Category: Corona Virus

New Yorks unequal recovery

In New York City, the Omicron wave is making the citys already lopsided recovery even more so.

Office workers were sent home again, reversing steady increases in subway ridership and hurting small businesses in central business districts. After border restrictions were lifted in November, overseas travelers were expected to give a boost to the hospitality industry, but hotel occupancy rates plummeted.

Even as the Omicron surge is subsiding, its effects linger. Service-sector employees worked fewer hours per week in December 2021, on average, than in December 2020. Working hours dropped even more in the first two weeks of January.

For a look at the recovery, I spoke to my colleague Nicole Hong, who covers New Yorks economy.

What does the recovery look like now?

Its been very uneven, and some of the metrics can feel contradictory.

For people who had jobs where they could work from home, and for people who had investments in the stock market, 2021 was a year when overall personal income in New York City actually went up. The real estate market is red hot right now. Rents and home sale prices are soaring from the lows that they hit earlier on in the pandemic. So for part of the city, people feel like things are back to normal and thriving and booming.

But New York City relies disproportionately on tourism and on office buildings, and we have hundreds of thousands of jobs in that ecosystem: everything from the shoeshine guy in Midtown, to the tour bus driver, to all the different restaurants and cafes and bars that serve tourists and office workers and commuters. As a result, at the start of the pandemic, New York had a bigger loss of jobs than pretty much any major American city, and it has taken longer to come back.

How is Covid affecting those workers?

With each new variant, and each new wave that causes things to slow down or shut down again, its disproportionately affecting people who have to show up in person to get paid. If white-collar workers are unable to go to the office because of a new variant, they can still work from home and get a paycheck. But for the restaurant that has to temporarily shut down because theres an Omicron outbreak, those waiters and dishwashers are typically not getting paid during that period.

The leisure and hospitality industries, which employ large numbers of lower-wage workers, have been especially slow to come back. I recently spoke to a tour guide who made a lot of money in 2019 because it was the best year for tourism in New York Citys history. Now, hes booking only a couple private tours a week.

What does the future look like?

The Independent Budget Office reported that New York City is not expected to recoup all the jobs it lost during the pandemic until late 2025, while the national economy is projected to surpass prepandemic employment this year. But its really hard to make an economic prediction this year for New York because we dont know yet the full impact of Omicron.

The future of our central business district is a huge uncertainty. So much of the citys economy is tied up in these office buildings from their underlying value, which feeds the citys property tax base, to pulling in commuters, which is essential to ridership on the commuter rails and subways. That unknown is huge, and well have to wait until the spring to see what the return-to-office situation is.

What are the ramifications of an inequitable recovery?

Its bad for economic growth when so many New Yorkers are unable to find a good-paying job, afford rent or access the kinds of opportunities that can pull them out of poverty. Its destabilizing, and it feeds into the broader conversation that city officials are having right now around how to deal with the overlapping crises of homelessness, mental health and substance abuse.

Italy has one of the highest vaccination rates in the world more than 80 percent of the population, including children, has had two doses.

The countrys high uptake holds the potential for a near future where the schism in society is no longer between the vaccinated and the unvaccinated, but between those who are comfortable taking risks in their daily lives and those who are not.

An increasing number of boosted people are entering a bring-it-on phase of the pandemic. Some are trying to time their resulting quarantines to a social and school calendar, or to have infections coincide with those of friends. Others are still coming to terms with a seemingly omnipresent virus, and forcing themselves to adjust their comfort levels and to be more social even to dine inside a restaurant.

Mariagiovanna Togna, for example, is willing to accompany her children to outdoor play dates. Her husband is still wearing rubber gloves and wiping down groceries. One of her sisters in Rome goes to yoga class and work. Her brother finally agreed to get vaccinated, she said, to keep going to bars, and he recently vacationed along the Amalfi Coast. But during Christmas vacation, their parents, in their 70s, asked him to stay in a bed-and-breakfast.

We are all vaccinated, many with the third dose already. We all have a civic sense about being careful for ourselves and for others, Togna said. But we have different styles of life.

I'm in my 70s, triple vaxed and done! I live alone and am more worried about my mental health than virus. Yesterday I took a Zumba class, no mask, and tonight Im meeting friends indoors for drinks. We are exhausted seniors and cant isolate and worry anymore.

Laurie, New York City

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Coronavirus Briefing: N.Y.C.s Lopsided Recovery - The New York Times

The vaccine sceptic and anti-lockdown campaigner Laurence Fox has said he has coronavirus.

The actor, who finished sixth in last years London mayoral elections, tweeted a picture on Sunday of a positive lateral flow test.

Above it, he wrote: In other news, felt shivery and crap yesterday. Turns out I have been visited by Lord Covid at last and have the Omnicold (if the LFT is to be believed!) On the #Ivermectin, saline nasal rinse, quercetin, paracetamol and ibruprofen. More man flu than Wu-flu at the moment.

Ivermectin is an anti-parasitic treatment used mainly on animals but which is approved in different doses to treat some parasitic worms in humans. It has not been proved to be effective at preventing or treating Covid, but has been promoted by vaccine-sceptic public figures such as the comedian and podcast host Joe Rogan, who said he used the drug to treat himself when he became sick with Covid, and the Fox News host Tucker Carlson.

