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  • MIT Research Reveals How Omicron Escapes From All Four Classes of Antibodies That Target COVID-19


    MIT Research Reveals How Omicron Escapes From All Four Classes of Antibodies That Target COVID-19


    A computational study shows that dozens of mutations help the virus’ spike protein evade antibodies that target SARS-CoV-2.


    A new study from MIT suggests that the dozens of mutations in the spike protein of the Omicron variant help it to evade all four of the classes of antibodies that can target the SARS-CoV-2 virus that causes Covid-19.


    This includes antibodies generated by vaccinated or previously infected people, as well as most of the monoclonal antibody treatments that have been developed, says Ram Sasisekharan, the Alfred H. Caspary Professor of Biological Engineering and Health Sciences and Technology (HST) at MIT.


    Using a computational approach that allowed them to determine how mutated amino acids of the viral spike protein influence nearby amino acids, the researchers were able to get a multidimensional view of how the virus evades antibodies. According to Sasisekharan, the traditional approach of only examining changes in the virus’ genetic sequence reduces the complexity of the spike protein’s three-dimensional surface and doesn’t describe the multidimensional complexity of the protein surfaces that antibodies are attempting to bind to.


    “It is important to get a more comprehensive picture of the many mutations seen in Omicron, especially in the context of the spike protein, given that the spike protein is vital for the virus’s function, and all the major vaccines are based on that protein,” he says. “There is a need for tools or approaches that can rapidly determine the impact of mutations in new virus variants of concern, especially for SARS-CoV-2.”


    Sasisekharan is the senior author of the study, which was published in Cell Reports Medicine. The lead author of the paper is MIT HST graduate student Nathaniel Miller. Technical associate Thomas Clark and research scientist Rahul Raman are also authors of the paper.

    Even though Omicron is able to evade most antibodies to some degree, vaccines still offer protection, Sasisekharan says.


    “What’s good about vaccines is they don’t just generate B cells, which produce the monoclonal [antibody] response, but also T cells, which provide additional forms of protection,” he says.


    Antibody escape

    After the Omicron variant emerged last November, Sasisekharan and his colleagues began to analyze its trimeric spike protein using a network-based computational modeling method they had originally developed several years ago to study the hemagglutinin spike protein on flu viruses. Their technique allows them to determine how mutations in the genetic sequence are related in the three-dimensional space through a network of inter-amino-acid interactions that critically impact the structure and function of the viral protein.


    The researchers’ approach, known as amino acid interaction network analysis, evaluates how one mutated amino acid can influence nearby amino acids depending on how “networked” they are — a measure of how much a given amino acid interacts with its neighbors. This yields richer information than simply examining individual changes in the one-dimensional amino acid sequence space, Sasisekharan says.

    With the network approach, you’re looking at that amino acid residue in the context of its neighborhood and environment,” he says. “When we started to move away from the one-dimensional sequence space toward multidimensional network space, it became evident that critical information about the interaction of an amino acid in its three-dimensional environment in the protein structure is lost when you look at just the one-dimensional sequence space.”


    Sasisekharan’s lab has previously used this technique to determine how mutations in the hemagglutinin protein of an avian flu virus could help it to infect people. In that study, he and his laboratory identified mutations that could change the structure of hemagglutinin so that it could bind to receptors in the human respiratory tract.


    When Omicron emerged, with about three dozen mutations on the spike protein, the researchers decided to rapidly use their method to study the variant’s ability to evade human antibodies. They focused their analysis on the receptor binding domain (RBD), which is the part of the spike protein targeted by antibodies. The RBD is also the part of the viral protein that attaches to human ACE2 receptors and allows the virus to enter cells.


    Using their network modeling approach, the researchers studied how each of the mutations on the RBD changes the protein’s shape and affect its interactions with four classes of human antibodies that target SARS-CoV-2. Class 1 and 2 antibodies target the RBD site that binds to the ACE2 receptor, while class 3 and 4 antibodies bind to other parts of the RBD.


