Virus World

The offshoot accounts for 40% of Covid cases in the US, raising fears of fresh waves of illness as it spreads to other countries. Scientists have raised concerns about a new Covid variant that is spreading fast in the US and threatening to cause further waves of infection. Here’s what we know so far.

What is the new variant called?

It’s known as XBB.1.5. It’s one of the latest descendants of Omicron, the highly transmissible version of Covid that caused cases to surge in the UK last winter. Offshoots of Omicron have dominated global Covid infections ever since. XBB.1.5 evolved from the XBB variant of Omicron, itself a fusion of two different BA.2 variants.

How fast is it spreading?

The variant seems to have arisen in or around New York state in late October. At the end of December, the number of cases in the US more than doubled in a week. It now accounts for about 40% of all Covid infections in the US. Hospitalisations are rising in New York, raising fears that XBB.1.5 is about to cause further waves of illness as it spreads to other countries. Some US estimates suggest that XBB.1.5 is spreading more than twice as fast as the BQ.1.1 variant, which is one of the most common variants found in the UK.

Why is it spreading so rapidly?

The variant has an unusual mutation known as F486P that is helping it spread. The mutation changes part of the Covid virus that many antibodies from vaccination or previous infection target. The change makes the antibodies less effective at neutralising the virus. The parent variant, XBB, has a different mutation at the same position. This makes XBB good at evading immune defences too, but the mutation comes with a cost: the virus cannot latch on to human cells as effectively, so the virus is actually less infectious. The XBB.1.5 offshoot suffers no such handicap: the F486P mutation allows it to evade antibodies without compromising how well it attaches to human cells. In fact, it binds to them even more strongly than XBB, driving up its infectivity. “The mutation can give that immune evasion without the cost to infectivity and that’s why it’s become so successful,” says Ravi Gupta, professor of clinical microbiology at the University of Cambridge.

Has the virus reached the UK?

Scientists in the UK analyse the genetics of only a fraction of Covid samples now, so there’s some uncertainty around XBB.1.5. But the variant has been detected here, and surveillance suggests it makes up at least 4% of Covid viruses being sequenced.

Does it cause more severe disease?

There is no evidence that XBB.1.5 causes more severe disease than other Omicron variants. But the fact that it is spreading fast is worrisome, as the virus is more likely to reach vulnerable people who could be hospitalised or die from the infection, especially if they have not received their latest booster.

Will it spark another wave?

That is the concern. In the US, scientists suspect XBB.1.5 is at least partly responsible for the rise in hospital admissions in New York, though cold weather and indoor gathering will also contribute. It is unclear whether the variant will drive a big surge in the UK, but some rise is anticipated. “It might drive an increase in cases, but I’m not convinced this will necessarily cause an explosive wave of infections in the UK,” says Gupta. “I don’t think there’s any cause to panic. The main thing we worry about is the severity of the disease, and there is no evidence that it’s more severe. People should, however, make sure they are up to date with their vaccines.” Paradoxically, the winter wave of influenza and other nasty respiratory viruses that are doing the rounds might blunt any spike in Covid. If you catch a virus it should activate the innate immune system, the body’s frontline defences against pathogens, offering at least some protection against viruses that follow soon after. So if you caught flu or another respiratory virus over Christmas, your immune defences might resist a brief encounter with Covid.

What do scientists advise?

Vaccines are still the best way to protect against severe Covid, but Sam Wilson, a professor of virology at the University of Glasgow, says taking familiar Covid precautions will also help. “Regardless of the impact of a new variant, the NHS is already under tremendous pressure from a cocktail of different viruses this winter,” he says. “Where it is possible, taking voluntary steps to reduce transmission – reducing contacts, wearing high-quality masks in crowded indoor spaces, and isolating if you have symptoms – will help reduce the pressure on the NHS.”

Lyme disease diagnoses have increased dramatically in the U.S. during the past 15 years, rising 357% in rural areas and 65% in urban areas, according to new data released by FAIR Health. 

