Will focus primarily on Omicron news here in North America (the United States and Canada) as it slowly spreads across North America. ---------- Omicron live updates: Variant found in 6 people in Nebraska, 1 person traveled to Africa Five were likely exposed through household contact with the first case. By Morgan Winsor, Emily Shapiro, and Meredith Deliso Last Updated: December 3, 2021, 5:44 PM ET As the COVID-19 pandemic has swept the globe, more than 5.2 million people have died from the disease worldwide, including over 785,000 Americans, according to real-time data compiled by Johns Hopkins University's Center for Systems Science and Engineering. Just 59.6% of the population in the United States is fully vaccinated against COVID-19, according to data from the Centers for Disease Control and Prevention. Latest headlines: 3 omicron cases detected in Maryland Omicron identified in Nebraska 'It's better to be vaccinated than unvaccinated,' CDC says Hawaii latest state to confirm omicron case https://abcnews.go.com/Health/live-updates/coronavirus/?id=81441585 ---------- Omicron puts scientists on red alert Scientists and companies race to study the latest coronavirus variant and what it means for therapies and vaccines by Ryan Cross December 2, 2021 | A version of this story appeared in Volume 99, Issue 44 Omicron, a new variant of the coronavirus, has put the world on red alert. Reports emerged from South Africa on Nov. 24, and 2 days later the World Health Organization dubbed Omicron a variant of concern. The news rattled financial markets and prompted countries to close their borders, though authorities found within a week that the variant was already in Australia, China, Europe, and the US. The international response to Omicron has been swifter and more severe than for previous variants for two reasons: cases in South Africa are rising more rapidly than expected, and the variant contains an unprecedented number of mutations. As soon as Omicron’s genetic sequence was shared, scientists began racing to understand whether it will pose a greater challenge to vaccines and therapies than its predecessors. “It is just a different beast, and that has sent the alarm bells ringing,” says Richard J. Webby, an influenza scientist at St. Jude Graduate School of Biomedical Sciences. Omicron contains more than 50 mutations, including at least 30 in its spike protein, which the virus uses to infect human cells. The COVID-19 vaccines are based on the original virus’s spike. They spur our immune systems to make antibodies that bind to a crucial region of the spike called the receptor-binding domain. The Delta variant has two mutations in that region, and the Beta variant has three. Omicron has between 10 and 15. “The list of mutations goes on so much longer in Omicron, and that was really startling to see,” says Rommie E. Amaro, a computational biologist and chemist at the University of California San Diego. The COVID-19 vaccines were less effective against the Beta variant, which had mutations that helped it partially evade immune responses. But Beta faded as a concern because of the far more transmissible Delta. Omicron shares mutations with Beta and Delta and has many more whose functions are unknown. “It is pretty clear we are going to take a hit, but we don’t know how big of a hit,” says Nicole Doria-Rose, chief of the Humoral Immunology Core at the US National Institutes of Health’s Vaccine Research Center. Academic, institutional, and industrial scientists are planning studies to see if antibodies produced from vaccination or natural infection can neutralize Omicron. These tests will take time, as scientists have to either grow the virus or create synthetic versions of it. The first results could come from South Africa in mid-December, and data from other groups should arrive later in the month. Firms including Johnson & Johnson, Moderna, Novavax, and Pfizer have also announced plans to make new versions of their vaccines tailored to Omicron. Gilead Sciences, Merck & Co., and Pfizer say their small-molecule antiviral therapies, which target coronavirus enzymes, should work against Omicron, although they plan further testing. Regeneron Pharmaceuticals says the mutations in Omicron’s spike could reduce the ability of its monoclonal antibody therapy, which targets the spike, to neutralize the virus. “There is a lot that we don’t know” about Omicron, says David Montefiori, an HIV scientist at Duke University Medical Center. Epidemiologists will watch to see if this variant spreads faster than Delta and whether its infections are more or less severe, he says. “I would guess over the next 4 weeks that we will be able to understand that from the way the infections play out in the real world.” https://cen.acs.org/pharmaceuticals/vaccines/Omicron-puts-scientists-red-alert/99/i44 ---------- wrbtrader