    The researchers compared the Omicron variant to the original SARS-CoV-2 virus, as well as the Beta and Delta variants. The Beta and Delta variants have mutations that help them evade class 1 and 2 antibodies, but not class 3 and 4. Omicron, on the other hand, has mutations that affect the binding of all four classes of antibodies.

    With Omicron you can see a significant number of sites being perturbed compared to Beta and Delta,” Sasisekharan says. “From the original strain to the Beta strain, and then the Delta strain, there is a general trend towards a greater ability to escape.” Those perturbations allow the virus to evade not only antibodies generated by vaccination or previous SARS-CoV-2 infection, but also many of the monoclonal antibody treatments that pharmaceutical companies have developed.


    As patients began to appear with Omicron infections, researchers and pharmaceutical companies sought to guide treatment by predicting which antibodies were most likely to retain their efficacy against the new variant.


    Based on their one-dimensional sequence and single point mutation analyses, pharmaceutical companies believed that their monoclonal antibodies were likely to bind Omicron and not lose any potency. However, when experimental data became available, the Omicron variant was found to substantially escape from monoclonal antibodies known as ADG20, AZD8895, and AZD1061, as predicted by the network analyses in this study, while the activity of monoclonal antibody S309 was also reduced by threefold.


    Additionally, the study revealed that some of the mutations in the Omicron variant make it more likely that the RBD will exist in a configuration that makes it easier to grab onto the ACE2 receptor, which may contribute to its enhanced transmissibility.


    The researchers plan to use the tools described in this paper to analyze future variants of concern that may emerge.


    Vaccine targets

    The findings from the new study could help to identify regions of the RBD that could be targeted with future vaccines and therapeutic antibodies. The Sasisekharan lab has previously engineered a therapeutic antibody that potently and specifically neutralized the Zika virus by targeting a highly networked envelope surface protein of the Zika virus. Sasisekharan hopes to identify RBD sites where mutations would be harmful to the SARS-CoV-2 virus, making it harder for the virus to escape antibodies that target those regions.


    “Our hope is that as we understand the viral evolution, we’re able to hone in on regions where we think that any perturbation would cause instability to the virus, so that they would be the Achilles heels, and more effective sites to target,” he says.


    To create more effective antibody treatments, Sasisekharan believes it may be necessary to develop cocktails of antibodies that target different parts of the spike protein. Those combinations would likely need to include class 3 and 4 antibodies, which appear to offer fewer escape routes for the virus to evade them, he says.


    Reference: “Insights on the mutational landscape of the SARS-CoV-2 Omicron variant receptor binding domain” by Nathaniel L. Miller, Thomas Clark, Rahul Raman and Ram Sasisekharan, 23 January 2022, Cell Reports Medicine.

    DOI: 10.1016/j.xcrm.2022.100527


    The research was funded by the National Institutes of Health and the Singapore-MIT Alliance for Research and Technology.

  • Scientists speak out on being silenced when raising concerns about COVID lab leak theory

    Scientists told Fox News that they incurred backlash and resistance to getting their work published


    Scientists speak out on being silenced when raising concerns about COVID lab leak theory
    Some scientists have begun speaking out about efforts to silence researchers who raised concerns about the possibility that COVID-19 could have originated in a…
    www.foxnews.com


    Some scientists have begun speaking out about efforts to silence researchers who raised concerns about the possibility that COVID-19 could have originated in a Chinese lab.


    "It shot from every direction from people who we now know were actually thinking exactly the same thing but have chosen to say the opposite, which is extraordinary," Australian Dr. Nikolai Petrovsky, a Flinders University Medicine professor, told Fox News of the backlash he received for voicing concerns that the pandemic may have originated in a lab.

    Petrovsky was not alone, according to reporting from Fox News' Benjamin Hall, who spoke with scientists from Israel, the U.S., Australia, Germany, the U.K., Australia and Germany. The scientists told Fox News that they received backlash and resistance to getting their work published, even from those who quietly believed in the possibility of the "lab-leak theory."