The trends show that tick-borne illnesses are becoming a more common concern nationally, not just in the areas where Lyme disease has been found historically. “Lyme disease remains a growing public health concern,” Robin Gelburd, president of FAIR Health, said in a statement. FAIR Health is a national, independent nonprofit group that highlights health care information by looking at data from its collection of more than 36 billion private insurance claims records. “FAIR Health will continue to use its repository of claims data to provide actionable and relevant insights to healthcare stakeholders seeking to better understand the ongoing rise of Lyme disease cases,” Gelburd said. The 15-year analysis included private insurance claims from 2007 to 2021, which showed a 357% increase in Lyme disease diagnoses in rural areas and a 65% increase in urban areas. In the past 5 years, from 2016 to 2021, diagnoses rose 60% in rural areas and 19% in urban areas.  The cases peaked in the summer months, when people spend more time outside in grassy areas, wooded areas, parks, and fields where ticks live. In June and July, Lyme disease diagnoses were more common in rural areas, but from November to April, diagnoses occurred more often in urban areas.

WASHINGTON (AP) — Dealing the White House a stinging setback, a government advisory panel overwhelmingly rejected a plan Friday to give Pfizer COVID-19 booster shots across the board, and instead endorsed the extra dose only for those who are 65 or older or run a high risk of severe disease.  The twin votes represented a heavy blow to the Biden administration’s sweeping effort, announced a month ago, to shore up nearly all Americans’ protection amid the spread of the highly contagious delta variant. The decision was made by an influential committee of outside experts who advise the Food and Drug Administration.  In a surprising turn, the panel rejected, by a vote of 16-2, boosters for almost everyone. Members cited a lack of safety data on extra doses and also raised doubts about the value of mass boosters, rather than ones targeted to specific groups. Then, in an 18-0 vote, it endorsed the extra shot for select portions of the U.S. population — namely, those most at risk from the virus. That would help salvage part of the White House’s campaign but would still be a huge step back from the far-reaching plan proposed by the administration a month ago to offer booster shots of both the Pfizer and Moderna vaccines to practically everybody eight months after they get their second dose. Friday’s vote was just the first step in the process. The FDA itself is expected to make a decision on boosters in the next few days, but it usually follows the committee’s recommendations. The offering of boosters is also subject to approval by the Centers for Disease Control and Prevention. A CDC advisory panel is expected to take up the question on Wednesday. The CDC has said it is considering boosters for older people, nursing home residents and front-line health care workers, rather than all adults.

Separate FDA and CDC decisions will be needed in order for people who received the Moderna or J&J shots to get boosters.

During several hours of vigorous debate Friday, members of the panel questioned the value of offering boosters to almost everybody 16 and over. “I don’t think a booster dose is going to significantly contribute to controlling the pandemic,” said Dr. Cody Meissner of Tufts University. “And I think it’s important that the main message we transmit is that we’ve got to get everyone two doses.” Dr. Amanda Cohn of the CDC said: “At this moment it is clear that the unvaccinated are driving transmission in the United States.” Scientists inside and outside the government have been divided in recent days over the need for boosters and who should get them, and the World Health Organization has strongly objected to rich nations giving a third round of shots when poor countries don’t have enough vaccine for their first. While research suggests immunity levels in those who have been vaccinated wane over time and boosters can reverse that, the Pfizer vaccine is still highly protective against severe illness and death, even amid the spread of the highly contagious delta variant.  The surprise turn of events could reinforce recent criticism that the Biden administration got out ahead of the science in its push for boosters. President Joe Biden promised early on that his administration would “follow the science,” following disclosures of political meddling in the Trump administration’s coronavirus response.

