Rutgers Team Develops Rapid Screening Test for Omicron and Other SARS-CoV-2 Variants

 

The test, which is up for approval for clinical testing, could guide treatment and identify high-risk patients  

A rapid test that detects all known COVID-19 variants, including the highly transmissible Omicron variant, has been developed by researchers at Rutgers New Jersey Medical School.

The test, which can be performed at laboratories experienced in COVID-19 testing can quickly detect clinical samples that contain the SARS-CoV-2 virus with signature mutations for each known variant of concern—namely, the Alpha, Beta/Gamma, Delta and Omicron variants. The test uses special probes called “sloppy molecular beacons” that perform particularly well at detecting mutations in organisms that mutate frequently. These probes work even if other mutations unexpectedly develop near a mutation of interest.

The Rutgers study appeared this week in the preprint journal MedRxiv, which publishes research that is not yet peer reviewed. The study demonstrates that their approach is 100 percent sensitive and specific for identifying the correct variant when tested on clinical samples. The test can be used in a variety of instruments and assay formats.

The test was developed in the laboratory of David Alland, director of the Rutgers New Jersey Medical School Public Health Research Institute and the Center for COVID-19 Response and Pandemic Preparedness within the Rutgers Biomedical and Health Sciences Institute for Infectious and Inflammatory Diseases, and project leader Padmapriya Banada, working with Patricia Soteropoulos, Raquel Green and Deanna Streck.

“Our approach is unusually flexible in being able to detect unanticipated mutations,” Alland said. “We had recently improved an older version of the assay, so that it could detect the Delta variant, but when Omicron appeared, we suspected that it would be able to specifically identify this variant as well, and we are happy to find that our testing shows that we were correct.”

The Rutgers Genomics Center Clinical Lab Team—Soteropoulos, Streck and James Dermody—are now working to obtain rapid approval from the New Jersey Department of Health to use the new test on patients, where it could help determine the correct type of antibody therapy and potentially help identify patients at high risk for severe COVID-19.

To bolster the world’s public health fight against COVID-19, the Rutgers team is releasing all of the information needed to create and run the test as well as supporting information on the preprint server MedRxiv, which will be updated periodically when needed.

https://www.rutgers.edu/news/rutgers-team-develops-rapid-screening-test-omicron-and-other-sars-cov-2-variants

California paid COVID sick leave would return under new agreement

 Gov. Gavin Newsom and state lawmakers announced on Tuesday that they reached an agreement on a framework to again require employers to provide paid COVID-19 supplemental sick leave.

Under the framework, employees would continue to have access to paid sick leave through Sept. 30, 2022, the governor’s office announced. It would be retroactive and cover COVID-19 absences from Jan. 1.

Workers at businesses with 26 or more employees who test positive for the virus, or have to care for a family member with COVID-19 would get up to two weeks of supplemental leave.

The framework will provide up to 40 hours of additional paid sick leave, and another 40 hours if a worker or a family member they take care of tests positive. 

“By extending sick leave to frontline workers with COVID and providing support for California businesses, we can help protect the health of our workforce, while also ensuring that businesses and our economy are able to thrive,” state officials said in a statement.

Companies would have to absorb the costs of the paid time off, the Los Angeles Times reported.

The paid leave would likely be finalized through early budget actions, which also include restoring business tax credits.

California previously had a COVID-19 supplemental paid sick leave law, but it expired on Sept. 30, 2021.

The law, signed by Newsom in March 2021, required that all employers with 26 or more employees provide 80 hours of paid COVID-19 sick leave.

It was meant to make sure that workers don’t show up at work while potentially infected, or miss out on getting vaccinated because they don’t want to take time off.

Under the now-expired law, employees got paid sick time if they couldn’t work because they had to quarantine or isolate, or because they had appointments to get the COVID-19 vaccine or were experiencing symptoms related to the shot. It also applied for employees experiencing COVID-19 symptoms and seeking a medical diagnosis, or caring for family members with the virus.

Officials are working to bring back paid sick leave as the state sees an omicron-fueled COVID-19 surge that has sent daily infection numbers skyrocketing since the holidays.