    "It's taken two years for that to finally come out and be exposed," Petrovsky said.


    The scientists say that there was a top-down effort aimed at protecting the scientific community from negative public attention, with fears spreading among scientists that a public realization that the pandemic may have spread due to gain-of-function research in a lab could hamper future experiments.


    Many in the scientific community who attempted to speak out about COVID-19's origins were labeled conspiracy theorists in the media and by fellow scientists early on in the pandemic, even though the possibility of human error has now gained renewed attention from experts.


    The scientists expressed fear to Fox News that the silencing of such voices has led to little change, with gain-of-function research continuing both in the U.S. and abroad despite growing calls for international regulation.

    But the scientists expressed outrage that there was more of an effort by China, some scientists and media to cover up how the pandemic may have started, leaving little hope for a push for stricter regulation.

  • So no-one EVER claimed vaccines would stop omicron in its tracks.

    They are now testing a new version of the mRNA vaccines that may work as well against omicron as the original vaccines worked against the first variant of COVID.


    Three doses of the present vaccines significantly reduce omicron infection, and even more than that, they reduce the average severity of the illness, and death. Reducing the infection rate even a small amount can reduce the transmission rate (Rt) until it is negative, so the total number of cases declines. An imperfect vaccine coupled with masks and social distancing may well reduce the Rt to a negative number. Masks by themselves can reduce transmission by ~80%. This has been common knowledge in Europe since the 14th century.


    An evidence review of face masks against COVID-19
    The science around the use of masks by the public to impede COVID-19 transmission is advancing rapidly. In this narrative review, we develop an analytical…
    www.pnas.org

  • “What’s good about vaccines is they don’t just generate B cells, which produce the monoclonal [antibody] response, but also T cells, which provide additional forms of protection,” he says.

    No this is fake news for most vaccines. Pfizer/Oxford astra --> monoclonal antibodies.

    Moderna is much broader but still very narrow antibodies. But infection generates at least 20 different antibodies. So a re-infection with Omicron is just a soft flu/cold.

    But the scientists expressed outrage that there was more of an effort by China, some scientists and media to cover up how the pandemic may have started, leaving little hope for a push for stricter regulation.

    $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ for new vaccines for self invented virus....

  • Update from Omicron land South Africa:: https://www.nicd.ac.za/disease…rveillance-datcov-report/


    The up-wave did progress with more than 100%/week. The down turn does, as predicted, proceed much slower with about 25..30% a week. So within 6 weeks we see now a bit less than 1/3 of the max cases. So it will take about 12 weeks to get down from top wave to 1/10 of wave and 24 weeks to 1/100. But here we face the sudden death phase where most virus find no new victims. So the full end can occur anytime after 20 weeks from peek.


    Best thing to do is to ASAP stop all CoV-19 measures! Else we cultivate new islands for new fires sources.

  • BBC UK the main FM/R/B source of CoV-19 fake information goes on with fake-fake fact checking in their own style:: https://www.bbc.com/news/60199614


    Have fun to see that the Cochrane Ivermectin fake review shines up again. Also the fake argument that heart issues are more frequent after CoV-19 than vaccination, where we know for age < 30 it > 20x more frequent after vaccination.


    So who still trusts BCC? Obviously only fools that still believe that once famous FM/R/B institutions like Cochrane or Lancet have any remaining value. These folks simply published to many constructed lies and now we must rate them on the same level as the Timbuktu journal for pregnant horses...

  • You seem to be resistant to facts. Boostered (Pfizer) get 4x more often Omicron than unvaxx....

    That is incorrect, to say the least. Probably you say this because you (or your sources) do not understand statistics, and the base rate fallacy. I would recommend you read the papers at this site:


    Home | Covid-19 Data Science
    This page aggregates and tries to provide a balanced discussion of research results, data sets, applications and models, and commentaries regarding Covid-19,…
    www.covid-datascience.com


    . . . but it would be a waste of your time. I am sure you would not understand them.

