New Coronavirus News from 3 Jan 2022

Wastewater samples reveal record levels of coronavirus across U.S. [NBC News, 3 Jan 2022]

By Alicia Victoria Lozano

"Wastewater is going to be a leading indicator for what's going on in a given community and what's to come," said a senior scholar at the Johns Hopkins Center for Health Security.

With at-home Covid-19 tests in high demand and their efficacy in question, health departments from California to Massachusetts are turning to sewage samples to get a better idea of how much the coronavirus is spreading through communities and what might be in store for health care systems.

Experts say wastewater holds the key to better understanding the public health of cities and neighborhoods, especially in underserved areas that do not have equal access to care.

“Every time an infected person uses the toilet, they’re flushing this information down the toilet, where it’s collecting and aggregating and mixing with poop from thousands of other people,” said Newsha Ghaeli, a co-founder and the president of Biobot Analytics, a wastewater epidemiology company based in Massachusetts.

“Even if you can’t access a test, you’re still pooping,” Ghaeli said. “It doesn’t depend on you having access to health care or health insurance.”

Monitoring sewage can also measure other public health concerns, such as obesity, opioids and even polio, said Sheree Pagsuyoin, an associate professor of civil and environmental engineering at the University of Massachusetts Lowell. The pandemic has ushered in a new era of wastewater analysis, once a maligned discipline, to inform public health policy.

“It’s sort of like mapping a trend,” Pagsuyoin said, adding that there has been a “paradigm shift” as more cities turn to sewage analysis to better understand local challenges.

Recent wastewater analysis from a variety of sources across the country indicates an unprecedented surge in infections at a time when millions of people are forced to reconsider travel and holiday plans.

According to Biobot Analytic's wastewater dashboard, coronavirus levels detected in sewage samples across the country are higher now than at any previous point in the pandemic.

Recent wastewater samples in Houston, for example, show that there has been a sharp increase in the amount of the coronavirus detected in the city’s sewage. As of Dec. 20, Houston’s viral load, or the amount of virus found in samples, was at 546 percent, and the positivity rate was at 14 percent, according to the city Health Department’s wastewater dashboard. The viral load is up from 142 percent last week and 76 percent the previous week.

More than 700 city employees have contracted the virus, Mayor Sylvester Turner said on Twitter. As a result, Turner announced the opening of two additional megasites that will offer free testing for residents.

Dr. Amesh Adalja, a senior scholar at the Johns Hopkins Center for Health Security, said: “Wastewater is going to be a leading indicator for what’s going on in a given community.

“It will also give an indication of what’s to come, because not every Covid case comes to clinical attention — many cases are mild or asymptotic,” he added. “But the fact is that people who are infected are going to shed the virus in their stool.”

Sewage monitoring also shows case numbers surging in parts of California, Colorado, Idaho, Massachusetts, Missouri and North Carolina, as well as Canada, Spain and the United Kingdom.

A team of researchers at the University of Missouri has been working with the state Department of Health and Senior Services and the Department of Natural Resources to track the virus through wastewater.

Researchers in Missouri separate the virus from larger particles of waste and extract its genetic material. They can also amplify the genetic material and study it in greater detail through a process known as quantitative reverse transcription polymerase chain reaction. In addition to detecting the presence of the virus that causes Covid-19 in human waste, researchers are also able to identify specific variants.

New data show that the highly contagious omicron variant is spreading quickly throughout the state.

Expanded testing conducted Dec. 20 found mutations associated with the omicron variant in 32 of 57 wastewater samples collected statewide, Jeff Wenzel, who oversees the wastewater surveillance program for the state health department, told The Associated Press. Testing conducted the week before found the mutation in 15 of 63 test locations.

Pagsuyoin is part of a team in Massachusetts developing a wireless sensor that could detect SARS-CoV-2, the virus that causes Covid-19, in the air and in wastewater days before an outbreak occurs. Researchers will undertake a three-year study using data from three monitoring sites, two of them in Massachusetts and the other in the Philippines.

“People are becoming a little bit more open about using wastewater data to know where a disease is supposedly coming out,” she said. “We can use this technology to more efficiently monitor population health.”

