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Thursday, December 2, 2021

Many Severe Covid-19 Survivors Go on to Die Within a Year

 New research this week finds that people who are hospitalized with severe covid-19 but survive often pay a heavy price afterward. The study concluded that these survivors were more than twice as likely to die in the subsequent 12 months compared to people who had tested negative for the virus. This relatively increased risk of death was even higher for people under the age 65.

While there remains much research to be done, studies thus far have made it clear that many covid-19 survivors can experience lingering symptoms even after the infection itself has cleared up. And those who are hospitalized are all the more vulnerable to these aftereffects. Severe covid often seriously damages the lungs and other organs, while life-saving interventions like steroids, ventilators, and life support devices like ECMO can take a toll on the body as well.

Researchers from the University of Florida had already published a study in July showing that hospitalized survivors were significantly more likely to be hospitalized again within six months, compared to those with mild to moderate covid-19. This new study of theirs, based on an examination of anonymous electronic health records, instead looked at the long-term mortality risk of patients up to a year later.

Nearly 14,000 patients in the same health care system were studied. These included 178 diagnosed with severe COVID-19 and 246 diagnosed with mild to moderate covid-19, as well as many others who tested negative for the virus but may have been sick for other reasons and received medical care in some way. Compared to covid-negative patients, and even after accounting for other factors like age and sex, those with severe covid were 2.5 times more likely to die in the next 12 months after their illness. Overall, just over 52% of severe covid patients died in a year’s time. There was no significant increased risk of mortality for mild to moderate cases, however.

]“This study provides evidence that the increased risk of death from covid-19 is not limited to the initial episode of covid-19, but a severe episode of covid-19 carries with it a substantially increased risk of death in the following 12 months,” the authors wrote in their study, published Wednesday in the journal Frontiers in Medicine.

About 20% of the deaths among these patients post-infection were attributed to problems with either the respiratory or cardiovascular system, the authors noted, the areas of the body that tend to be affected directly by infection from the coronavirus. But it’s well known that the symptoms of severe covid are often the result of an overzealous immune response, one that can wreak havoc all throughout the body. And it’s this potential for widespread damage that is likely to blame for the majority of added deaths seen in these survivors.

“Since these deaths were not for a direct covid-19 cause of death among these patients who have recovered from the initial episode of covid-19, this data suggests that the biological insult from covid-19 and physiological stress from covid-19 is significant,” they wrote.

Older people are more likely to develop severe illness and die from covid-19. But among patients in this study, the associated risk of dying was actually relatively greater for survivors of severe covid under age 65 than it was for patients over 65. Compared to similarly aged but non-infected people, they were more than three times more likely to die in the months after their hospitalization.

The results are yet another reminder that the harms of the pandemic run deeper than any official death toll can illustrate. As many as 7.5 million Americans have been hospitalized by covid-19, the Centers for Disease Control and Prevention has estimated. Given the risks that hospitalized survivors will face even after their initial ordeal, the authors say it’s “clear that prevention of significant covid-19 infection is the most effective way to decrease the risk of death following covid-19.”

https://gizmodo.com/many-severe-covid-19-survivors-go-on-to-die-within-a-ye-1848144418

Omicron has 'substantial' ability to evade immunity from prior COVID infection

 Omicron has a "substantial" ability to evade immunity from a previous COVID infection, according to the first real-world study of the variant's effect.

The finding suggests the new variant could cause a substantial wave of infections, even in populations with high levels of antibodies.

Researchers at South Africa's National Institute for Communicable Diseases (NICD) warn their finding has important public health implications.

They add: "Urgent questions remain regarding whether Omicron is also able to evade vaccine-induced immunity and the potential implications of reduced immunity to infection on protection against severe disease and death."

The scientists looked at almost 2.8 million confirmed cases of COVID-19 in South Africa since March 2020 and found 35,670 were reinfections.

The risk of a reinfection was lower in the Beta and Delta waves than the first surge of cases in March 2020 that was caused by the Wuhan strain of the virus.

But significantly they found the risk of reinfection in the current Omicron wave is 2.4 times higher than in the first wave.