The FDA panel’s overwhelming initial rejection came despite full-throated arguments about the need for boosters from both Pfizer and health officials from Israel, which began offering boosters to its citizens in July. Sharon Alroy-Preis of Israel’s Ministry of Health said the booster dose improves protection tenfold against infection in people 60 and older. “It’s like a fresh vaccine,” bringing protection back to original levels and helping Israel “dampen severe cases in the fourth wave,” she said. And representatives for Pfizer argued that it is important to shore up immunity before protection against severe disease starts to erode. A company study of 44,000 people showed effectiveness against symptomatic COVID-19 was 96% two months after the second dose, but had dropped to 84% by around six months. Both Pfizer and the Israeli representatives faced pushback from panelists. Several were skeptical about the relevance of Israel’s experience to the U.S. Another concern was whether third doses would exacerbate serious side effects. Meissner said he was worried about extra doses for younger age groups, given the risk of heart inflammation that has been seen in mostly younger men after a second dose. While the condition is very rare, he said, it is not clear if that risk would increase with another dose. Pfizer pointed to Israeli data from nearly 3 million boosters to suggest side effect rates would be similar to that seen after second doses. Dr. Paul Offit, a vaccine expert at Children’s Hospital of Philadelphia, said he was supportive of a third dose for adults over 60 or 65, but “I really have trouble” supporting it for anyone down to age 16. While an extra shot likely will at least temporarily decrease cases with mild or no symptoms, “the question becomes what will be the impact of that on the arc of the pandemic, which may not be all that much,” Offit said. Biden’s top health advisers, including the heads of the FDA and CDC, first announced plans for widespread booster shots in mid-August, targeting the week of Sept. 20 as an all-but-certain start date. But that was before FDA staff scientists had completed their own assessments of the data.

Earlier this week, two top FDA vaccine reviewers joined a group of international scientists in publishing an editorial rejecting the need for boosters in healthy people. The scientists said continuing studies show the shots are working well despite the delta variant. On Friday, U.S. Surgeon General Dr. Vivek Murthy said that in announcing its booster plan, the Biden administration was not trying to pressure regulators to act but was instead trying to be transparent with the public and be prepared in the event that extra shots won approval. “We have always said that this initial plan would be contingent on the FDA and the CDC’s independent evaluation,” Murthy said. The Biden plan has also raised major ethical concerns about impoverished parts of the world still clamoring for vaccine. But the administration has argued that the plan is not an us-or-them choice, noting that the U.S. is supplying large quantities of vaccine to the rest of the globe. The U.S. has already approved Pfizer and Moderna boosters for certain people with weakened immune systems, such as cancer patients and transplant recipients. Some Americans, healthy or not, have managed to get boosters, in some cases simply by showing up and asking for a shot. And some health systems already are offering extra doses to high-risk people.

Widespread human SARS-CoV-2 infections combined with human-wildlife interactions create the potential for reverse zoonosis from humans to wildlife. We targeted white-tailed deer (Odocoileus virginianus) for serosurveillance based on evidence these deer have ACE2 receptors with high affinity for SARS-CoV-2, are permissive to infection, exhibit sustained viral shedding, can transmit to conspecifics, and can be abundant near urban centers. We evaluated 624 pre- and post-pandemic serum samples from wild deer from four U.S. states for SARS-CoV-2 exposure. Antibodies were detected in 152 samples (40%) from 2021 using a surrogate virus neutralization test. A subset of samples was tested using a SARS-CoV-2 virus neutralization test with high concordance between tests. These data suggest white-tailed deer in the populations assessed have been exposed to SARS-CoV-2.

Preprint available in bioRxiv (July 29, 2021):

 https://doi.org/10.1101/2021.07.29.454326 

In this Viewpoint, two Harvard economists estimate the cumulative financial costs of the COVID-19 pandemic in the US to date from lost domestic output and health reduction at more than $16 trillion, as a way to put the lesser costs of public health measures, such as population testing.

The estimated cumulative financial costs of the COVID-19 pandemic related to the lost output and health reduction are shown in the Table. The total cost is estimated at more than $16 trillion, or approximately 90% of the annual gross domestic product of the US. For a family of 4, the estimated loss would be nearly $200 000. Approximately half of this amount is the lost income from the COVID-19–induced recession; the remainder is the economic effects of shorter and less healthy life.

Output losses of this magnitude are immense. The lost output in the Great Recession was only one-quarter as large. The economic loss is more than twice the total monetary outlay for all the wars the US has fought since September 11, 2001, including those in Afghanistan, Iraq, and Syria. By another metric, this cost is approximately the estimate of damages (such as from decreased agricultural productivity and more frequent severe weather events) from 50 years of climate change....

Published in JAMA (October 12, 2020):

https://doi.org/10..1001/jama.2020.19759

High profile inmates like ex-Trump lawyer Michael Cohen are among those who have asked for early release. 