Foxs tweet came four days after he posted a picture of himself wearing a T-shirt with a slogan saying, No vaccine needed, I have an immune system. In another tweet posted on Sunday, he said he was on day two of the virus.

After a number of people commented in response to Foxs tweet asking where he had got the ivermectin and why he was taking it, he responded by saying: Not only do you only have to sign a form saying you feel well to get into Mexico, but you can also buy drugs like Ivermectin over the counter that the vaccinaholics dont want you to get hold of here. Im so happy to be joining the natural immunity club. Going to have a nap.

Launching his mayoral campaign last year, Fox said he would not get the Covid jab until after 2023, by which time he claimed all the tests needed to convince him of its safety would be completed.

He has also cast doubt on the UKs death toll from the pandemic, claiming that some doctors were seeking to add non-Covid deaths including that of his mother in 2020 to the official tally to support the governments fear-based narrative.

And Fox has questioned the scientific basis of long Covid, which the Office for National Statistics estimates is affecting 1.3 million people, or 2% of the population, in the UK, based on people self-reporting symptoms that last more than a month after a Covid infection.

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Laurence Fox says he has coronavirus and is taking ivermectin - The Guardian

The omicron variant of Covid-19 was discovered less than three months ago, but it rocketed case numbers to record highs. Yet almost as rapidly as they rose, new infections plummeted in countries like the United Kingdom, South Africa, and now the United States.

Omicron caused some of the pandemics tallest, sharpest spikes in Covid-19 infections as it overtook previous variants like delta, but several waves triggered by earlier variants followed a remarkably similar pattern. Almost as steeply as cases rose, they fell.

Why did this happen? Why didnt omicron cases rise and fall slowly or level out at a high or moderate level?

I think you may get different answers from different experts, said Eleanor Murray, an epidemiologist at Boston University, in an email. This isnt just a curiosity: Researchers are trying to tease out the reasons in the hope of flattening peaks in the future.

Understanding why cases are rising and falling is crucial for figuring out what kinds of public health strategies are working. Its also important for anticipating what comes next and how to deploy resources like medical workers, hospital beds, vaccines, and treatments.

The Covid-19 spikes were seeing are not just an intrinsic fact of nature. Theyre partly a consequence of how we respond or dont to changes in the virus and in our society. And as steep spikes are eventually replaced by shallower slopes, they will also reveal when the acute Covid-19 pandemic has ebbed and given way to an endemic disease.

The omicron variant of SARS-CoV-2, the virus that causes Covid-19, appeared at just the right time to cause a huge infection spike. It took root in the Northern Hemisphere as holiday travel picked up and cooler temperatures pushed people indoors, helping it travel long distances and spread locally through person-to-person contact.

Omicron also had the right mix of traits to catch fire. The omicron variant contains mutations that allow it to better evade immune protection while spreading faster than any prior known variant. Even people vaccinated against Covid-19 began getting infected in large numbers as protection from their initial doses started to waver, though most experienced mild symptoms. All these factors together led to lots of infections happening very quickly.

It has infected everybody that could be infected out and about and that means automatically it will run out of people to infect and start coming down as fast as it went up, said Ali Mokdad, an epidemiologist at the Institute for Health Metrics and Evaluation at the University of Washington.

While omicron has been the most extreme example of this phenomenon, earlier variants also caused sharp spikes and declines. South Africa, for instance, saw distinct peaks associated with different variants. Most of these peculiar stalagmites in South Africa were symmetrical except for the delta wave last summer, which saw a brief resurgence on its way down.

[T]he shape of a spike then decline is what we generally expect in a single population, said Justin Lessler, a professor of epidemiology at the University of North Carolina School of Public Health, in an email.

A key variable is the basic reproductive number of the virus, or R0, which is the average number of people that one infected individual tends to infect. If that number is above one, the epidemic grows exponentially; if it is below one, it declines exponentially, Lessler said.

As more people get infected with a coronavirus variant, there are fewer people left to infect. When the basic reproductive number falls below one, new infections reach their peak and then decline. To plateau, the rate of new infections has to stabilize somewhere near one, but that would require an unusual set of conditions, according to Lessler.

The idea that disease outbreaks are generally symmetrical is an old one. William Farr observed in the 1840s that smallpox epidemics followed a mathematical pattern, though his formula, known as Farrs law, resulted in a bell-shaped curve. But diseases rarely follow such neat curves.

That has been generally discredited as a law since it doesnt allow for things like changes in susceptibility due to different levels of immunity/immune waning, movement in and out of populations, and changes to risk and exposure behaviors, said Murray.

Thats been evident during the Covid-19 pandemic. Some countries like South Korea saw more gentle hills as different variants took root, while others like Brazil experienced asymmetrical, jagged peaks throughout the pandemic. Some of that is due to delays in identifying and reporting cases. In some places, variants like delta and omicron overlapped. At the country level, case curves can change shape as the pandemic spreads over time from urban to rural areas or can peak at different times depending on the region.

Then one has to account for public health interventions. Vaccines offer significant immune protection (and recovery from Covid-19 can be protective too). Measures like wearing face masks, limiting public gatherings, more rigorous testing, and boosting vaccination efforts also assist in flattening the curve and help waves to crest. People also change their behavior in response to rising infections. In the US, surges in vaccination and testing followed spikes in cases.