The results have been published as a pre-print on the MedRxiv server and have not been peer reviewed.

The researchers say: "We find evidence of a substantial and ongoing increase in the risk of reinfection that is temporally consistent with the timing of the emergence of the Omicron variant in South Africa, suggesting that its selection advantage is at least partially driven by an increased ability to infect previously infected individuals.

"Immune escape from prior infection, whether or not Omicron can also evade vaccine derived immunity, has important implications for public health globally."

Professor Paul Hunter, of The Norwich School of Medicine, University of East Anglia, said: "The implications of this paper are that Omicron will be able to overcome natural and probably vaccine induced immunity to a significant degree.

"But, the degree is still unclear though it is doubtful that this will represent complete escape.

"The other big uncertainty is whether this increases the risk of severe disease, hospital admissions and deaths.

"With previous variants epidemiological studies showed that protection against severe disease from other variants was better maintained than protection against infection."

Although only around a quarter of the population in South Africa is fully vaccinated, immunity from natural infection is high because the country has had several large waves of COVID.

Earlier, the World Health Organisation (WHO) said it will deploy a surge team to South Africa to help deal with the variant outbreak.

The team will be sent to Gauteng province to help with surveillance and contact tracing.

However, Barry Schoub, chair of the South African government's committee on COVID vaccines, told Sky News initial signs were "good news".

"Certainly, at this stage, the news does look to be promising - the great majority of the breakthrough infection (in other words, individuals that have had infection despite vaccination) is mild.

"Our hospital surveillance is showing a little bit of an uptick but certainly nothing as dramatic as we've seen in the previous waves."


https://news.sky.com/story/covid-19-omicron-has-substantial-ability-to-evade-immunity-from-previous-coronavirus-infection-12484840

Over 42,000 Adverse Reaction Reports Revealed In 1st Batch Of Pfizer Vax Docs

 The FDA's excruciatingly slow release of data related to Pfizer's COVID-19 vaccine has already borne fruit, and it's damning despite a trickle of just 500 pages per month out of 329,000 pages - which will take until 2076 to complete.

As first reported by Kyle Beckerthere were a total of 42,086 case reports for adverse reactions (25,379 medically confirmed, 16,707 non-medically confirmed), spanning 158,893 total events.

More than 25,000 of the events were classified as "Nervous system disorders."

Since the vaccine has been publicly administered, there have been over 913,000 reports of adverse events in the OpenVAERS global database.

And that's just what's been reported.

https://www.zerohedge.com/covid-19/over-42000-adverse-reaction-reports-revealed-first-batch-pfizer-vax-docs

3rd US omicron case detected in Colorado

 Colorado health officials on Thursday reported that the third confirmed U.S. case of the COVID-19 omicron variant has been detected in their state.

The Colorado Department of Public Health and Environment (CDPHE) said in a statement that it has confirmed the first omicron case in Colorado.

"The case was identified in an adult female resident of Arapahoe County who had recently traveled to Southern Africa for tourism," the CDPHE said. "She is experiencing minor symptoms and is isolated and recuperating at home. She had been fully vaccinated and was eligible for the booster vaccine but had not received it yet."

Omicron in Colorado, per @CDPHE pic.twitter.com/DambvNffWN

Omicron cases have also previously been confirmed in California and Minnesota.

Colorado State Epidemiologist Rachel Herlihy said in a press conference on Thursday that the infected resident had followed public health guidelines when traveling, such as wearing a mask.

According to Herlihy, whole genome sequencing of the the woman's test was completed Thursday morning. Close contacts of the resident have so far tested negative.

Herlihy told reporters that the infected Colorado resident travelled through numerous countries in Africa and returned to Colorado late last week. At the time of her return, she was not symptomatic.

The Colorado health official noted that mild cases of omicron have been reported anecdotally, but pointed out that these cases appear to have been clustered in younger people who are less likely to develop severe illness due to COVID-19.

The Centers for Disease Control and Prevention (CDC) on Wednesday confirmed the first U.S. case of the omicron variant in California. Like the Colorado woman, the San Francisco resident who tested positive was fully vaccinated and had recently travelled to southern Africa.