New York City is releasing "vulnerable" prisoners, the mayor said on Wednesday, days after Los Angeles and Cleveland freed hundreds of inmates. Prison reform advocates say those in jail are at higher risk of catching and passing on Covid-19. There have been more than 9,400 cases of Covid-19 and 152 deaths in the US so far, according to estimates. Globally there are some 220,000 confirmed cases and over 8,800 deaths.

New York City Mayor Bill de Blasio said on Wednesday that city officials will this week identify individuals for release, including people who were arrested for minor crimes and those most vulnerable to infection due to underlying health problems. His announcement came hours after a guard and a prisoner tested positive for coronavirus at Rikers Island prison, where disgraced former Hollywood producer Harvey Weinstein, 68, is a high-profile inmate. Weinstein will be moved to a different state prison, an official said on Wednesday. Other New York prisons, such as Sing Sing, have had inmates test positive for coronavirus and one employee for the state's corrections department has died from it.

The Biden administration has proposed using a less common injection method that would allow a single dose of the monkeypox vaccine to be split into five. As the monkeypox virus continues to spread in the United States, the Biden administration has adopted a strategy of vaccine-splitting to stretch the nation’s limited supply. A method known as intradermal vaccination allows a single-use vial to be split into five injections. Bavarian Nordic makes Jynneos, the only monkeypox-specific vaccine approved in the United States. It was initially approved by the Food and Drug Administration for a single 0.5 milliliter subcutaneous injection, followed by a second 0.5 milliliter dose four weeks later....

The latest omicron offshoot, BA.5, has quickly become dominant in the United States, driving a wave of reinfections across the country.  America has decided the pandemic is over. The coronavirus has other ideas. The latest omicron offshoot, BA.5, has quickly become dominant in the United States, and thanks to its elusiveness when encountering the human immune system, is driving a wave of cases across the country. The size of that wave is unclear because most people are testing at home or not testing at all. The Centers for Disease Control and Prevention in the past week has reported a little more than 100,000 new cases a day on average. But infectious-disease experts know that wildly underestimates the true number, which may be as many as a million, said Eric Topol, a professor at Scripps Research who closely tracks pandemic trends. Antibodies from vaccines and previous covid infections offer limited protection against BA.5, leading Topol to call it “the worst version of the virus that we’ve seen.”  Other experts point out that, despite being hit by multiple rounds of ever-more-contagious omicron subvariants, the country has not yet seen a dramatic spike in hospitalizations.

About 38,000 people were hospitalized nationally with covid as of Friday, according to data compiled by The Washington Post. That figure has been steadily rising since early March, but remains far below the record 162,000 patients hospitalized with covid in mid-January. The average daily death toll on Friday stood at 329 and has not changed significantly over the past two months. There is widespread agreement among infectious-disease experts that this remains a dangerous virus that causes illnesses of unpredictable severity — and they say the country is not doing enough to limit transmission. Restrictions and mandates are long gone. Air travel is nearly back to pre-pandemic levels. Political leaders aren’t talking about the virus — it’s virtually a nonissue on the campaign trail. Most people are done with masking, social distancing, and the pandemic generally. They’re taking their chances with the virus. “It’s the wild west out there,” said Ziyad Al-Aly, an epidemiologist at Washington University in St. Louis. “There are no public health measures at all. We’re in a very peculiar spot, where the risk is vivid and it’s out there, but we’ve let our guard down and we’ve chosen, deliberately, to expose ourselves and make ourselves more vulnerable.” Angela Rasmussen, a virologist at the University of Saskatchewan, would like to see more money for testing and vaccine development, as well as stronger messaging from the Biden administration and top health officials. She was dismayed recently on a trip to southern California, where she saw few people wearing masks in the airport. “This is what happens when you don’t have politicians and leaders taking a strong stand on this,” she said. The CDC said it has urged people to monitor community transmission, “stay up to date on vaccines, and take appropriate precautions to protect themselves and others....”

