisers are cautiously optimistic that the UK has passed the ‘test’ of Omicron but scientists are clear that global vaccination rates need to be higher for the pandemic to be declared a thing of the past

‘Endemic’ Covid? The pandemic will only be over when the world is jabbed

An Israeli government advisory panel has recommended offering a fourth COVID-19 vaccine dose to all adults, on condition that at least five months have passed since they received the third or recovered from the illness, the Health Ministry said on Tuesday.

Israel mulls offering 4th COVID vaccine dose to all adults

We analyzed the differences in viral environmental stability between the SARS-CoV-2 Wuhan strain and all variants of concern (VOCs). On plastic and skin surfaces, Alpha, Beta, Delta, and Omicron variants exhibited more than two-fold longer survival than the Wuhan strain and maintained infectivity for more than 16 h on skin surfaces. The high environmental stability of these VOCs could increase the risk of contact transmission and contribute to their spread.

ifferences in environmental stability among SARS-CoV-2 variants of concern: Omicron has higher stability

Maryland 24,183 new cases South Korea 8,571 new cases Maryland population 6.2 million South Korea population 51.82 million Perspective, even w SK sharply rising & MD headed down (hope it continues).

For the BA.2 watchers, looks like it doubling roughly every 4 days in the UK at the moment. Would make it the dominant strain around about February 14th. Maybe it is time to move away from the Greek alphabet and move onto their Gods instead. Eros variant?

NYC update Positive rate 6.6%. Cases fewest since 12/13. Hospital census lowest since 1/1/2022. Hospital admits lowest since 12/22/2021. All indicators (except deaths) declining rapidly, but still well above pre-Omicron levels. Expect more swift progress this week.

Smart people change their minds. They reconsider things they thought they'd already figure out when offered compelling data contradicting their previous understanding. Last week we saw the Swiss data. This is from #USA. #scicomm #dataviz #VaccinesSaveLives (h/t @OurWorldInData)

10.31234/osf.io/b9qrj

While vaccinations are vital to managing pandemics, attitudes toward vaccines are not uniformly positive. During the COVID-19 vaccines development and enrollment phase, we studied the temporal dynamics of COVID-19 vaccination intention in relation to attitudes toward COVID-19 vaccines and the pandemic, vaccination in general, and social norms and trust. The data are derived from a longitudinal survey study with Dutch participants (N = 744; six measurements between December 2020 – May 2021) and analyzed with vector-autoregression network analyses. While cross-sectional results indicated that vaccination intention was relatively strongly related to attitudes toward the vaccines, results from temporal analyses showed that vaccination intention mainly predicted and was not predicted by other vaccination-related variables. Vaccination intention thus influences other variables but barely vice versa. This underlines the challenge of stimulating uptake of new vaccines developed during pandemics, and the importance of examining directions of effects in research into vaccination intention.

Why COVID-19 vaccination intention is so hard to change: a longitudinal study

As the WHO Executive Board resumes talks this week on a much-discussed Pandemic Accord, and other preparedness measures, three noted infectious disease experts chart a course for “eliminating” SARS-COV2 – warning that will take more sustained global coordination and determination than what has been seen so far.

Backed by Science: Here’s How We Can Eliminate COVID-19

10.1021/acs.estlett.1c00877

Exhaled respiratory droplets and aerosols can carry infectious viruses and are an important mode of transmission for COVID-19. Recent studies have been successful in detecting airborne SARS-CoV-2 RNA in indoor settings using active sampling methods. The cost, size, and maintenance of these samplers, however, limit their long-term monitoring ability in high-risk transmission areas. As an alternative, passive samplers can be small, lightweight, and inexpensive and do not require electrical power or maintenance for continual operation. Integration of passive samplers into wearable designs can be used to better understand personal exposure to the respiratory virus. This study evaluated the use of a polydimethylsiloxane (PDMS)-based passive sampler to assess personal exposure to aerosol and droplet SARS-CoV-2. The rate of uptake of virus-laden aerosol on PDMS was determined in lab-based rotating drum experiments to estimate time-weighted averaged airborne viral concentrations from passive sampler viral loading. The passive sampler was then embedded in a wearable clip design and distributed to community members across Connecticut to surveil personal SARS-CoV-2 exposure. The virus was detected on clips worn by five of the 62 participants (8%) with personal exposure ranging from 4 to 112 copies of SARS-CoV-2 RNA/m3, predominantly in indoor restaurant settings. Our findings demonstrate that PDMS-based passive samplers may serve as a useful exposure assessment tool for airborne viral exposure in real-world high-risk settings and provide avenues for early detection of potential cases and guidance on site-specific infection control protocols that preempt community transmission.