Sewage analysis is most effective as an early warning signal between surges — particularly because people are not testing as often when rates are down — and in tracking cases when waves begin to dissipate. It can also help fill in some gaps during waves when testing is insufficient and serve as a way to compare waves, said Dr. Albert Ko, a professor of public health, epidemiology and medicine at Yale University’s School of Public Health.

“What it is useful for is looking at trends over time and comparing, let’s say, ‘Are we as bad in transmission this wave as compared to the last one?’” Ko said, although he added that variants and seasonality can “hamper interpretation” of such comparisons.

Ko said wastewater surveillance is best used as part of a broader analysis of an outbreak that takes other data points into consideration, like testing.

Why this Covid-19 surge is 'unprecedented in this pandemic' [CNN, 3 Jan 2022]

By Christina Maxouris and Holly Yan

(CNN)The new year is starting with a massive influx of Covid-19 that's different from any other during this pandemic, doctors say.

"We're seeing a surge in patients again, unprecedented in this pandemic," said Dr. James Phillips, chief of disaster medicine at George Washington University Hospital.

"What's coming for the rest of the country could be very serious. And they need to be prepared."

Even health care workers are getting sidelined during the rapid rise of the Omicron variant, the most contagious strain of novel coronavirus to hit the US.

"Our health system is at a very different place than we were in previous surges," emergency medicine professor Dr. Esther Choo said.

"This strain is so infectious that I think all of us know many, many colleagues who are currently infected or have symptoms and are under quarantine," said Choo, associate professor at Oregon Health and Science University.

"We've lost at least 20% of our health care workforce -- probably more."

Don't get a false sense of security with Omicron
Early studies suggest the Omicron variant may cause less severe disease than the Delta variant, which still makes up a considerable portion of US Covid-19 cases.

But because Omicron is much more contagious, the raw number of Covid-19 hospitalizations could get worse, Dr. Anthony Fauci said.

"When you have so many, many cases, even if the rate of hospitalization is lower with Omicron than it is with Delta, there's still the danger that you're going to have a surging of hospitalizations that might stress the health care system," said Fauci, director of the National Institute of Allergy and Infectious Diseases.

And Omicron might be more problematic for young children, said Dr. Scott Gottlieb, former commissioner of the US Food and Drug Administration.

"It does appear now, based on a lot of experimental evidence that we've gotten just in the last two weeks, that this is a milder form of the coronavirus," Gottlieb told CBS' "Face the Nation" on Sunday.

"It appears to be more of an upper airway disease than a lower airway disease. That's good for most Americans. The one group that that may be a problem for is very young children -- toddlers -- who have trouble with upper airway infections," said Gottlieb, a current board member at Pfizer.

"This new strain could have a predilection, again, for the upper airway, which could be a bigger challenge in young kids, because of the way it binds to the airway cells."

School districts go remote after record-high child Covid-19 hospitalizations
Just as millions of students prepared to return to school, new pediatric Covid-19 hospitalizations reached a record high.

For the week ending December 28, an average of 378 children were admitted to hospitals every day with Covid-19, according to CDC data.

That's a 66% jump from the previous week. It also breaks the previous record of 342 set during the Delta variant surge at the beginning of the school year.

With the more transmissible Omicron variant, some schools might want to postpone in-person learning, pediatrician Dr. Peter Hotez said.

"It may be the case in some school districts, where things are so raging right now in terms of Omicron for the next couple of weeks, and it may be prudent to delay things a couple more weeks," said Hotez, dean of the National School of Tropical Medicine at Baylor College of Medicine in Houston.

"It's going to be a very challenging time," Hotez said. "People are going to have to be patient."
In Georgia, at least five large Atlanta-area school districts will be starting class remotely this week.

"Due to the rapid rise in positive cases in the metro Atlanta area, students will begin virtual classes Tuesday, Jan. 4 through Friday, Jan. 7," Atlanta Public Schools said Saturday.

"Our current plan is to resume in-person instruction on Monday, Jan. 10," the school district said.

"All APS staff are required to report to their work location Monday, Jan. 3, for mandatory COVID-19 surveillance testing, unless they are ill. The data collected from staff testing will be used for future planning."

APS said the goal is to allow students and staff to be tested and to isolate and quarantine as needed, according to CDC and health department guidelines.

Four other nearby school districts -- in Fulton County, DeKalb County, Rockdale County and Clayton County -- announced they would have temporary remote learning following the holiday break.