WASHINGTON — President Biden on Thursday used the full force of his presidency to push two-thirds of American workers to be vaccinated against the coronavirus, reaching into the private sector to mandate that all companies with more than 100 workers require vaccination or weekly testing. Mr. Biden also moved to mandate shots for health care workers, federal contractors and the vast majority of federal workers, who could face disciplinary measures if they refuse. The sweeping actions, which the president announced in a White House speech, are the most expansive he has taken to control the pandemic and will affect almost every aspect of society. They also reflect Mr. Biden’s deep frustration with the roughly 80 million Americans who are eligible for shots but have not gotten them. “We’ve been patient,” Mr. Biden said in a sharp message to those who refuse to be vaccinated. “But our patience is wearing thin. And your refusal has cost all of us.”  Initially reluctant to enact mandates, Mr. Biden is now moving more aggressively than any other president in modern history to require vaccination, experts say. In his remarks, he promised to “protect vaccinated workers from the unvaccinated.” “We can and we will turn the tide on Covid-19,” he said. Even so, Mr. Biden conceded that the mandates would take time to “have full impact.” They are also all but certain to be the subject of legal challenges; already, the largest union representing federal workers has raised questions. It is also unclear how many workers subject to the new mandates have already been vaccinated.

Mr. Biden is acting through a combination of executive orders and new federal rules. Under his plan, private-sector businesses that have 100 or more employees will have to require vaccination, or mandatory weekly testing, after the Occupational Safety and Health Administration drafts a rule. Roughly 17 million health care workers employed by hospitals and other institutions that accept Medicare and Medicaid reimbursement will also face strict new vaccination requirements, as will federal contractors and most federal workers. Experts say Mr. Biden has the legal authority to impose vaccine requirements on the private sector, through laws that require businesses to comply with evidence-based federal health safety standards. OSHA, which enforces workplace safety, has already imposed other pandemic precautions, such as a rule in June requiring health care employers to provide protective equipment and adequate ventilation and ensure social distancing, among other measures. Robert I. Field, a law professor at Drexel University, said that OSHA had the authority to protect workers’ safety, keeping them from being exposed to a potentially deadly virus, by requiring vaccinations.  Lawrence O. Gostin, a Georgetown University law professor who specializes in public health, added: “The president’s plan is bold, audacious and unprecedented. But I do think it’s entirely lawful. He’s on extremely strong legal ground.” The moves, which Mr. Biden said would cover 100 million people, are part of a broader White House effort to curb the pandemic, which began to spin out of control in July even as Mr. Biden and his top aides were forecasting a “summer of joy” and declaring independence from the virus. Since then, the highly infectious Delta variant has spread rapidly, fueling a spike in cases and deaths. Also on Thursday, Mr. Biden ordered mandatory vaccination for nearly 300,000 educators in the federal Head Start Program and at more than 200 federally run schools. He announced that he would use the Defense Production Act to increase the production of rapid testing kits and would work with retailers, including Amazon and Walmart, to expand their availability. And he said the Transportation Security Administration would now double fines on passengers who refuse to wear masks.....

Nearly all COVID-19 deaths in the U.S. now are in people who weren’t vaccinated, a staggering demonstration of how effective the shots have been and an indication that deaths per day — now down to under 300 — could be practically zero if everyone eligible got the vaccine.  An Associated Press analysis of available government data from May shows that “breakthrough” infections in fully vaccinated people accounted for fewer than 1,200 of more than 853,000 COVID-19 hospitalizations. That’s about 0.1%. And only about 150 of the more than 18,000 COVID-19 deaths in May were in fully vaccinated people. That translates to about 0.8%, or five deaths per day on average. The AP analyzed figures provided by the Centers for Disease Control and Prevention. The CDC itself has not estimated what percentage of hospitalizations and deaths are in fully vaccinated people, citing limitations in the data.  Among them: Only about 45 states report breakthrough infections, and some are more aggressive than others in looking for such cases. So the data probably understates such infections, CDC officials said. Still, the overall trend that emerges from the data echoes what many health care authorities are seeing around the country and what top experts are saying. Earlier this month, Andy Slavitt, a former adviser to the Biden administration on COVID-19, suggested that 98% to 99% of the Americans dying of the coronavirus are unvaccinated. And CDC Director Dr. Rochelle Walensky said on Tuesday that the vaccine is so effective that “nearly every death, especially among adults, due to COVID-19, is, at this point, entirely preventable.” She called such deaths “particularly tragic.” Deaths in the U.S. have plummeted from a peak of more than 3,400 day on average in mid-January, one month into the vaccination drive. 