Labor groups, like the California Labor Federation, have been calling for the Legislature to reinstate the paid leave.

“The Omicron surge is making workers risk losing their jobs or going to work sick,” tweeted the California Labor Federation, which is made up of more than 1,200 unions representing workers in manufacturing, retail, hospitality, health care and other sectors.

The California Teachers Association applauded the supplemental paid COVID-19 leave agreement, saying it will ensure that employees quarantine, recover and return to their classrooms.

“The fast-spreading Omicron COVID-19 variant has brought unprecedented challenges to our schools and colleges as thousands of students and educators have tested positive or fallen ill with COVID. This has put undue pressure on teachers and school employees faced with having to choose between going without pay or spreading the virus to their school communities.”

https://ktla.com/news/california/california-paid-covid-sick-leave-would-return-under-new-deal/

Pharmacies Turn Away Immunocompromised Patients Seeking 4th Covid Shot

 Patients with weakened immune systems — who are at high risk from covid-19 — say pharmacies are turning them away when they seek additional vaccine doses recommended by federal health officials.

Alyson Smith became eligible this month for a fourth vaccine dose because her medications leave her immunocompromised.

Although the Centers for Disease Control and Prevention encourages most adults to receive a total of three mRNA vaccines — two “primary” vaccinations and a booster — the agency now advises people with weak immune systems to receive three primary shots plus a booster, for a total of four doses.

Many people are confused about the difference between a primary vaccine series and a booster. A primary vaccine series helps people build antibodies to a new pathogen, while a booster combats waning immunity.

As Smith learned, many pharmacists are unaware that the CDC’s vaccine guidance has changed.

Smith booked her vaccine appointment online. But when she showed up at a Chicago-area Walgreens for the appointment Jan. 19, an employee told her the pharmacy chain wasn’t administering fourth doses to anyone.

Smith said she’s frustrated that vulnerable people are being forced to make multiple visits to crowded pharmacies and supermarkets, where many customers are unmasked.

“I feel for the pharmacists, because they’re overwhelmed like everyone else,” said Smith, 52. “But two years into the pandemic, there is a corporate responsibility to take action when the guidance comes down.”

In a written statement, Walgreens said it has administered thousands of fourth doses to immunocompromised people. “As vaccination guidelines continue to evolve, we make every effort to continuously update our pharmacy teams.”

The confusion stems from recent updates in vaccine advice for immunocompromised people, as well as a change in the interval between the end of a primary vaccine series and a booster.

• In August, the CDC began allowing immunocompromised people to receive a third dose of mRNA vaccine as part of their primary vaccination.
• In October, the CDC quietly updated its website to allow people with suppressed immune systems to receive a fourth shot as a booster.
• In January, the agency shortened the time that anyone must wait for a booster from six months to five.

People who received the one-dose Johnson & Johnson vaccine are eligible for a single booster, for a total of two shots, according to the CDC.

Given how often vaccine guidelines have been revised in recent months, some pharmacists have had a hard time keeping pace, said Mitchel Rothholz, chief of governance and state affiliates at the American Pharmacists Association. Pharmacy employees have coped with an ever-expanding workload but a deepening shortage of employees during the pandemic, he said.

“I don’t know any provider who wants to turn away a patient,” Rothholz said. “The CDC continues to make updates, and it’s becoming very difficult for providers at the grassroots level to keep up. I can understand why a pharmacist would say, ‘Corporate hasn’t given us the green light.’”

Confusion about who is eligible for a fourth shot “was inevitable, although I’m not saying it’s right or wrong,” he said.

Yet many patients and their doctors are frustrated.

If patients keep up with the latest guidelines, they ask, why can’t their pharmacy?

“It’s ridiculous,” said Dr. Dorry Segev, a transplant surgeon and researcher at Johns Hopkins University. “CDC makes it very clear that it’s allowed, and even people who print out the CDC guidance and take it to their pharmacies are being turned away.”

Charis Hill, 34, joined a chorus of immune-suppressed people venting their concerns on social media in recent days. When Hill tweeted Jan. 21 that Rite Aid should better educate its staff, the retailer tweeted back that day, saying, “We’re very sorry you didn’t have a great experience, Charis. Please check back with us early next month for more information regarding the fourth dose.”