'Omicron is truly everywhere'
Across the country, the rapid spread of Omicron variant has impacted businesses, transportation and emergency services.

"Omicron is truly everywhere," said Dr. Megan Ranney, an emergency medicine professor at Brown University's School of Public Health.

"What I am so worried about over the next month or so is that our economy is going to shut down -- not because of policies from the federal government or from the state governments, but rather because so many of us are ill."

In New York, staffing issues led to the suspension of several subway lines, New York City's Metropolitan Transportation Authority announced last week.

And the city's emergency medical services were instructed to not transport stable patients with influenza-like symptoms so they could prioritize those in emergencies, according to a directive issued New Year's Eve by the fire commissioner, chief of department, chief of EMS and the chief medical director. The directive, which includes limited exceptions, applies to the New York Fire Department and voluntary hospital providers in the city's 911 system.

In Ohio, the mayor of Cincinnati declared a state of emergency after a spike in Covid-19 infections led to staffing shortages in the city's fire department.

The mayor said if the problem goes unaddressed, it would "substantially undermine" first responders' readiness levels.

And thousands of flights have been canceled or delayed as staff and crew call out sick.

Vast majority of patients are unvaccinated, experts say
While Americans who have been fully vaccinated might get infected with Omicron, they are less likely than the unvaccinated to get seriously ill, health experts say.

Doctors across the country say most people hospitalized for Covid-19 are unvaccinated.

"What we're seeing is that our vaccinated patients aren't getting sick, and our frail, multiple comorbidities-vaccinated patients do need admission, but their admissions are shorter and they're able to leave the hospital after several days," said Dr. Catherine O'Neal, chief medical officer at Our Lady of the Lake Regional Medical Center in Baton Rouge, Louisiana.

"Our unvaccinated patients are the sickest patients," she said. "They're the patients most likely to be on the ventilator.

"We're running out of tests," O'Neal added. "We're running out of room. We're inundated in the ER."
Despite a year of calls from public health experts to get vaccinated -- and now boosted -- only about 62% of the US population is fully vaccinated, according to US Centers for Disease Control and Prevention data.

And about 33.4% of those who are fully vaccinated have received their booster doses, the data shows.

"If you're unvaccinated, that's the group still at highest risk," said Dr. William Schaffner, a professor at Vanderbilt University Medical Center. "The adults that are being admitted to my institution, the vast majority continue to be unvaccinated."

New Coronavirus News from 2 Jan 2022

Puerto Rico Faces Staggering Covid Case Explosion [The New York Times, 2 Jan 2022]

By Frances Robles

The island had a 4,600 percent increase in cases in recent weeks after mounting one of the nation’s most successful vaccination campaigns.

Armed with her vaccine passport and a giddy urge to celebrate the holiday season, Laura Delgado — and 60,000 other people in Puerto Rico — attended a Bad Bunny concert three weeks ago.

Three days later, she was sick with Covid-19, one of about 2,000 people who fell ill as a result of the two-day event.

“We did so well; we followed the rules,” said Ms. Delgado, a 53-year-old interior designer. “We followed the mask mandate. Our vaccination rate was so high that we let our guard down. The second Christmas came, we were like, ‘We’re going to party!’”

Puerto Rico Coronavirus Cases
The superspreader concert helped usher in an explosion of Covid-19 cases in Puerto Rico, which until then had been celebrating one of the most successful vaccination campaigns in the United States. The concert was one of a series of business events, company holiday parties and family gatherings that fueled a 4,600 percent increase in cases on the island, a surge that public health officials worry could linger into the New Year; the Puerto Rican holiday season stretches to Three Kings Day on Jan. 6.

While the Omicron variant has besieged the entire country, it is especially worrisome in Puerto Rico, a U.S. territory already overwhelmed by government bankruptcy, an exodus of health professionals and a fragile health care system. Officials imposed a new wave of tough restrictions on travelers and diners in hopes of staving off the new wave of cases.

Rafael Irizarry, a Harvard University statistician who keeps a dashboard of Puerto Rico Covid-19 data, tweeted the daunting facts: A third of all coronavirus cases the island has recorded since the start of the pandemic occurred in the past month. The number of cases per 100,000 residents jumped to 225, from three, in three weeks.

In December, the number of hospitalizations doubled — twice.