In Minnesota, a fully vaccinated adult man was confirmed to have tested positive for the omicron variant on Thursday. The Minnesota man's mild symptoms had resolved by the time he got tested for COVID-19.

Though no cases of omicron have been confirmed in New York, New York City Mayor Bill de Blasio (D) said on Thursday that people should assume the variant is already present in the city.

"We are aware of a case of the Omicron variant identified in Minnesota that is associated with travel to a conference in New York City, and we should assume there is community spread of the variant in our city,” he said.

Since omicron's emergence, health experts have stated that it is still unclear how well the strain evades immunity offered by currently available COVID-19 vaccines. Numerous vaccine developers have hypothesized that oral COVID-19 treatments and booster shots should be effective against the variant.

Officials and health experts have said it will take a few weeks of testing before the omicron variant is better understood.

In response to the omicron variant's spread, the Biden administration has implemented a travel ban on eight African countries where the strain is believed to be prevalent. This measure has been blasted by health officials as being ineffective, though administration officials have argued it will buy time for the U.S. to better prepare for omicron.

https://thehill.com/homenews/state-watch/584090-third-us-omicron-case-detected-in-colorado

Most advanced lab-grown human embryos prompt question: Are they getting too real?

 The stem cells were no more than a week old when scientists moved them from their slick-walled plastic wells into ones lined with a thin layer of human endometrial tissue. But in that time, the cells had multiplied and transformed, organizing themselves into semi-hollow spheres. Per the instructions of the chemical cocktail in which they’d been steeping, they were trying to turn into embryos.

Video cameras captured what happened next: The balls of cells rotated until they were cavity-side-up, before finally touching down and grabbing onto the endometrial layer, a cellular proxy for a human uterus. Days later, when the scientists dipped paper test strips into the wells, pink lines appeared. Their Petri dishes were pregnant.

“These experiments clearly point out the fact that we are able to model in the dish the first touch between the embryo and the mother,” stem cell biologist Nicolas Rivron told reporters at a press conference.

On Thursday, Rivron and his colleagues at the Institute of Molecular Biotechnology of the Austrian Academy of Sciences in Vienna reported in Nature that they’ve learned to efficiently manufacture realistic models of human embryos from stem cells. These so-called blastoids aren’t the first successful attempt to recapitulate the developmental stage that embryos reach between four and seven days post-fertilization — when they’re a blastocyst made up of about a hundred cells and ready to implant into the walls of the uterus — but they appear to be the most advanced yet.

These synthetic embryos were made by mixing induced pluripotent stem cells with a brew of biochemical signals capable of coaxing them into forming spherical structures that include the beginnings of three distinct cell lineages — outer layers representing the future placenta and amniotic sac, and an inner clump of cells with the potential to develop into a fetus.

“This is a very, very close model of a real, complete human embryo,” said Insoo Hyun, director of research ethics at the Harvard Medical School Center for Bioethics, who was not involved in the study. “It’s probably the closest I’ve seen.”

The field of synthetic embryology has exploded in recent years. A parade of increasingly lifelike models that mimic portions of an embryo’s journey to personhood promise to shed light on critical moments of human development while providing a more flexible and ethical alternative to the study of human embryos, which has been historically limited by regulations and the willingness of IVF donors.

As the science of synthetic embryology gets more sophisticated, the models become more useful. But each advance raises a new round of ethical questions about where embryo models end and embryos begin. If it divides, organizes, and develops like an embryo, does it matter how it was made? Should an embryo derived from stem cells get the same legal and ethical rights as one produced when sperm met egg?

“At some point we have to ask, ‘when does an embryo model become so good that it functionally becomes an embryo?’” said Hyun. “And for me, that question starts to get raised here.” It’s not that the latest work on blastoids was unethical, he clarified. On the contrary, it met all the guidelines issued by the International Society for Stem Cell Research (ISSCR), which Hyun helped write. The latest version, issued in May, prohibits scientists from transferring blastoids, which contain all the cell types necessary for development, into a human or animal uterus. “It was a really well-done paper, I thought it was kind of stunning actually,” said Hyun. “It just opens up these other questions.”