That increase in testing and implementation of public health interventions helps us not only reduce transmission, but also more accurately and timely identify dips in cases, said Saskia Popescu, an infectious disease epidemiologist at George Mason University, in an email. These are also good examples of how effective the vaccines have been and our ability to rapidly respond to spikes and novel variants.

So both the shape and the size of an infection spike can be altered with public health tactics. Over time, as immunity builds up in the population, experts expect to stop seeing tall, sharp spikes in Covid-19 cases. The virus probably wont go away entirely, but case counts could form seasonal waves as new variants arise, immunity wanes, and exposure opportunities increase, according to Mokdad.

Covid-19 cases spurred by omicron appear to have peaked already in the US, but the health care system is still facing a stressful time ahead.

When an outbreak peaks in a given community, 50 percent of the infections have occurred and now another 50 will happen as we come down, Mokdad said. So we still have a couple of weeks ahead of us that are dangerous in the United States. ... A small fraction of them are going to the hospitals, but a small fraction of a huge number is a lot.

If public health measures like masking and social distancing are relaxed too soon, cases can bounce back up on their way down. The UK, for instance, reopened schools and relaxed Covid-19 rules before the omicron wave flattened out. Then infections stopped dropping.

The same thing could happen to other countries. That sharp decline will slow down at one point, then it goes back [down] sharply again, Mokdad said. Thats what we are noticing globally.

Even after the omicron wave recedes, the US will still have to contend with people who remain unvaccinated against Covid-19, both inside the country and around the world. And the virus is always changing: Omicron now has a subvariant called BA.2 that is gaining some ground, though its not yet clear what it means for the pandemic overall.

The more the virus spreads, the more likely it is to mutate in dangerous ways. As the current variants have shown, they can quickly spread around the world, regardless of where they originate.

The recurring spikes of Covid-19 cases, fueled in part by variants, should inspire us to redouble our efforts at controlling the disease, especially with vaccines. Were still struggling to avoid these peaks as vigilant infection prevention efforts and global vaccine equity have been a challenge, said Popescu.

A more robust global vaccination effort, coupled with better disease surveillance to catch variants before they spell trouble, could prevent the next wave and finally start to bring the pandemic under control.

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Omicron surge: Why Covid-19 cases often spike sharply and fall rapidly - Vox.com

On the cusp of the third year of the COVID-19 pandemic, the United States is battling back the biggest surge of the virus yet with the omicron variant.

Cases, even while receding in some places, are near record levels. And daily deaths, while lower than the peak of last winter, are still averaging more than 2,000 nationwide.

Despite pitched battles over masks and vaccines, life appears somewhat normal in many respects -- kids are going to school, people are going into work and large indoor gatherings and events are being held.

So, while it may be hard to imagine, many experts suggest 2022 could be the year COVID becomes an endemic disease, meaning it is always circulating within the population but at low rates or causing just seasonal outbreaks.

During a press conference Wednesday, Dr. Anthony Fauci, the nation's top infectious diseases expert, said the U.S. can get "sufficient control" over COVID-19 so it "does not disrupt us in society, does not dominate our lives, not prevent us [from doing] the things that we generally do under normal existence."

This is because the virus will start running out of people to infect as people become immune and follow mitigation measures such as mask-wearing and testing if they have symptoms.

"We have the tools with vaccines, with boosts, with masks, with tests and with antivirals," Fauci said.

As an endemic disease, COVID-19 would shift from becoming a global health emergency to a virus that the world learns to live with.

Travelers walk past a sign offering free COVID-19 vaccinations and booster shots at a pop-up clinic in the international arrivals area of Los Angeles International Airport in Los Angeles, Calif., Dec. 22, 2021.

Public health experts say many societal changes are needed for a time when the virus circulates but is not as disruptive, such as targeted testing, more vaccination, better treatments and allowances for staying home when you're sick.

"We really need to be shifting our thinking to how do we live with this virus rather than can we make it completely go away," Dr. Timothy Brewer, a professor of epidemiology at UCLA Fielding School of Public Health, told ABC News. "So I think we need to sort of move into the mode of minimizing the impact of the virus as much as possible in terms of health, economic and social disruption -- recognizing this virus is going to be there."

People who are sick will be advised to stay home or wear masks in public

When the virus does become endemic, experts say people will be advised not go into school or work while sick and instead stay home, unlike before the pandemic.

If you have to leave the house, it could remain common to wear a mask on public transit or in indoor spaces.

"It will become a culture of if you're sick you stay home," Dr. Wafaa El-Sadr, a professor of epidemiology and medicine at Columbia University Mailman School of Public Health, told ABC News. "Don't come to work, don't go to school, don't send your kids to school. There will be more of an appreciation of the collective responsibility that we have for each other."

Currently, federal law does not require employers to provide paid sick leave to employees although some states, such as California, New York and Washington, have laws requiring it.

Antivirals may become more common in doctor's offices and hospitals

In addition to vaccines, some antiviral treatments, from Pfizer and Merck, have come out in the past several months, specifically for those who test positive or had symptoms recently developed.

Studies have shown that these antivirals can help prevent hospitalization, especially those who are at high risk of severe illness.

Experts stress that even after the emergency phase is over, antivirals should not be considered a substitute for vaccines, but rather an extra layer of protection, specifically for at-risk groups.