Some experts suggest Omicron variant may have evolved in an animal host By Helen Branswell Dec. 2, 2021 When Covid-19 variants arise, the accepted wisdom is that the constellation of mutations they contain developed in an immunocompromised person who contracted the virus and couldn’t shake the infection. But some scientists have an alternative theory for where the latest variant of concern, Omicron, may have acquired the unusual mutations that stud its spike protein. They speculate the virus could have evolved in another animal species. The theory goes that some type of animal, potentially rodents, was infected with the SARS-CoV-2 virus sometime in mid-2020. In this new species, the virus evolved, accumulating roughly 50 mutations on the spike protein before spilling back over into people. Kristian Andersen, an immunologist at the Scripps Research Institute, is among those who has been raising the idea that Omicron may have emerged from a reverse zoonotic event. (A zoonotic event is when an animal pathogen starts to infect and spread among people. A reverse zoonosis is when such a virus passes back into an animal species.) “I know that most people think that these [come from] immunocompromised individuals, and I do think that that’s plausible, but to be perfectly honest, I actually think this reverse zoonosis followed by new zoonosis seems more likely to me given just the available evidence of the really deep branch, and then the mutations themselves, because some of them are quite unusual,” Andersen told STAT. “I don’t think we should dismiss that possibility, because I think it’s definitely on the table.” A number of other scientists who study the evolution of viruses have told STAT they think the idea isn’t out of the question. Some place more weight on the theory that variants develop in immunocompromised people, while others feel there isn’t enough evidence at this point to favor one option over the other. “Personally, I think it’s probably more likely it was circulating undetected, in an immunocompromised individual,” Emma Hodcroft, a molecular epidemiologist at the Institute of Social and Preventive Medicine in Bern, Switzerland, said via email. Having said that, though, Hodcroft insisted that it is important to explore the hypothesis. “I would certainly consider it a plausible alternative hypothesis to the evolution during a persistent infection in a human,” said Andrew Rambaut, a professor of molecular evolution at the Institute of Evolutionary Biology in Edinburgh. He cautioned that coming up with a definitive answer won’t be quick. “I am not sure we will be in a position to say for sure for a while,” Rambaut wrote in an email. One of the peculiar traits of SARS-2 underpins this thinking. It is what virologists describ e as a promiscuous virus; it is capable of infecting a number of species. Dogs and house cats. Large cats. Mink. White-tailed deer. Given how easily the virus seems to jump from species to species, people studying it assume this list will grow. The original virus that came out of Wuhan, China, in early 2020 did not infect rodents. But as variants — Alpha, Beta, Delta — started to emerge, those viruses could infect rodents. Robert Garry, a professor of microbiology and immunology at Tulane Medical School, has been tracking the SARS-2 mutations that have arisen. Seven are associated with rodent adaptation — the changes that seemed to allow the virus to infect mice, rats, and related species. All seven of those mutations are in Omicron, Garry noted. He believes it’s a toss-up whether the variant developed in an animal or a human host, but if it’s the former, his bet would be on rodents. Getting a firm answer might require enormous luck. Scientists are looking at various animal species to see if they can be infected with SARS-2; were they to find viruses like Omicron in any, that would swing the needle. But Michael Worobey, a professor of evolutionary biology at the University of Arizona, thinks one could do some experiments on selected species of wild animals to see if they can be infected and if, when infected, similar patterns of viral evolution occur. Studying the molecular clock of viruses that spread in animals — looking at the speed at which they evolve and comparing it to SARS-2 evolution in humans — could also provide some clues, said Worobey, who initially thought Andersen’s idea was not impossible, but not the likeliest of explanations for Omicron. After hearing details of the explosive outbreak in white-tailed deer, he’s rethinking the idea. For Worobey, the question is whether any animal species can become chronically infected with SARS-2 — in effect, whether there are animal species in which SARS-2 lingers in the way it does in immunocompromised people. That could put positive selective pressure on the virus — in other words give it an incentive to mutate to stay ahead of the animal’s immune response. “It does move my thinking in terms of Omicron possibly having come from a reservoir, if there are [animal] reservoirs that do chronic infections,” he said. Part of what leads Andersen to wonder about an animal source is the fact that the variant traces back to viruses that were spreading over a year ago. “That in itself you need to be able to explain,” he said. Angela Rasmussen, a coronavirus virologist at the University of Saskatchewan’s Vaccine and Infectious Disease Organization, agreed. “I think it’s pretty obvious to everybody … that this virus has been on an independent evolutionary track for quite some time and it’s very surprising, which to me just kind of goes back to say well, the idea that this could be … plausible,” she said. Regardless of whether this variant emerged in another species or not, given SARS-2’s ability to jump species, it is possible the world will face animal-derived variants in the future, Garry warned. The upshot of that? “We’re going to have to keep tweaking the vaccines.”