Without the polarizing politics that have plagued the debate over vaccines in other parts of the country, nearly 85 percent of those in Puerto Rico have received at least one vaccine dose, and about 75 percent have gotten both shots.

But in the face of a highly contagious new variant, a high vaccination rate is not that meaningful anymore, Mr. Irizarry said. Most in Puerto Rico have passed the six-month limit beyond which the vaccine’s effectiveness begins to wane, yet at least 40 percent have yet to receive their booster shots, health officials said.

At one point this week, the daily case count had surpassed 11,000, a very high figure for an island with just 3.2 million inhabitants. The exponential increases have begun to taper off, but case numbers are still climbing, Mr. Irizarry said.

“I first noticed something going on on Dec. 13, and I alerted the Department of Health,” he said. “By the 14th and 15th, it was obvious. I called the guy who runs the database and said, ‘Is there some kind of glitch in the database?’”

The Coronavirus Pandemic: Latest Updates
There are currently 317 people hospitalized with Covid-19, more than a quarter of whom are children, according to the island’s Department of Health. That’s about half the number of people who were hospitalized with the illness at this time last year, before so many people were vaccinated. But it is still proving to be a challenge for hospitals.

“The problem is, let’s suppose Omicron is half as bad,” Mr. Irizarry said. “If you have eight times more cases, the math doesn’t work out in your favor.”

Gov. Pedro R. Pierluisi has ordered lower capacity limits in restaurants. To attend large public events, people now have to be vaccinated and present a negative Covid-19 test. Passengers arriving on domestic flights must show a negative test taken within 48 hours before arrival, regardless of their vaccination status. Similar rules were already in place for international flights.

Mass public events, including an important celebration to commemorate the 500th anniversary of the island’s capital, San Juan, have been canceled. “Dick Clark’s New Year’s Rockin’ Eve,” which ABC had planned to broadcast live from Puerto Rico in front of big crowds, was downgraded to a virtual event.

The Coronavirus Pandemic: Key Things to Know

The global surge. As the Omicron variant sweeps across the planet, the global tally of new coronavirus cases has for the first time passed one million per day on average. The previous daily average global case record set last April has already been broken three times this week.

Canceled flights. With Covid surge, has come thousands of flight cancellations, as airlines are unable to adequately staff their flights. Looking for relief, the airline industry pushed the CDC to shorten its recommended isolation period for Americans infected with Covid-19. On Monday, it reduced the recommended quarantine period to five days for those without symptoms.

Around the world. South Africa announced that its Omicron wave had passed without a large spike in deaths. Case counts in the country are down 30 percent in the last week. The announcement offered cautious hope to other countries grappling with the fast-spreading variant.

Staying safe. Worried about spreading Covid? Keep yourself and others safe by following some basic guidance on when to test and how to use at-home virus tests (if you can find them). Here is what to do if you test positive for the coronavirus.

After a few dozen Miss World contestants got sick, the pageant finals in Puerto Rico were canceled.

On Thursday, the Scientific Coalition, a group of scientists and health professionals that has been advising the governor, recommended even stricter measures, such as limits on alcohol sales and shorter hours for bars and other establishments. On Friday, the governor followed the recommendation and ordered businesses closed between midnight and 5 a.m. from Jan. 4 until Jan. 18. He also mandated booster shots for restaurant employees and public safety workers.

“It’s a message that’s hard to digest when two weeks ago the case numbers here were among the lowest in the world,” said Daniel Colón-Ramos, a Yale University professor who is president of the coalition.

The measures are particularly hard in Puerto Rico, he said, where it is hard to overstate the importance of a holiday season that starts at Thanksgiving and lasts until Jan. 6. He described it as “Fourth of July plus the Super Bowl.”

“Christmas is a week that Puerto Ricans celebrate their identity,” he said. “They celebrate their family. They celebrate their faith. They celebrate their heritage.”

The average age of people who become infected on the island is 33, health officials said. But experts worry that if young people who become infected while attending parties and other events visit elders for New Year’s and Three Kings Day, the number of sick older people is certain to rise. With so many of its young professionals moving in recent years to Florida, Texas and other states, Puerto Rico has a disproportionately high percentage of older adults, many of whom suffer from diabetes, obesity and other ailments that put them at higher risk for coronavirus complications.