In a written statement, Rite Aid said it continually educates its staff as CDC advice changes, and “is looking into the response that was provided to the customer on social media.”

Dr. Shikha Jain, an assistant professor of medicine at the University of Illinois Cancer Center in Chicago, said patients in rural areas often drive long distances to look for vaccines. One of her patients was “almost in tears” after being turned away. Jain tried to help by calling the pharmacy but was on hold so long that she had to hang up to see patients.

Jain said the CDC needs to do a better job educating doctors, pharmacists, and patients.

The CDC did not respond to a request for comment before publication.

Teresa Strahlman, 61, said she’s immunocompromised due to medications she takes for lupus, an autoimmune disease. But the Maryland woman said she didn’t realize she was eligible for a fourth dose until reading a KHN post on Facebook. “I had no idea, and I have a million doctors,” Strahlman said. “No one has said anything to me.”

The CDC estimates that 2.7% of adults — or 7 million people — are immunocompromised, a group that includes people with medical conditions that dampen their immune response, as well as those taking immune-suppressing drugs because of organ transplants, cancer, or autoimmune diseases.

Some immunocompromised people say that being turned away from a pharmacy is especially frustrating, given all that they have sacrificed during the pandemic.

Linda Rushing, 74, has given up attending church services in person, although she’s deeply religious, because of a weakened immune system that leaves her prone to a variety of infections.

Rushing made three visits to local pharmacies before finding someone to administer her fourth shot.

“It’s a tragedy to need help and not be able to get it,” said Rushing, of Rowlett, Texas, whose daughter and granddaughter are also immunocompromised. “I don’t want covid. I don’t want to give it to anybody, and I’m trying to do everything I can not to die from it.”

https://khn.org/news/article/pharmacies-are-turning-away-immunocompromised-patients-seeking-4th-covid-shot/

COVID-19 deaths climb in Los Angeles area

 Los Angeles County has reported an uptick in COVID-19 deaths, with daily fatalities resulting from the virus doubling in just one week. 

On Thursday, the county reported 102 COVID-19 deaths, marking the most fatalities it has seen in a day since March 10, 2021, according to the county’s public health department. 

The department said most of those fatalities are likely the result of the highly transmissible omicron variant, which was first detected in South Africa last November and has since spread around the world. 

Ninety percent of those fatal infections came after Dec. 24, a timeline suggesting that the omicron variant was the cause of the spike in those cases, the department reported.

The county's Director of Public Health Barbara Ferrer also noted that Black and Latinx residents had higher rates of cases, hospitalization and deaths, marking “a tragedy that reflects both long standing inequities to the resources that promote good health and policies and practices that marginalize the concerns of people of color.” 

Early studies have indicated that the omicron variant tends to be more mild than other COVID-19 strains and less likely to cause hospitalizations.

But for the people for whom the variant does become deadly, their condition tends to worsen more quickly than those infected with previous variants, Ferrer said, according to The Los Angeles Times.

“It means that for the people who are, in fact, ending up passing away from COVID, if they were infected with omicron, it looks like they get hit pretty hard earlier on,” Ferrer explained.

On Monday, Los Angeles County's public health department reported 25,784 daily cases and 27 deaths resulting from the virus.

Los Angeles Mayor Eric Garcetti (D) stressed the devastation of the death toll, but said he believes that “we’re in a better place” compared to last winter, The Times reported. 

“We’re still walking through … the shadow of the valley of death right now when we see 100-plus people in my city, my county, die in a single day like we did last week,” the mayor said. “And somehow that’s become normalized, or we don’t think about it as hard as we used to. I do. I still think about it. I pray on it each night. I pray on it in the morning when I wake up.”

https://thehill.com/homenews/state-watch/591323-covid-19-deaths-climb-in-los-angeles-area

COVID-19 test provider says it'll sue LA sheriff for alleging company has links to China

 The company providing COVID-19 testing in Los Angeles County said it would sue Sheriff Alex Villanueva for defamation after he claimed the company was connected to China. 