People have drinks and dine on the outdoor patio at La Boheme in West Hollywood as coronavirus surges on July 8, 2020, in Los Angeles, Calif.

"The distribution of antivirals is really important in terms of making sure immunocompromised people and people with disabilities have that sort of protection," Abdulah Shihipar, a public health researcher at Brown University, told ABC News.

Brewer agrees and says he thinks the treatments for COVID-19 will be similar to those for HIV in that they will get better and better over time.

"HIV is no less pathogenic today than it was 40 years ago but the difference is we have very effective treatments, we have excellent antivirals against HIV," he said. "So I think as antivirals become available that they will play a very important role" in combating COVID-19.

Shihipar says he hopes the federal government comes up with a long-term plan for distribution whether that means a program people can sign up for to get cheap subsidized drugs, setting up at pharmacies, delivering it to rural areas and so on.

Testing will be more strategic such as just screening people with symptoms

Currently, the U.S. has a model based on two types of testing: diagnostic for symptomatic people to see if they are positive for COVID, and preventive for asymptomatic people to make sure they are not infected before participating in activities or seeing others.

But in a world in which COVID-19 is more seasonal of a virus, experts say the country will have to shift to more focused testing, particularly focusing on the symptomatic.

"Now we kind of test just to test everybody, it should be more focused," said El-Sadr. "For people who are symptomatic, if you have symptoms, it is a good idea to get tested, absolutely. So I think focusing on people who are asymptomatic will be very important."

Right now, an average of 1.7 million tests is being administered per day in the U.S., according to the Centers for Disease Control and Prevention. Experts say that, during peaks, a minimum of 2 million is needed to keep up with demand. Supplies have been short in some cases as manufacturers ramp up production of at-home tests and omicron redefines infection levels in the country.

El-Sadr also says testing can be used for specific high-risk activities such as eating indoors with family members who are unvaccinated or having a social gathering with someone who is immunosuppressed as opposed to generally for indoor gatherings.

"We have to think of what is the strategic use of testing," El-Sadr added.

Medical personnel from Riverside (CA) University Health Systems hospitals administer a COVID-19 test at drive-through testing site in the parking lot of Diamond Stadium, March 22, 2020 in Lake Elsinore, Calif.

Brewer believes testing programs currently in place at schools, such as students testing before returning and then undergoing weekly testing, won't work in the long run.

"It's logistically and financially too cumbersome and expensive and slow," he said. "Given that we know up to 40% or more of people can be asymptomatic when infected and we know asymptomatic people can spread disease, we just kind of need to operate under the assumption that anyone is potentially infected and do things like hand hygiene and vaccination rather than relying on a testing strategy."

Improved ventilation standards in workplaces and schools could be implemented

Experts say that improving indoor air quality will be one of the most important tasks, specifically as states begin to roll back mandates and mitigation measures.

Making sure indoor air is being recirculated will lower rates of cases and prevent outbreaks.

Shihipar says the Occupational Safety and Health Administration had standards for health care settings (which have since expired) that need to be expanded to all workplaces.

"We need to change the way we deal with indoor air, like how do we properly ventilate these spaces -- not just for COVID but for flu and all these other diseases," he said. "How do we make the air cleaner so that the disease spreads less?"

He continued, "We need emergency temporary workplace standards from OSHA. One for all workers would actually regulate employers to make their workplaces safe in terms of ventilation, in terms of capacity."

Shihipar added that he'd like to see the government giving each teacher a certain number of portable air filters for their rooms and the governments and setting up clear standards of air regulation for school districts.

Students pass a beach ball to the next person on the list during roll call on the first day of class at Laguna Niguel Elementary School in Laguna Niguel, Calif. on Aug. 17, 2021.

We may need annual COVID vaccines

Experts have suggested that annual COVID-19 vaccines, just like the flu shot, could become a reality in a world where the virus is endemic to keep antibody levels high.

They could even be adapted to combat variants just the flu shot is manufactured to combat which strains researchers think will be the most dominant.

Brewer said it will depend on two factors: how long immunity lasts after vaccination and how much the virus changes.

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Experts say the COVID-19 emergency could end this year. What would it look like? - ABC News

OREM, Utah Federal officials worried that more than 174,000 coronavirus patient test results from an Orem lab used by TestUtah were potentially wrong but none of the people who were tested early in the pandemic were told, documents obtained by The Salt Lake Tribune show.

Testing at Timpanogos Regional Hospital may have produced accurateresults.Or its lab may have produced false negatives or false positives, according to documents and interviews with people familiar with the matter.

State health officials knew for months that federal regulators were questioning whether the hospitals lab was following requirements designed to ensure tests are processed accurately, according to interviews and documents. Public officials knew as early as May 2020 about problems at the lab, which did not suspend COVID-19 testing until Aug. 23, 2020.

In the hospitals plan for correcting deficiencies, submitted to regulators the day after it halted its processing of coronavirus tests, it acknowledged:

Once it was determined that verification and validation had not been properly performed, Timpanogos Lab suspended the processing of COVID-19 specimens on the non-validated and non-verified instruments.

Read the full report on The Salt Lake Tribune's website.

The Utah Department of Health sent the following statement to FOX 13 News:

The UDOH was not a party to the CLIA audit. However, our contract with Nomi Health requires that Nomi Health ensure any concerns raised in the audit are resolved. The final audit results from CLIA did not include a requirement or recommendation that any entity notify any patients of potential issues with their test results.