  • Around 10% of travellers wearing masks - supposed to be a 'condition of carriage' - but there's no enforcement.

    People keep saying "I am through with COVID," but COVID is not through with them.


    The response to the 1918 pandemic also fell apart in the last years, because people were fed up with it. See:

    What We Can Learn From How the 1918 Pandemic Ended

    Opinion | What We Can Learn From How the 1918 Pandemic Ended
    Overconfidence, indifference and weariness are perhaps the biggest dangers.
    www.nytimes.com


    QUOTE:


    Nearly all cities in the United States imposed restrictions during the pandemic’s virulent second wave, which peaked in the fall of 1918. That winter, some cities reimposed controls when a third, though less deadly wave struck. But virtually no city responded in 1920. People were weary of influenza, and so were public officials. Newspapers were filled with frightening news about the virus, but no one cared. People at the time ignored this fourth wave; so did historians. The virus mutated into ordinary seasonal influenza in 1921, but the world had moved on well before.

  • Nearly all cities in the United States imposed restrictions during the pandemic’s virulent second wave, which peaked in the fall of 1918.

    200 years earlier they did burn witches and it also didn't help. The only mean is social distancing. Masks other than FP95/98 are simply crap. Same for gene therapy today. Why did Pfizer sabotage J&J and Novavax vaccine production? Take a real vaccine not crap. May be its to late already..

  • Johns Hopkins researchers: Lockdowns had ‘little to no effect’ on COVID-19 deaths but ‘imposed enormous economic and social costs’ – White House Wire


    Johns Hopkins researchers: Lockdowns had ‘little to no effect’ on COVID-19 deaths but ‘imposed enormous economic and social costs’

    Lockdowns in the U.S. and Europe “had little to no effect on COVID-19 mortality” but “imposed enormous economic and social costs” in the places where they were implemented, researchers at Johns Hopkins University said in a new analysis released this week.

    What are the details?

    The researchers reportedly reviewed two dozen unique studies conducted during the early stages of the pandemic as a part of their meta-analysis and ultimately found that lockdowns in the U.S. and Europe only reduced COVID-19 mortality by an average of 0.2%.

    Temporary shelter-in-place orders were also found to be ineffective, only reducing COVID-19 mortality by 2.9% on average, the researchers noted.

    The analysis was published by the Johns Hopkins Institute for Applied Economics, Global Health, and the Study of Business Enterprise, an organization led by one of the analysis’ authors, Steve H. Hanke.

    Hanke, a professor of applied economics at the renowned university, was joined by Jonas Herby, a special advisor at the Center for Political Studies in Copenhagen, Denmark, and Lars Jonung, professor emeritus in economics at Lund University, Sweden, in conducting the research.

    Together, they concluded, “We find no evidence that lockdowns, school closures, border closures, and limiting gatherings have had a noticeable effect on COVID-19 mortality.”

    What else?

    Yet while lockdowns during the initial phase of the pandemic failed to prevent the spread of the deadly pathogen as many public health experts promised, they did impose “devastating effects” on the places that implemented them, the researchers noted.

    “They have contributed to reducing economic activity, raising unemployment, reducing schooling, causing political unrest, contributing to domestic violence, and undermining liberal democracy,” the researchers said. “These costs to society must be compared to the benefits of lockdowns, which our meta-analysis has shown are marginal at best.”

    “Such a standard benefit-cost calculation leads to a strong conclusion: lockdowns should be rejected out of hand as a pandemic policy instrument,” they concluded.

    In fact, the only shutdown policy that may have achieved marginal success in reducing COVID deaths was bar and restaurant closures. But even in that case, the researchers said more studies were needed.

    Why does it matter?

    The conclusion stands in complete contrast to the widely accepted notion presented by public health experts during the early stages of the pandemic.