Already this year, five other groups around the world have independently reported methods for making blastoids, with varying degrees of efficiency and complexity. Two teams — one at Monash University in Australia, one from the University of Texas Southwestern Medical Center in Dallas and Kunming Medical University in China — published their results in Nature in March. Both teams also showed that their artificial structures formed similarly to real blastocysts. But both reported that only about 10% of the reprogrammed cells made the transition, and some of the structures contained cells not typically found in human blastocysts. Two other teams, one based in China and one based in the U.S. and the U.K., showed similar results while working with extended pluripotent stem cells. Another group, from the U.K., reported in Cell Stem Cell in June achieving much higher efficiencies — between 30% and 80% of their stem cells expanded into blastoids. The Austrian group’s blastoids were even more efficient, forming more than 70% of the time.

“It’s been a big year for blastoids,” said Jianping Fu, a bioengineer at the University of Michigan whose lab created some of the earliest human embryo models from stem cells in 2017.

In 2018, Fu and Rivron joined Hyun and several others in writing an editorial urging lawmakers to ban the use of stem-cell based synthetic embryos for reproductive purposes while preserving their use for some types of research. They encouraged regulators to treat embryo models in the same way many nations dealt with cloning in the late 1990s and early 2000s. “We think that the intention of the research should be considered the key ethical criterion by regulators, rather than surrogate measures of the equivalence between the human embryo and a model,” they wrote.

Hyun said he still stands by those recommendations, to a point, even if it makes the slippery-slope crowd nervous. “The further along you get in modeling pregnancy, the harder it is to justify those experiments on the grounds that there’s no other way to answer your research question,” said Hyun. Scientists have been able to glean insights into the earliest stages of development by studying human embryos donated by families who’ve undergone IVF. Tissue from aborted fetuses has provided clues about later stages of pregnancy. But from the time an embryo implants until the time a person realizes they’re pregnant, scientists have virtually no way of knowing what’s going on.

“It’s a total black box,” said Hyun. “But it maxes out at about 28 days. And what most people don’t realize is that means there’s a natural limitation on how long you could justify an experiment with synthetic embryos. Once you traverse the black box of development, there’s no need to keep going in the dish.”

Although it’s not required by law or the latest ISSCR guidelines, which relaxed the long-held “14-day rule” barring research on embryos older than two weeks, the Austrian researchers did not allow their artificial embryos to develop past 13 days. But Rivron said he does not expect any of the blastoids to have the ability to develop into a complete embryo, even if allowed the chance.

A few years ago, his team successfully grew blastocysts in the lab from mouse stem cells. Ever since, they’ve been implanting the blastoids into the uteruses of living mice and crossing their fingers. But they’ve never successfully made any mice pups. Rivron said he’d expect the same thing for their human blastoids if they were implanted into a functioning uterus (an experiment the ISSCR’s guidelines, as well as laws in a handful of countries, expressly forbid). After implantation on the uterus-in-a-dish, the blastoids didn’t grow or organize as well as what you’d expect from real embryos in a real womb, said Rivron. “These are very nice models, but we are far from any potential of using them for reproduction.”

So how does he expect scientists might use them instead? A logical application would be to use them for drug discovery and screening — a process that would require large numbers of these embry(ish)os. “Now that we have formed a reliable embryo model, we can uniquely understand the molecules at play, and I believe that these molecules will actually become tomorrow’s medicines to enhance fertility or to be used as contraceptives,” said Rivron. His group is already working with collaborators to test an FDA-approved drug that prevented the innermost cells of the blastoid from forming. Because those cells instruct the outer cells to become sticky, disrupting them could offer a hormone-free way to prevent embryos from implanting.

Other as-yet-discovered drugs could possibly enhance the implantation process, thereby improving the odds of getting pregnant. Compared to creating a fully competent synthetic embryo, using existing models to find and develop drugs is achievable on a relatively short timescale, said Rivron. “This is not something that requires 10 years.”