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174,000 people in Utah werent told their coronavirus test results couldve been wrong - fox13now.com

Researchers from Oxford, Sheffield, Cardiff and Manchester have identified abnormalities in the lungs of long COVID patients who are experiencing breathlessness. These abnormalities can't be detected with routine tests, the researchers have said.The study uses hyperpolarized xenon MRI scans to find possible lung damage in long COVID patients who have not been hospitalised with COVID-19 but who continue to experience breathlessness. The research paper is available in medRxiv, pre-print server.The study, known as EXPLAIN, had 36 participants in its pilot stage in three broad groups: the first group is patients diagnosed with long COVID, who have been seen in long COVID clinics and who have normal CT (computerized tomography) scans; the second group is people who have been in hospital with COVID-19 and discharged more than three months previously, who have normal or nearly normal CT scans and who are not experiencing long COVID, and the third group is an age- and gender-matched control group who do not have long COVID symptoms and who have not been hospitalised with COVID-19.

In this study patients are required to lie in the MRI scanner and breathe in a litre of the inert gas xenon. Xenon behaves in a very similar way like oxygen, which helps radiologists to observe how the gas moves from the lungs into the bloodstream.

The result obtained from the pilot study shows significantly impaired gas transfer from the lungs to the bloodstream in long COVID patients.

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Coronavirus: Study finds lung abnormalities in long COVID patients with breathlessness - Times of India

To understand how the coronavirus keeps evolving into surprising new variants with new mutations, it helps to have some context: The viruss genome is 30,000 letters long, which means that the number of possible mutation combinations is mind-bogglingly huge. As Jesse Bloom, a virologist at the Fred Hutchinson Cancer Research Center, told me, that number far, far exceeds the number of atoms in the known universe.

Scientists try to conceptualize these possibilities in a fitness landscapea hyper-dimensional space of peaks and valleys. The higher peaks the coronavirus discovers, the fitter, or better at infecting people, it becomes. The more the virus replicates, the more mutations it tries out, the more ground it explores, and the more peaks it may find. To predict what the coronavirus could do next, we would simply need to know the topography of the entire fitness landscapewhich, maybe youve guessed, we do not. Not at all. Not even close. We dont actually know what peaks are out there. We didnt know the Omicron peak was out there, says Sarah Otto, an evolutionary biologist at the University of British Columbia. We cant really guess what more is possible.

What we can say is that the overwhelming majority of mutations will make a virus less fit (valleys) or have no effect at all (ridges), but a very small proportion will be peaks. We dont know how high those peaks are or exactly how frequently they appear. When Delta took over the world, it seemed like it would sweep all other lineages away. I would have for sure thought the next variant was going to come from Delta, says Katia Koelle, a biologist at Emory University. Then Omicron popped up on a distant peak, in a direction no one had thought to look.

The next variant may surprise us again. It could, by chance, become more virulent. It could become more transmissible. It will definitely alight upon new ways to escape the antibodies weve built up. The virus will keep finding those fitness peaks.

To make predictions about viral evolution even harder, the fitness landscape is continuously being remodeled as our mix of immunity shifts through vaccination and infection by new variants. This in effect changes what it means for the virus to be fit. Some mountains will sink; some hills will uplift. Still, the virus is extremely unlikely to mutate so much that our immunity against severe infection is reset to zero. As more and more of the world gains initial immunity from vaccines or infection, that will dampen the most severe outcomes. Whether future variants will still cause huge numbers of infections will depend on how quickly the virus can keep evolving and how well our immunity holds up after repeated exposures. Unlike other pathogens that have been criss-crossing the fitness landscape in humans for a very long time, the coronavirus has only just gotten started.

The coronaviruss variants keep surprising us because its evolutionary leaps look like nothing else weve seen before. Omicron racked up more than 50 mutations, with more than 30 in its spike protein alone. Of the four seasonal coronaviruses that cause common colds, two accumulate only 0.3 or 0.5 adaptive mutations a year in their spike proteins. A third doesnt seem to change much at all. The fourth is a mysterywe dont have enough long-term data on it. Influenza is capable of big jumps through a process called reassortment, which can cause pandemics (as H1N1 did in 2009), but the seasonal flu averages just one or two changes a year in its key protein, Koelle told me.

There are three possible explanations for why the evolution of SARS-CoV-2 looks so different from that of other viruses, and they are not mutually exclusive. First of all, we really havent looked that hard at other respiratory viruses. More than 7.5 million genomes of SARS-CoV-2 have been sequenced; just a few hundred or a few dozen for each of the four seasonal coronaviruses have been. When scientists try to reconstruct the relationship among these sequenced viruses in evolutionary trees, the trees are so sparse, says Sarah Cobey, a biologist at the University of Chicago. A whole suite of other viruses also cause common colds: rhinoviruses, adenoviruses, parainfluenza, respiratory syncytial virus, metapneumovirus, and so on. These, too, are poorly sampled. More than 100 types of rhinoviruses alone infect humans, but we dont have a great understanding of how that diversity came to be or evolved over time.