    Many leading epidemiologists — including Dr. Neil Ferguson of the Imperial College London and scientists at the Institute for Health Metrics and Evaluation at Washington University — argued early on that lockdowns were absolutely necessary to avoid mass fatalities.

    The analysis made specific reference to Imperial College London’s initial estimate that lockdowns would reduce COVID deaths by as much as 98%. That estimate, according to the researchers, proved not even close to correct.

    Furthermore, after examining deaths early during the pandemic, they found that by end of the lockdown period studied, on May 20, 2020, a total of 97,081 people had died of COVID-19 in the U.S. Another prominent model at the time had predicted there would be 99,050 deaths without lockdowns.

    The analysis is sure to garner widespread attention over the next several days and weeks as many around the globe continue to debate over the efficacy of lockdown policies to combat the ongoing pandemic.

  • and maybe entertainment can release fear
    "church for some"

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  • Is China’s Sinopharm Inactivated COVID-19 Vaccine Compromising Healthy People’s Immune System?


    Is China’s Sinopharm Inactivated COVID-19 Vaccine Compromising Healthy People’s Immune System?
    A team of scientists led by members of Shanghai Institute of Stem Cell Research and Clinical Translation at the Shanghai East Hospital’s School of
    trialsitenews.com


    A team of scientists led by members of Shanghai Institute of Stem Cell Research and Clinical Translation at the Shanghai East Hospital’s School of Medicine, Tongji University, report on some disturbing trends associated with mass COVID-19 vaccinations across multiple nations with inactivated SARS-CoV-2 vaccines from China.


    Led by corresponding authors Zhongmin Liu, Congrong Wang, and Yi E. Sun, the authors report that the vaccination program is impacting persons above and beyond simply generating neutralizing antibodies. They report seemingly constant changes in hemoglobin A1c, serum sodium and potassium levels, not to mention coagulation profiles as well as kidney functions in 100% healthy study volunteers post a jab with inactive vaccines (e.g., Sinopharm, etc.). However, the medical researchers also discovered in their study that comparable modifications have been observed in COVID-19 patients, suggesting vaccination “mimicked an infection.” After conducting single-cell mRNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) looking at the samples prior to and after 28 days post the first jab the study authors report numerous and uniform changes in gene expression of several immune cell types. Among other findings the authors note lower counts of CD8+ T cells, mediators of adaptive immunity, as well as more classic monocyte contents. Additional sequences (snRNA-seq) also exhibited greater NF-kB signaling (associated with production of cytokine and inflammation generally) as well as lower amounts of type I interferon responses, confirmed via biological assays, also known to occur post COVID-19 infection with severe symptoms. The study authors suggest potentially adverse impacts from the mass vaccination program, recommending caution when vaccinating persons with pre-existing conditions such as diabetes, electrolyte imbalances, renal dysfunction, and coagulation disorders.


    Study Type

    Longitudinal Follow up study


    The Vaccine Under Investigation

    SARS-CoV-2 vaccine (Vero Cell) inactivated by the Beijing Institute of Biological Products Co. Ltd. (Sinopharm)



    Background

    The authors report in Nature, Cell Discover indicate that based on their observations inoculation with inactivated COVID-19 vaccines that “in addition to stimulating the generation of neutralizing antibodies” the products also “influenced various health indicators including those related to diabetes, renal dysfunction, cholesterol metabolism, coagulation problems, electrolyte imbalance” in such a way as it almost seems like actual SARS-CoV-, the virus behind COVID-19 is triggered by the inactivated vaccines.


    Dramatic Changes Post Vaccination

    For example, the authors from China used sophisticated sequencing methods such as scRNA-seq of the PBMCs from vaccine study volunteers pre-and post- the jab finding “dramatic changes in immune cell gene expression, not only echoing some of the clinical laboratory measures but also suggestive of increased NF-kB-elated inflammatory responses” occurring in classical monocytes. Post-vaccination, the sequencing observation suggests impacts to “the gene set positively contributing to MVS scores, also known to be associated with severe symptom development” and highly expressed in monocytes.