Other scientists have other ideas. Fu said an obvious immediate application would be to use large numbers of blastoids to systematically figure out better recipes for the medium that IVF clinics use to culture embryos prior to implantation. “There are a lot of unknowns in how culture medium conditions affect the growth and development of human embryos, including successful implantation,” said Fu. “Those are questions that can better be answered now.”

To Martin Pera, a stem cell researcher at the Jackson Laboratory, an even more powerful application would be to use these models to better understand how organisms precisely alter the expression of genes in different types of cells during early development. “It’s a very dynamic time, epigenetically,” said Pera.

Since the 1990s, some scientists have argued for the fetal origins of adult disease; that the intrauterine environment, especially during times of bodily stress, may predispose a developing fetus to worse health outcomes later in life. “We need models to replicate that, and this is an important start,” Pera said.

https://www.statnews.com/2021/12/02/lab-grown-human-embryos-prompt-question-are-they-getting-too-real/

Some suggest Omicron variant may have evolved in animal host

 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 describe as a promiscuous virus; it is capable of infecting a number of species. Dogs and house cats. Large cats. MinkWhite-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/some-experts-suggest-omicron-variant-may-have-evolved-in-an-animal-host/

Second U.S. case of Omicron variant indicates domestic transmission

 Health officials on Thursday reported the country’s second Covid-19 infection from the Omicron variant in a Minnesota resident who notably did not travel internationally recently, unlike the first case.

The case in Minnesota is an adult male who had been vaccinated and, in early November, received a booster shot. He lives in Hennepin County, which includes Minneapolis, state health officials said. He developed mild symptoms on Nov. 22, was tested on Nov. 24, and no longer has symptoms. 

The man had been in New York City in the days leading up to feeling sick and attended the Anime NYC 2021 convention at the Javits Center from Nov. 19 to Nov. 21. Minnesota health officials are collaborating with New York City authorities and the Centers for Disease Control and Prevention on their case investigation.

“The primary goal of vaccination all along has been to prevent severe disease so it’s very encouraging that vaccines are still successful in that regard,” Jan Malcolm, Minnesota’s health commissioner, said at a briefing.

State officials said one close contact of the man has tested positive on a rapid test, but they haven’t yet confirmed the case or sequenced the virus from that possible infection.

The new case demonstrates that there is at least some local transmission of the Omicron variant and that it had arrived in the U.S. before the Biden administration imposed travel restrictions on Botswana and South Africa — where early cases of the variant were detected — and six neighboring countries. Some two dozen countries have now reported cases. 

The case also indicates that the variant was in the United States even before the global research community knew about the threat the variant potentially posed. It will likely add fuel to the calls for the Biden administration to lift its travel ban on the southern African nations, which are seen by scientists as penalizing the region where researchers have simultaneously been praised for their speedy detection work and for sharing their findings quickly and transparently. 

Experts have said it was likely Omicron was spreading in the United States at some level, and it was just a matter of time before genomic sequencing of infections started detecting it. 

According to the anime convention’s website, attendees had to show they had at least one dose of a Covid-19 vaccine, but could attend immediately after getting a shot. It takes days if not more than a week for the vaccine-elicited protection to kick in.

Some 46,000 people attended the convention in 2019, according to its site.

The first U.S. Omicron infection was detected by researchers in San Francisco and announced Wednesday. The person, whose age and sex were not provided, had recently returned from a trip to South Africa. The person was vaccinated and had not had a booster shot, and reported only mild symptoms.

Experts urge people showing symptoms of Covid-19 to get tested and to report relevant travel history to authorities. 

Scientists are scrambling to better understand the Omicron variant. They initially raised alarms about because its number and combination of mutations suggested it may be able to escape some amount of immune protection, and because limited epidemiological evidence in South Africa suggests it can compete with the highly transmissible Delta variant. But experts stress they still need to learn much more about Omicron’s transmissibility, severity, and immune evasion before they can assess how much of a threat it is to the world, and to vaccine protection. 

https://www.statnews.com/2021/12/02/second-us-case-omicron-variant-indicates-domestic-transmission/