Development and Application of a Polydimethylsiloxane-Based Passive Air Sampler to Assess Personal Exposure to SARS-CoV-2

Both Victoria and New South Wales are seeing continued improvement in COVID-19 hospitalisation

A story told in three parts

Of 51,141 deaths due to ischaemic heart diseases 32,872 (64.3%) had pre-existing conditions. Do those 33k heart disease deaths not count? Or is an absence of pre-existing conditions only required for Covid deaths... Source: ONS England 2019

10.1371/journal.pone.0258191

Face coverings are a key component of preventive health measure strategies to mitigate the spread of respiratory illnesses. In this study five groups of masks were investigated that are of particular relevance to the SARS-CoV-2 pandemic: re-usable, fabric two-layer and multi-layer masks, disposable procedure/surgical masks, KN95 and N95 filtering facepiece respirators. Experimental work focussed on the particle penetration through mask materials as a function of particle diameter, and the total inward leakage protection performance of the mask system. Geometric mean fabric protection factors varied from 1.78 to 144.5 for the fabric two-layer and KN95 materials, corresponding to overall filtration efficiencies of 43.8% and 99.3% using a flow rate of 17 L/min, equivalent to a breathing expiration rate for a person in a sedentary or standing position conversing with another individual. Geometric mean total inward leakage protection factors for the 2-layer, multi-layer and procedure masks were <2.3, while 6.2 was achieved for the KN95 masks. The highest values were measured for the N95 group at 165.7. Mask performance is dominated by face seal leakage. Despite the additional filtering layers added to cloth masks, and the higher filtration efficiency of the materials used in disposable procedure and KN95 masks, the total inward leakage protection factor was only marginally improved. N95 FFRs were the only mask group investigated that provided not only high filtration efficiency but high total inward leakage protection, and remain the best option to protect individuals from exposure to aerosol in high risk settings. The Mask Quality Factor and total inward leakage performance are very useful to determine the best options for masking. However, it is highly recommended that testing is undertaken on prospective products, or guidance is sought from impartial authorities, to confirm they meet any implied standards.

The protective performance of reusable cloth face masks, disposable procedure masks, KN95 masks and N95 respirators: Filtration and total inward leakage

Robert Malone claims to have invented mRNA technology. Why is he trying so hard to undermine its use?

The Vaccine Scientist Spreading Vaccine Misinformation

A month ago, Dr. Robert Malone announced the “Defeat the Mandates” rally on Joe Rogan’s podcast, to be held this Sunday. I sensed many echoes of Jenny McCarthy’s 2008 “Green Our Vaccines” rally, although what’s different is even more disturbing than the antivaccine misinformation that’s the same.

Defeat The Mandates: Green Our Vaccines reconstituted for COVID-19

So this is political vetting of public health decisions. By an education Secretary.

Black Americans who were initially hesitant about receiving a COVID-19 vaccine were more likely than whites to warm up to the idea as the pandemic wore on and to view vaccines as necessary for protection, a new study has found.

Vaccine hesitance dropped faster among Blacks, study finds

Hospitality, leisure and travel firms feel impact of Covid variant in January

Omicron pushes UK business growth to 11-month low

Gov: Its all about managing personal risk, No not that like that Right, ill have to ban you then

10.1101/2021.12.23.21268276

In an updated self-controlled case series analysis of 42,200,614 people aged 13 years or more, we evaluate the association between COVID-19 vaccination and myocarditis, stratified by age and sex, including 10,978,507 people receiving a third vaccine dose. Myocarditis risk was increased during 1-28 days following a third dose of BNT162b2 (IRR 2.02, 95%CI 1.40, 2.91). Associations were strongest in males younger than 40 years for all vaccine types with an additional 3 (95%CI 1, 5) and 12 (95% CI 1,17) events per million estimated in the 1-28 days following a first dose of BNT162b2 and mRNA-1273, respectively; 14 (95%CI 8, 17), 12 (95%CI 1, 7) and 101 (95%CI 95, 104) additional events following a second dose of ChAdOx1, BNT162b2 and mRNA-1273, respectively; and 13 (95%CI 7, 15) additional events following a third dose of BNT162b2, compared with 7 (95%CI 2, 11) additional events following COVID-19 infection. An association between COVID-19 infection and myocarditis was observed in all ages for both sexes but was substantially higher in those older than 40 years. These findings have important implications for public health and vaccination policy.