    Meanwhile, the authors point out that while type 1 interferon (IFN-α/β) are considered beneficial against SARS-CoV-2 infection, they were actually “downregulated after vaccination.”


    Summary

    Mass vaccination may be damaging innocent volunteers during study and in association with mass vaccination as the inactivated vaccines, in addition to eliciting neutralizing antibody responses, could be seriously compromising people’s immune systems.


    The Academic Medical Center

    The study leads to work out of the Shanghai East Hospital, School of Medicine, Tongji University. Based in Pudong, Shanghai, this teaching hospital is affiliated with Tongji University. Founded in 1920, the Shanghai East Hospital and the Shanghai Tongji University School of Medicine cover two campuses including 61 clinical and technical departments and offices.


    A large hospital with 2,000 beds, what’s known as the “South-Campus” is known for medical procedures, disease prevention, and medical education as well as clinical research. Combined both campuses employ 2,800 staff and at least 400 attending physicians. This complex serves 3 million walk-in patients as well as emergency room patients per annum—including about 4000 international patients.


    Lead Research/Investigator

    Zhongmin Liu, Shanghai Institute of Stem Cell Research and Clinical Translation at the Shanghai East Hospital’s School of Medicine, Tongji University


    Yi E. Sun, Shanghai Institute of Stem Cell Research and Clinical Translation at the Shanghai East Hospital’s School of Medicine, Tongji University


    Congrong Wang, Shanghai Institute of Stem Cell Research and Clinical Translation at the Shanghai East Hospital’s School of Medicine, Tongji University; Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Department of Endocrinology & Metabolism


    Comprehensive investigations revealed consistent pathophysiological alterations after vaccination with COVID-19 vaccines

  • Omicron: a chimera of two early SARS-CoV-2 lineages


    Omicron: a chimera of two early SARS-CoV-2 lineages
    Research Square is a preprint platform that makes research communication faster, fairer, and more useful.
    www.researchsquare.com


    Abstract

    The current global epidemiology of COVID-19 is now characterized by the emergence and rapid spread of the SARS-CoV-2 Omicron variant on a global scale1,2. Despite the variant’s prompt predominance, there remain knowledge gaps in its origin and evolution history3–6. Here, we show that Omicron lineage SARS-CoV-2 is characterized by the feature of chimera. It was generated by genomic recombination of two early PANGO lineages of SARS-CoV-2. In the recombination event, strains with medium or high circulating intensity like SARS-CoV-2/human/USA/COR-21-434196/2021 belonging to PANGO lineage BA.1 provided the fundamental genome and served as the major parents, while the rare lineage strains like SARS-CoV-2/human/IRN/Ir-3/2019 belonging to B.35, as the minor parents, hybridized their genomic fractions into the major genomes at position 21593-23118nt. This recombination event results in 22 amino acid residue substitutions for the variant of Omicron, including 16 in the pivotal RBD of the spike protein. These substitutions have led to some subtle variations in the spatial structure and the affinity to hACE2 receptor of the spike protein7,8, thereby raising concerns about the effectiveness of available vaccines and antibody therapeutics9–12. The global spread and explosive growth of the SARS-CoV-2 in human population increase opportunities for future recombination13–15.

  • The data show miscarriages and cancer increased 300% in 2021 over the previous five-year average. Neurological disorders increased 1000% in 2021 over the past five-year average, increasing from 82,000 to 863,000 in one year.

    Now we have the response of the US military:

    They did take database down because of a "data glitch". Usually a "data glitch" is a malfunction.. But no malfunction has been seen or noted by anybody.

    So second explanation:: The 2021 data is correct!! wow! But the old data is incorrect in fact 5 year data is missing. It did not disappear just never entered...Why? An administration glitch??

    So not 5 year data is missing all data is missing .... as we have a 1000% increase for one year... How could they miss all data for certain diagnoses ??? Same as VAERS ???


    It will be interesting to see what they try to fake/correct.

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