About 63% of all vaccine-eligible Americans — those 12 and older — have received at least one dose, and 53% are fully vaccinated, according to the CDC. While vaccine remains scarce in much of the world, the U.S. supply is so abundant and demand has slumped so dramatically that shots sit unused. Ross Bagne, a 68-year-old small-business owner in Cheyenne, Wyoming, was eligible for the vaccine in early February but didn’t get it. He died June 4, infected and unvaccinated, after spending more than three weeks in the hospital, his lungs filling with fluid. He was unable to swallow because of a stroke. “He never went out, so he didn’t think he would catch it,” said his grieving sister, Karen McKnight. She wondered: “Why take the risk of not getting vaccinated?” The preventable deaths will continue, experts predict, with unvaccinated pockets of the nation experiencing outbreaks in the fall and winter. Ali Mokdad, a professor of health metrics sciences at the University of Washington in Seattle, said modeling suggests the nation will hit 1,000 deaths per day again next year.  In Arkansas, which has one of the lowest vaccination rates in the nation, with only about 33% of the population fully protected, cases, hospitalizations and deaths are rising. “It is sad to see someone go to the hospital or die when it can be prevented,” Gov. Asa Hutchinson tweeted as he urged people to get their shots. In Seattle’s King County, the public health department found only three deaths during a recent 60-day period in people who were fully vaccinated. The rest, some 95% of 62 deaths, had had no vaccine or just one shot.

“Those are all somebody’s parents, grandparents, siblings and friends,” said Dr. Mark Del Beccaro, who helps lead a vaccination outreach program in King County. “It’s still a lot of deaths, and they’re preventable deaths.” In the St. Louis area, more than 90% of patients hospitalized with COVID-19 have not been vaccinated, said Dr. Alex Garza, a hospital administrator who directs a metropolitan-area task force on the outbreak. “The majority of them express some regret for not being vaccinated,” Garza said. “That’s a pretty common refrain that we’re hearing from patients with COVID.” The stories of unvaccinated people dying may convince some people they should get the shots, but young adults — the group least likely to be vaccinated — may be motivated more by a desire to protect their loved ones, said David Michaels, an epidemiologist at George Washington University’s school of public health in the nation’s capital. Others need paid time off to get the shots and deal with any side effects, Michaels said. The Occupational Safety and Health Administration this month began requiring health care employers, including hospitals and nursing homes, to provide such time off. But Michaels, who headed OSHA under President Barack Obama, said the agency should have gone further and applied the rule to meat and poultry plants and other food operations as well as other places with workers at risk. Bagne, who lived alone, ran a business helping people incorporate their companies in Wyoming for the tax advantages. He was winding down the business, planning to retire, when he got sick, emailing his sister in April about an illness that had left him dizzy and disoriented. “Whatever it was. That bug took a LOT out of me,” he wrote. As his health deteriorated, a neighbor finally persuaded him to go to the hospital. “Why was the messaging in his state so unclear that he didn’t understand the importance of the vaccine? He was a very bright guy,” his sister said. “I wish he’d gotten the vaccine, and I’m sad he didn’t understand how it could prevent him from getting COVID.”

___

The Associated Press Health and Science Department receives support from the Howard Hughes Medical Institute’s Department of Science Education. The AP is solely responsible for all content.

The new coronavirus spread across much of the interior of the United States by tagging along with people moving from state to state, but US coastal regions were seeded with SARS-CoV-2 imported from other countries — perhaps in 2019, according to models. Alessandro Vespignani at Northeastern University in Boston, Massachusetts, and his colleagues studied air traffic, commuting patterns and other data to understand how and when the coronavirus took hold in the United States (J. T. Davis et al. Preprint at medRxiv http://doi.org/d3mf; 2020). The team found that in several coastal states, international travel drove introduction of the virus. In California and New York, SARS-CoV-2 might have begun circulating as early as December 2019.

But in many non-coastal states, domestic travelers rather than international visitors were the source of the first wave of infections. Infections spread across the country from late January to early March but were largely undetected, the authors say. The findings have not yet been peer reviewed.

Preprint of original study available at medRxiv (July 7, 2020):

https://doi.org/10.1101/2020.07.06.20140285