..... https://www.statnews.com/2021/12/02...n-variant-may-have-evolved-in-an-animal-host/ -------- This is another possible sources of Covid Variants of Concern...experiments in laboratories by evolutionary biologists or zoonosis involving Covid naturally infecting a human host and then infecting an animal host (e.g. rodent) to then reinfect a human host again as a mutated virus. More importantly, this source of Variants of Concern can occur anywhere in the world...including in the United States or Canada. In my opinion, evolutionary biologists should not be doing these types of zoonosis experiments. I just don't like the ethics involved and there are too many laboratories in the world that do not have proper safety protocols to control such types of experiments. wrbtrader
It's here, it's in every state, and everyone will get it. It doesn't mean the world is fucking doomed. Move along. Fer cryin' out loud! As for rodentia getting the thing? Uh huh, yeah, sure. I guess owners of pet rats and mice need to stop french-kissing their pets. WTF?!?
Stop being a drama queen. It's not in every state and the world is not doomed...just fucked. Also, Omicron has not been found in wild animals although prior variants have been found in wild animals (e.g. mink farms) in which they needed to be destroyed to prevent Covid from jumping from animal to host...increasing the risk of Variant of Concern. https://www.nationalgeographic.com/animals/article/what-the-mink-coronavirus-pandemic-has-taught-us Right now, as stated multiple times in other threads...they can not stop Omicron but they can slow the spread so that governments can be prepared just in case shit does hit the fan. Better safe than sorry Regardless, I'm more interested in the science of Covid and how our immune system defenses do battle against it and how we fuck ourselves with stupidity about Covid. wrbtrader
How Scientists Can Update COVID Vaccines against Omicron A microbiologist explains how Pfizer and Moderna would rapidly adjust mRNA vaccines If the omicron variant of the coronavirus is different enough from the original variant, it’s possible that existing vaccines won’t be as effective as they have been. If so, it’s likely that companies will need to update their vaccines to better fight omicron. Deborah Fuller is a microbiologist who has been studying mRNA and DNA vaccines for over two decades. Here she explains why vaccines might need to be updated and what that process would look like. 1. Why might vaccines need to be updated? Basically, it’s a question of whether a virus has changed enough so that antibodies created by the original vaccine are no longer able to recognize and fend off the new mutated variant. Coronaviruses use spike proteins to attach to ACE-2 receptors on the surface of human cells and infect them. All mRNA COVID-19 vaccines work by giving instructions in the form of mRNA that direct cells to make a harmless version of the spike protein. This spike protein then induces the human body to produce antibodies. If a person is then ever exposed to the coronavirus, these antibodies bind to the coronavirus’s spike protein and thus interfere with its ability to infect that person’s cells. The omicron variant contains a new pattern of mutations to its spike protein. These changes could disrupt the ability of some – but probably not all – of the antibodies induced by the current vaccines to bind to the spike protein. If that happens, the vaccines could be less effective at preventing people from getting infected by and transmitting the omicron variant. 2. How would a new vaccine be different? Existing mRNA vaccines, like those made by Moderna or Pfizer, code for a spike protein from the original strain of coronavirus. In a new or updated vaccine, the mRNA instructions would encode for the omicron spike protein. By swapping out the genetic code of original spike protein for the one from this new variant, a new vaccine would induce antibodies that more effectively bind the omicron virus and prevent it from infecting cells. People already vaccinated or previously exposed to COVID-19 would likely need only a single booster dose of a new vaccine to be protected not only from the new strain but also other strains that may be still in circulation. If omicron emerges as the dominant strain over delta, then those who are unvaccinated would only need to receive 2-3 doses of the updated vaccine. If delta and omicron are both in circulation, people would likely get a combination of the current and updated vaccines. 