Second, the coronavirus could indeed be an outlier that is inherently better than other viruses at exploring its fitness landscape. It helps to be an RNA viruswhich acquires mutations more quickly than a DNA virusand then it helps to be moving really fast, Cobey told me. Measles takes, on average, 11 or 12 days between infecting one person and that person infecting another; the coronavirus takes only 1.5 to three. The more people it can infect, the more of the fitness landscape it can explore.

Third, the coronavirus was a novel pathogen. Whatever intrinsic transmissibility it may have had, it was also unimpeded by immunity when it first arrived in the human population. That means SARS-CoV-2 has been able to infect a simply staggering proportion of the world in two yearsfar more people than older viruses are typically capable of infecting. And each time it infects someone, it copies itself billions of times. Some copies created in every infection will harbor random mutations; some mutations will even be beneficial to the virus. But these mutations can have a hard time becoming dominant in the short course of a typical COVID-19 infection. It takes a while typically for a mutation to go from zero to even 5 to 10 percent of viruses in an infected person, says Adam Lauring, a virologist at the University of Michigan. That person then transmits only a tiny number of virus particles to the next person, so most of that diversity gets lost. Across millions of infections, some of those mutations are passed on, and they gradually accumulate into one viral lineage. Delta seems to have evolved this way. The coronaviruss ubiquity could have also seeded an unusual number of chronic infections all at once, which experts think are another big driver of viral evolution. In a chronic infection, over weeks and months, those beneficial viral mutations have time to become dominant and then transmit. This may be how Alpha originated.

Omicrons origins are still unknown. It may have evolved in a piecemeal fashion like Delta, but some experts think that its ancestors would have been found via sequencing if so. Two other possibilities exist: a chronic infection in someone immunocompromised or an animal reservoir that spilled back into humans. In both cases, the selection pressures within one immunocompromised patient or in an animal population are slightly different from those on a virus that is transmitting between humans. That may be what allowed the virus to cross a fitness chasm and discover a new peak in Omicron. Understanding the evolutionary forces that created Omicron can help us understand the realm of what is possibleeven if it cant tell us exactly what the next variant will look like.

With Omicron, I think we got lucky, says Sergei Pond, an evolutionary biologist at Temple University. The set of mutations that makes the variant so good at infecting even vaccinated people just happens to also make it a little less inherently virulent. Theres no reason this will always be the case. The coronaviruss virulence is a by-product of two other factors under more direct evolutionary pressure: how inherently transmissible it is and how good it is at evading previous immunity. How deadly it is doesnt matter so much, because the coronavirus is usually transmitted early on in an infection, long before it ever kills its host.

Across the immense fitness landscape, the coronavirus has many, many different paths to higher inherent transmissibility or immune escape. Take the example of transmissibility, Otto says. A virus could replicate very, very fast, so that patients shed high levels of it. Delta seems to do this, and it was more virulent. Or the virus could switch to replicating mostly in the nose and throat, where it might be easier to transmit, rather than deep in the lungs. Omicron seems to do this, and it is less virulent. The next variant could go either wayor it might chart an entirely new course. A version of Omicron called BA.2 is now outcompeting the classic Omicron variant in the United Kingdom and Denmark, though its still unclear what advantage it might have.

Omicron doesnt just have a lot of mutations; it has some really unusual ones. Thirteen of the mutations cluster in sites where scientists havent seen many changes before. That suggests mutations there normally make the virus less fit and get weeded out. But according to a preprint from Ponds group, these 13 individually maladaptive changes might be adaptive when present all together. You can imagine, he told me, a virus under pressure to escape from existing antibodies. It acquires a series of mutations that make it less recognizable to antibodies but perhaps worse at entering cells. Under the slightly different selection environment inside an immunocompromised patient or an animal reservoir, the virus still might be able to lingeruntil it finds just the right combination of mutations to compensate for previous changes. In Omicron, this process remodeled key parts of the spike protein so that it both became less recognizable to existing antibodies and found a different strategy for entering cells. The coronavirus normally has two ways of infecting cells, either fusing directly with them or entering through a bubble. Omicron has become a specialist in the latter, which happens to work less well in lung cells than in nose and throat cells, and may explain the variants lower intrinsic severity. To get around the immune system, the virus ended up changing one of its most basic functions.

Do other sets of mutations interact in unknown ways to change key viral functions? Almost certainly. We just dont know what they are yet. Well have to wait and watch SARS-CoV-2 in the years and decades to come. If you look at human influenza or seasonal coronaviruses, theyve been evolving in humans for a long time and they havent stopped evolving, Bloom, the virologist, said.

There are limits to how inherently transmissible the virus can get. Measles, the most transmissible known virus, has an R0 of 12 to 18, compared with Deltas R0 of 5. Omicrons R0 is still unclear, because a lot of its advantage over Delta seems to come from evading existing antibodies rather than inherent transmissibility. As the coronavirus has fewer and fewer nonimmune people to infect, though, immune evasion will become a more and more important constraint on its evolution. And here, the virus will never run out of new strategies, because what is optimal is always shifting. This Omicron wave, for example, is generating a lot of Omicron immunity as it moves through the population, which has in effect made Omicron less fit than when it emerged. The next variant is more likely to be not Omicron, or something as antigenically distinct from Omicron as possible, says Aris Katzourakis, a virologist at the University of Oxford. But exactly what that looks like? Perhaps we know enough now to know we shouldnt try to predict that.