“We have a health system that is — it’s not a secret — fragile,” said Carlos R. Mellado López, the island's secretary of health. He urged people not to unnecessarily overwhelm testing centers and insisted that Puerto Rico had the tools necessary, such as monoclonal antibody treatments, to combat the crisis.

But experts also caution that thousands of medical professionals have left Puerto Rico in recent years in search of higher salaries, which could complicate the island’s ability to attend to large numbers of sick people. The number of doctors on the island has dropped by 5,000 since 2006, and another exodus of primary care doctors is anticipated because they were left out of recent tax incentives designed to keep specialists from leaving, said Víctor M. Ramos Otero, president of the Puerto Rico doctors’ association.

“The problem we have is not the beds,” Mr. Ramos said. “The principal issue is the personnel.”
José R. López de Victoria, an epidemiologist who helped design coronavirus protections for Puerto Rican basketball teams, said the crisis was still stretching ahead.

“From what we are seeing at testing sites, this is not over,” he said. “It’s going to be two more weeks. The expectation is that the case rate will go up.”

Covid is rampant among deer, research shows [NBC News, 2 Jan 2022]

By Evan Bush

The findings are a reminder that human health is intertwined with that of animals and that inattention to other species could prolong the pandemic.

Humans have infected wild deer with Covid-19 in a handful of states, and there’s evidence that the coronavirus has been spreading among deer, according to recent studies, which outline findings that could complicate the path out of the pandemic.

Scientists swabbed the nostrils of white-tailed deer in Ohio and found evidence of at least six separate times that humans had spread the coronavirus to deer, according to a study published last month in Nature.

About one-third of the deer sampled had active or recent infections, the study says. Similar research in Iowa of tissue from roadkill and hunted deer found widespread evidence of the virus.

The research suggests that the coronavirus could be taking hold in a free-ranging species that numbers about 30 million in the U.S. No cases of Covid spread from deer to human have been reported, but it’s possible, scientists say.

It’s a reminder that human health is intertwined with that of animals and that inattention to other species could prolong the pandemic and complicate the quest to control Covid.

Widespread, sustained circulation of the virus in deer could represent a risk to people if mutations in deer create a new variant. A population of wild animals harboring the virus could also retain variants that are no longer circulating among humans now and allow them to return later.

“The sheer possibility that these things are happening and it’s unknown makes this very unsettling,” said Suresh Kuchipudi, a virologist at Pennsylvania State University. “We could be caught by surprise with a completely different variant.”

Early in the pandemic, scientists grew concerned that the virus could jump from humans to other animals. One study found many mammals with receptors that could allow the virus to bind in their cells, with deer among those at high risk.

They began to investigate.

First, in a laboratory study, researchers spritzed four fawns’ noses with infectious coronavirus to test whether the virus could infect them. They also took two uninfected deer into the same room, keeping them separated with a plexiglass barrier that didn’t reach the ceiling.

“We had four inoculated animals and two contact animals. Everybody got infected and shed significant amounts of infectious virus. That was a surprise,” said Diego Diel, an associate professor of virology at Cornell University, who helped lead the research.

The deer most likely shared the virus through nasal secretions that traveled over the barrier by air, he said. The infected deer didn’t exhibit noticeable symptoms.

Deer often travel in herds and touch noses, making transmission a concern.

So federal scientists tested blood samples of wild deer in Illinois, Michigan, New York and Pennsylvania. They eventually tested 624 samples, finding that about 40 percent of samples that were collected last year had antibodies that suggested past infection.

The latest studies provide evidence of active and recent infection.

In the peer-reviewed Ohio State University study, 35.8 percent of 360 free-ranging deer tested positive through nasal swabs. The researchers were able to culture the virus for two samples, meaning they could grow live virus.

And after they reviewed genetic relationships among viruses from 14 deer, “we’ve got evidence we have deer-to-deer transmission occurring,” said an author of the study, Andrew Bowman, an associate professor of veterinary preventive medicine at Ohio State University. The researchers found six mutations in deer that are uncommon in people.

A preprint study led by Kuchipudi of Penn State found the coronavirus in lymph nodes of 94 of 283 deer that were hunted or killed by vehicles in Iowa in 2020.

Both studies suggest that the virus spilled over from humans to deer several times in several places. The common viral genomes circulating in humans at the time were also circulating in deer, the studies say.