3. How do scientists update a vaccine? To make an updated mRNA vaccine, you need two ingredients: the genetic sequence of the spike protein from a new variant of concern and a DNA template that would be used to build the mRNA. In most organisms, DNA provides the instructions for making mRNA. Since researchers have already published the genetic code for the omicron spike protein, all that’s left to do is make a DNA template for the spike protein that would be used to produce the mRNA part of new vaccines. To do this, researchers mix DNA templates with synthetic enzymes and four molecular building blocks that make mRNA – G, A, U and C for short. The enzymes then build an mRNA copy of the DNA template, a process called transcription. Using this process, it takes only minutes to produce a batch of the mRNA for vaccines. Researchers then place the mRNA transcripts within fatty nanoparticles that protect the instructions until they are safely delivered into cells in your arm. 4. How long until a new vaccine might be ready? It takes only three days to generate the DNA template needed to make a new mRNA vaccine. Then it would take about a week to produce sufficient doses of the mRNA vaccine for testing in the lab and another six weeks to perform the pre-clinical tests on human cells in test tubes to make sure a new vaccine works as it should. So within 52 days, scientists could have an updated mRNA vaccine ready to plug into the manufacturing process and begin producing doses for a human clinical trial. That trial would likely require at least another few weeks for a total of around 100 days to update and test a new vaccine. While that trial is going on, manufacturers could start switching their current process to making a new vaccine. Ideally, once the clinical trial is complete – and if the vaccine gets authorized or approved – a company could immediately start rolling out doses of a new vaccine. 5. Does an updated vaccine need full clinical trials? It’s currently not clear how much clinical data would be required to get FDA approval or authorization for an updated COVID-19 vaccine. However, all the ingredients would be the same in a new vaccine. The only difference would be a few lines of genetic code that would ever so slightly change the shape of the spike protein. From a safety perspective, an updated vaccine is essentially identical to the already tested vaccines. Because of these similarities, clinical testing may not need to be as extensive as what was needed for the first-generation COVID-19 vaccines. At a minimum, clinical trials for updated vaccines would likely require safety testing and confirmation that an updated vaccine induces antibody levels on par with the response of the original vaccine against the original, beta and delta strains. If these are the only requirements, then researchers would enroll only hundreds – not tens of thousands – of people to obtain the clinical data needed. One important thing to note is that if vaccine manufacturers decide to update their vaccines for the omicron variant, it wouldn’t be their first time making this kind of change. A previous variant, B.1.351, emerged in October 2020 and was sufficiently resistant to then-current vaccines to warrant updating them. Manufacturers quickly responded to the potential threat by developing an updated mRNA vaccine to match this variant and performed clinical trials to test the new vaccine. Fortunately, this variant did not become the dominant variant. But if it had, vaccine manufacturers would have been ready to roll out an updated vaccine. If it turns out that omicron – or any future variant, for that matter – warrants a new vaccine, companies have already completed the dress rehearsals and are ready to meet the challenge. https://www.scientificamerican.com/article/how-scientists-can-update-covid-vaccines-against-omicron/ ---------- wrbtrader
Scientists see a ‘really, really tough winter’ with Omicron Another major pandemic wave seems inevitable. The big question is how much severe disease it will bring People line up outside a vaccination center in London on 13 December. The United Kingdom is accelerating its booster program in response to the rise of the Omicron variant.Rob Pinney/Getty Images When South African scientists first alerted the world to the rapid spread of a new SARS-CoV-2 variant, some speculated it might not take off in other countries. After all, an earlier variant named Beta, which dominated in South Africa between November 2020 and May, did not spread much beyond its borders and has since petered out. Today it’s clear that the world will not be so lucky this time. Although many questions remain, scientists feel increasingly confident that the new arrival, Omicron, is likely to dramatically alter the trajectory of the pandemic—and not for the better. Omicron has now been found in more than 70 countries and is rapidly gaining ground. As Science went to press, for example, Danish scientists estimated Omicron was just days away from replacing Delta as the most common variant. “What we see is an extraordinary, rapid spread,” says Troels Lillebæk, an infectious disease researcher at the University of Copenhagen. Despite very high vaccination rates, the country of 5 million is now seeing more than 6000 cases a day, roughly twice the number seen during the highest previous peak. (The growth seemed to show signs of slowing down early this week, but that may be in part because the country is reaching the limits of its testing capability.) Neighboring Norway, which has about the same population, is now projecting more than 100,000 cases a day in a matter of weeks, unless people drastically reduce social contacts. Even if Omicron causes milder disease, as some scientists hope, the