Originally posted here:

What Will the Next Variant Look Like After Omicron? - The Atlantic

A Hong Kong hamster that evaded the cull. Bertha Wang/AFP via Getty Images hide caption

A Hong Kong hamster that evaded the cull.

Each week, we answer frequently asked questions about life during the coronavirus crisis. If you have a question you'd like us to consider for a future post, email us at goatsandsoda@npr.org with the subject line: "Weekly Coronavirus Questions." See an archive of our FAQs here.

I read that Hong Kong killed thousands of hamsters after a report that 11 hamsters in a pet store, as well as a human employee, tested positive for COVID. Should I be worried about my hamster ... or cat or dog?

So yes, animals can get COVID. And it can even prove fatal. In November, a snow leopard at the zoo in Sioux Falls, South Dakota, died after reportedly experiencing COVID-like symptoms.

But human-to-animal transmission is "rare, very rare," says Charlotte Baker, an assistant professor of epidemiology at Virginia Tech. The same goes for pet-to-human transmission (although, keep in mind that the virus did almost certainly cross from animals to humans to start this pandemic). One study shows that infected cats can transmit virus for up to 5 days, but did not find evidence of transmission from dogs.

So Hong Kong's massive hamster cull, says transmission experts, was ... overkill.

If you do have COVID and are an extremely cautious person, you might not cuddle as much with your pooch or feline or ... pet rodent. Of course, a hamster won't be jumping in your lap and begging for a hug.

And if you're worried that your pet does have COVID? "I wouldn't suggest testing your dog," says Dr. Preeti Malani, an infectious disease doctor at University of Michigan Health in Ann Arbor. "That's not a good use of test kits since they're in low supply." If your canine seems under the weather, call the vet!

A relative who's on dialysis caught COVID, was hospitalized and now is back home in her assisted living apartment building. Is it safe for me to visit her? Would I pose any risk to her?

Good questions.

When someone who is immunocompromised catches the virus, they typically take longer to clear the virus out of their body. That's because their immune system isn't super strong.

So "they'll shed virus for a longer period," says Dr. Abraar Karan, an infectious disease physician at Stanford University. That's why the Centers for Disease Control and Prevention suggests a 20-day waiting period from either the date of the first positive COVID test or the onset of symptoms in an immunocompromised individual.

Obviously, the patient should be free of symptoms at that 20-day marker and test negative if they're able to get access to a test before a visit can be considered.

But that doesn't mean you should just pop in.

After all, 20 days is just a number set by the CDC based on data to establish a reasonable waiting period for an immunocompromised person to recover from COVID. Viruses (as far as we know) do not understand and abide by numbers.

And there are different degrees of being immunocompromised a category that includes those on dialysis, chemotherapy patients and individuals with autoimmune diseases. An individual might be considered moderately or severely immunocompromised. That's why our medical experts say to check with your friend or family member to see if their physician can offer guidance about visits.

Also, the visitor should take precautions to protect the immunocompromised individual and anyone you'd be in contact with during a visit. Wear a mask in the highly protective N95 family as the CDC recommends. Even though it's unlikely that you'd reinfect a newly recovered patient, it's not impossible. What if your friend had the delta version and you have a budding case of omicron but don't yet know it, says Karan (although these days, he says, it's pretty much all omicron).

Meanwhile, it's not just COVID you need to worry about. You could be coming down with a cold or the flu, for example, and sure don't want to pass such pathogens on to the immunocompromised person you're visiting.

Let your acquaintance know you'll be careful. Baker, the epidemiology professor, is herself immunocompromised. When friends come to visit, "they stay masked as much as possible and I really appreciate that someone else is considering that they don't want to give me anything."

For those reasons, you should build in other precautions: visiting outside or with open windows since airflow disperses pathogens keeping six feet of distance during the visit and practicing good hand hygiene.

"By layering these strategies you take the risk to minimal," says Malani. Visits are important, she says. "It's important to try and take care of people's social needs during all this being isolated isn't good."

Of course "some people are perfectly happy never seeing anyone," Malani says. "But for individuals whose health is poor, those visits can be something they look forward to.

"If for any reason you have to delay [a visit], find other ways to express your love and support." Maybe that'll mean a virtual schmooze via Zoom or a video call.

If it's not yet advisable to drop by, "send them some food!" says Baker. And if your friend has a sweet tooth, remember the wise words from an episode of The Mary Tyler Moore Show: "Chocolate solves everything."

Continue reading here:

Can a pet give you COVID? Is it risky to visit an immunocompromised pal? : Goats and Soda - NPR

How to prepare kids for the return to school

Associate Professor MargieDanchin from the Murdoch Children'sResearch Institute joined the Weekend Breakfast team on the News Channel to talk through some common questions and concerns parents have upon the return to school this year.

Q: What happens if a child does contract COVID? What are the implications for the child? How does it play out within the body?

A: So if a child gets COVID, and particularly with Omicron variant, we have seen on an individual basis that it presents pretty much like many other respiratory infections andprimary school-aged children are at the lowest risk of severe disease.

So what we see particularly is they may have a runny nose, a cough, a fever, chills and sweats, some experience very, very mild symptoms and some may be in bed for a couple of days and take a week or so to recover. And about one-in-five children have no symptoms at all. But we do know that between 1 to 2 per centof children who test positive with symptoms will need admission to hospital and it's those kids that we want to prevent being admitted to hospital and also make sure that these kids are vaccinated now and we have seen a fantastic response to vaccination as well.