Risk of myocarditis following sequential COVID-19 vaccinations by age and sex

2) Florida governor’s new anti-COVID testing surgeon general doesn’t seem well either…

Our list of retracted COVID-19 papers is up to 206. For context and denominators, please see the post. https://retractionwatch.com/retracted-coronavirus-covid-19-papers/…

We’ve been tracking retractions of papers about COVID-19 as part of our database. Here’s a running list, which will be updated as needed. (For some context on these figures, see this post, our letter in Accountability in Research and the last section of this Nature news article. Also see a note about the terminology regarding preprint servers at the end.)

Retracted coronavirus (COVID-19) papers

Florida governor Ron DeSantis and politicians in Texas say research does not support mask mandates. Many studies show they are wrong

Masks Protect Schoolkids from COVID despite What Antiscience Politicians Claim

My cousin wanted to get tested. She waited in an auto testing line for 6.5 hours, and stayed in it bc she was traveling to bury her Daddy. How many people give up in such long lines? How many cases upwards of a million are we losing bc Biden et all failed on home tests?

You get the public health outcomes that your system is willing to support

minority whose actions are tolerated by the state? And what how polarising is *that*? All thoughts/data appreciated 3/311

2/3 the majority that is? Many have gone along with measure after measure out of a sense of collective responsibility and/or because they were told doing so would end the pandemic. What effect will it have on *their* future compliance to see the undermining of that effort by a ..

Just a thought on this and the general vaccine mandate debate. As a behavioural scientist currently stuck in Germany where this is a live debate, it strikes me that the thoughts below address only part of the population: those not currently vaccinated. But what about ... 1/2Quote Tweet

there are many things I would not have believed about the pandemic pre 2020, but top of them is the fact that Western nations would completely ignore 24 months worth of *actually implemented* policies that were vastly more successful

I've had people mention rising case numbers in Japan and South Korea. But let's really put that rise into perspective. Nations that have early accepted that #COVIDisAirborne simply fair better

Yes, Neoliberal John Snow wins the Internet today H/T @gregggonsalves Reminds me of this….

Update on Omicron by Dr @mvankerkhove from @WHO's Q&A

The rise of Omicron Translated from @numeroteca

Impact of social distancing OVER a month. 15 vs 406 infections. See below and avoid gatherings

It was always likely that immunity to COVID-19 would wane, and we now know the median time to waning is around 1.5-2 years post infection for most people, sometimes less

10.2337/dc21-0969

OBJECTIVEThe aim of this study was to investigate the incidence of type 1 diabetes in children and adolescents during the coronavirus disease 2019 (COVID-19) pandemic in Germany compared with previous years.RESEARCH DESIGN AND METHODSBased on data from the multicenter German Diabetes Prospective Follow-up Registry, we analyzed the incidence of type 1 diabetes per 100,000 patient-years in children and adolescents from 1 January 2020 through 30 June 2021. Using Poisson regression models, expected incidences for 2020/21 were estimated based on the data from 2011 to 2019 and compared with observed incidences in 2020/21 by estimating incidence rate ratios (IRRs) with 95% CIs.RESULTSFrom 1 January 2020 to 30 June 2021, 5,162 children and adolescents with new-onset type 1 diabetes in Germany were registered. The observed incidence in 2020/21 was significantly higher than the expected incidence (24.4 [95% CI 23.6–25.2] vs. 21.2 [20.5–21.9]; IRR 1.15 [1.10–1.20]; P < 0.001). IRRs were significantly elevated in June 2020 (IRR 1.43 [1.07–1.90]; P = 0.003), July 2020 (IRR 1.48 [1.12–1.96]; P < 0.001), March 2021 (IRR 1.29 [1.01–1.65]; P = 0.028), and June 2021 (IRR 1.39 [1.04–1.85]; P = 0.010).CONCLUSIONSA significant increase in the incidence of type 1 diabetes in children was observed during the COVID-19 pandemic, with a delay in the peak incidence of type 1 diabetes by ∼3 months after the peak COVID-19 incidence and also after pandemic containment measures. The underlying causes are yet unknown. However, indirect rather than direct effects of the pandemic are more likely to be the cause.

Incidence of Type 1 Diabetes in Children and Adolescents During the COVID-19 Pandemic in Germany: Results From the DPV Registry

Norfolk and Waveney CCG pilot will care for up to 15 patients who are not well enough to be sent home

‘Care hotel’ set up in Norwich to relieve ‘unprecedented’ pressure on hospitals