astronomical case projections mean the outlook is grim, warns Emma Hodcroft, a virologist at the University of Bern. “A lot of scientists thought Delta was already going to make this a really, really tough winter,” she says. “I’m not sure the message has gotten across to the people who make decisions, how much tougher Omicron is going to make this.” For Hodcroft and other virologists, immunologists, and epidemiologists, Omicron is another dizzying plunge on the pandemic roller coaster, right before the holidays—a time of frenzied phone calls, late night work, and little sleep. “We have people working the whole weekend again,” says Florian Krammer, a vaccine researcher at the Icahn School of Medicine at Mount Sinai. “It doesn’t matter if something needs to be done at 10 p.m., it’s getting done.” As with earlier variants, a handful of countries are providing the world with most of the early data. South Africa, where scientists first observed the spread of Omicron, has sequenced a wealth of genomes and produced data about early cases. Denmark, with one of the best genomic surveillance systems in the world, has provided an in-depth view of how Omicron can explode on top of a Delta surge. And scientists in the United Kingdom are conducting a host of studies to nail down how well Omicron transmits in households and elsewhere, and how vaccines are doing against the variant. “We should be pretty grateful” to these countries, Hodcroft says. How good Omicron is at immune escape is also becoming clearer. Preliminary data from South Africa showed its rise coincided with an unexpected surge in reinfections. This past week, laboratory assays by several groups have shown antibodies, whether elicited by vaccines or a previous infection, are significantly less effective at neutralizing Omicron than other variants. And based on the first cases, scientists in the United Kingdom have estimated that protection from symptomatic illness is much lower in people who have received two doses of the AstraZeneca or messenger RNA vaccines. The good news is that boosters appear to bring protection against disease back to about 75%, and probably even higher against hospitalization. “I think it all boils down in the end to protection from severe disease,” Krammer says. Early data from Discovery, South Africa’s largest health insurer, presented on 14 December, offered some additional reassurance that Omicron’s immune escape isn’t complete. The data showed hospital admissions in the country are growing more slowly than in previous waves. That could mean the protection from severe disease is still robust in vaccinated and recovered people—or the virus is inherently a bit milder than Delta. But Harvard University epidemiologist William Hanage says the question of severity is still impossible to answer. Recent genomic comparisons suggest Omicron only began to spread in mid-October—earlier work had estimated late September—so the variant hasn’t infected enough people to conclude much of anything, he says. By chance, many of the early cases in South Africa happened to be in younger people, who are less likely to develop severe disease. And even if the variant turns out to be inherently milder, the volume of cases will likely overwhelm health systems. “A colleague put it really well in one of our little depressing Slack channels,” Hanage says: “There’s not much that can spread this fast and be benign to a society that’s already got full hospitals without it.” Scientists also worry Omicron—which represented a massive leap from known variants in genomic terms—may bring other, unpleasant evolutionary surprises. For instance, roughly one-tenth of Omicron genomes sequenced so far have an additional mutation in the spike protein called 346K that is predicted to make it even better at evading the immune system. “Omicron has most of the greatest hits for antibody escape already, so there aren’t a ton of additions that it could make, but 346K is one of them,” says Stephen Goldstein, a virologist at the University of Utah. “We have to keep an eye on it.” Given its divergence from earlier variants, Krammer thinks vaccine manufacturers should develop booster shots tailored to Omicron. Obtaining regulatory approval and making such boosters available in large numbers would take months, however—too long to address the crisis many scientists expect. And if the past year is any indicator, they are unlikely to be available to low- and middle-income countries in any meaningful quantities. For now, most European countries are hoping that providing existing boosters widely, in tandem with added control measures such as a ban on large gatherings, mask mandates, better ventilation, and working from home, will help lower the wave of Omicron infections and prevent hospitals from buckling. Maria Van Kerkhove, an epidemiologist at the World Health Organization, says vaccinating those who have not received any shots at all is still very important—even though it may be too late to get the numbers up substantially. “Get the vaccine into the arms of people who are most at risk,” Van Kerkhove says. “Look to see who you’re missing and focus on these.” https://www.science.org/content/article/scientists-see-really-really-tough-winter-omicron ---------- wrbtrader