Q: If a child was to contract COVID,how soon and, of course, recovers,how soon before they can then gettheir booster shot, their secondshot, or their firstvaccine?

A: At the moment we're recommending if the child has had COVID infection that they wait about four weeks. Now, of course, that will potentially vary on an individual basis. If a parent has an early appointment, it would be fine to get them vaccinated at two or three weeks. The key point is that they need to have fully recovered and we do know that the severer presentation of COVID infection called MISCin children which happens in about one-in-3,000 kids, that happens about two to six weeks after the acute illness. So in general, we'd like to at least wait a month, make sure the child has recovered. And also that initial COVID infection does stimulate the immune system, the child will have antibodies on board and then having a pause and then giving the vaccine will give a really strong immuneboost to the child.

Q: What happens to the rest of the family if a child contracts COVID?

A: So if the child tests positive, they need to go home and isolate for seven days and the family members who are close contacts also need to test and isolate. But what is different now, so particularly in New South Wales, Victoria, ACT,if childrentest negative, they can go back to school as long as they don't have symptoms. So that is a bit of a difference now COVID is starting to be treated a bit like other infections in children, parents are notified, if the children around them have symptoms they need to test.

And thenwe have also seen the introduction of the asymptomatic surveillance of twice weekly rapid antigen testing for most kids in schools and of course that's five times a week for children who are at higher risk in special school settings. So testing, unfortunately, is going the become at least for the first month quite common for a lot of children in the school environment, you know, testing at home before they come to school, so I think we need to do a lot of reassurance around that as well.

Q: How do you talk to children about the pandemic, about COVID, without, you know, raising their anxiety levels?

A: Yeah, this has been a challenge for the last two years, hasn't it, with children and it's quite amazing to think now that we are entering the third year of the pandemic.The most important thing is to understandwhere the child is developmentally and then pitch the conversation appropriately depending on their age. But the key is to just sit down with the child, have an honest conversation, ask what the questions they have are (we know all kids will have questions),what they might be concerned about, and then really start the conversation from there.

We need to let them know, a bit like last term, school is going to look different. We know that kids are going to be asked to wear masks. I mean, here in Victoria, they are mandatory for grade 3 and above and prep to grade 2 obviously it's recommended. So children will be wearing masks. They'll be aware of the changes to the air filters in the classroom. They may even be having some outdoor learning lessons,we have seen the shade cloths and the sales installed in many schools here in Victoria. The school environment will look different so preparing kids for that is really important.

And also again talking them through the rapid antigen testing to demystify that, helping them practice with cotton buds, showing what it might be like to do it on another adult or themselves before to do the test. It's all about giving them a sense of control and you do that by explaining to them what to expect so that they're not frightened or caught off-guard.

See the rest here:

COVID live updates: Get up to speed on all the coronavirus news from across Australia - ABC News

With scientists from China's Wuhan flagging a concern regarding a more contagious and possibly deadlier strain of coronavirus NeoCov, World Health Organization (WHO) asserted that it still needs to be studied whether it poses threats for humans.

The scientists have clarified, NeoCov is related to the Middle East respiratory syndrome or MERS-coronavirus. The virus is discovered in a bat population in South Africa and is currently spreading only among animals," the scientists said and further warned, Just one mutation is enough for the virus to be able to infiltrate human cells."

"Whether the virus detected in the study will pose a risk for humans will require further study," WHO told Russian news agency Tass.

"Animals, particularly wild animals are the source of more than 75% of all emerging infectious diseases in humans, many of which are caused by novel viruses. Coronaviruses are often found in animals, including in bats which have been identified as a natural reservoir of many of these viruses," WHO said.

WHO is aware of the new finding of Wuhan scientists and is in touch with the World Organization for Animal Health, the Food and Agriculture Organization to respond to this.

NeoCoV was found in a population of bats in South Africa and to date has spread exclusively among these animals. However, the study, not yet peer-reviewed and released on the bioRxiv website, found, NeoCoV and its close relative, PDF-2180-CoV, can use some types of bat Angiotensin-converting enzyme 2 (ACE2) and human ACE2 for entry.

Just one mutation is enough for the virus to be able to infiltrate human cells, claim scientists.

According to Chinese researchers, NeoCoV carries the potential combination of MERS-high CoVs mortality rate (one in every three infected person dies) and the current SARS-CoV-2 coronaviruss high transmission rate.

The MERS-CoV virus is similar to SARS-CoV-2 in terms of symptoms like fever, cough and shortness of breath. The disease was first identified in Saudi Arabia in 2012 and was prevalent in the middle-eastern countries in 2012 and 2015.

Most of the human cases of MERS-CoV infections spread through human-to-human infections. Many people have lost their lives due to MERS-CoV.

The researchers further noted that infection with NeoCov could not be cross-neutralised by antibodies targeting SARS-CoV-2 or MERS-CoV.

"Considering the extensive mutations in the RBD regions of the SARS-CoV-2 variants, especially the heavily mutated Omicron variant, these viruses may hold a latent potential to infect humans through further adaptation," the authors of the study added.

(With inputs from agencies)

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NeoCov: What WHO says on this new coronavirus variant possibly deadlier than previous strains - Mint