Villanueva alleged late last year that Fulgent Genetics had "strong ties" to Chinese technology and genomics companies but did not provide details of those ties. In a letter to the Board of Supervisors, the sheriff said DNA collected as a result of the tests were “not guaranteed to be safe and secure from foreign governments.”

The company, which was contracted to conduct testing and track the vaccination status of county employees, claims the sheriff's remarks were “in a last-ditch effort” to avoid vaccine mandates, according to The Los Angeles Times. 

Fulgent's attorneys asserted that the sheriff “made these and other false claims about Fulgent even though the FBI neither accused Fulgent of wrongdoing nor alluded to any evidence that Fulgent provided or would provide private medical information to China,” the Times reported.

Following the sheriff's claims, Lisa M. Garrett, the county’s director of personnel, denied that data was shared with Beijing. 

“The County has no evidence from any law enforcement agency or any other source that any County employee data has been or will be shared with the Chinese government,” Garrett said in an email to employees last month, the Times added. 

Fulgent is also contracted by federal agencies including the Department of Homeland Security and is certified by the Food and Drug Administration.

Villanueva has been outspoken against the county's vaccine mandate. He has previously asserted that the mandates would cause a "mass exodus” among his employees and said that he could not enforce "reckless mandates that put the public's safety at risk."

The Hill has reached out to Fulgent Genetics and to the sheriff's department for comment. 

https://thehill.com/regulation/court-battles/591376-covid-19-test-provider-says-itll-sue-la-sheriff-over-allegation

Gottlieb Suggests End To Mask, Vaccine Mandates

 by Jack Phillips via The Epoch Times (emphasis ours),

Dr. Scott Gottlieb, former director of the Food and Drug Administration (FDA) and current board member at Pfizer, said that declining COVID-19 cases should signal to policymakers that it is time to lift more pandemic-related restrictions.

“I think certainly on the east coast where you see cases declining dramatically we need to be willing to lean in and do that very soon I think as conditions improve we have to be willing to relax some of these measures with the same speed that we put them in place,” he told “The Squawk Box” in a Monday interview when asked about whether mask mandates should be dropped.

Gottlieb said that “a lot of the acrimony” in the United States stems from a lack of “clear goalposts” about when some of the measures will end.

The former FDA commissioner also cited the Connecticut government’s recent decision to rescind vaccine mandates for state workers as a policy that other policymakers should adopt in the near future as COVID-19 cases decline nationwide.

“The only way to get compliance from people and get accommodation [is] if we demonstrate the ability to withdraw these [mandates] in the same manner in which we put them in,” Gottlieb added.

The call for COVID-19 restrictions to be dropped comes as the overall infection rate in the United States has sharply declined in recent days. Data from the Johns Hopkins-run Our World in Data shows that 4,110 out of every one million Americans recorded infections on Jan. 10, but that rate was 2,643 as late as Friday and dropped to 615 per one million as of Sunday.

Outside the United States, more and more European countries have moved to rescind certain COVID-19-related rules, including vaccine passports and mask mandates. For example, UK Prime Minister Boris Johnson said that starting Jan. 27, people in England won’t have to wear masks in public or show proof that they’ve been vaccinated to enter some venues.

But on Monday, World Health Organization’s (WHO) director-general, Tedros Adhanom Ghebreyesus, warned that more COVID-19 variants may emerge and alleged that it’s dangerous to assume Omicron is the last one or that “we are in the endgame.”

“There are different scenarios for how the pandemic could play out and how the acute phase could end. But it’s dangerous to assume that omicron will be the last variant or that we are in the endgame,” Tedros told a WHO board meeting. “On the contrary, globally, the conditions are ideal for more variants to emerge.” He didn’t provide evidence or data to back up his claim.

https://www.zerohedge.com/covid-19/pfizer-board-member-suggests-end-mask-vaccine-mandates

Omicron BA.2 Variant May Be Extra Transmissible

 The Omicron sublineage BA.2 is making headlines for its potentially increased transmissibility as its prevalence rises in some countries, but experts aren't too concerned about the variant just yet.

Late last week, the U.K. Health Security Agency designated BA.2 a "variant under investigation" as cases were doubling every 4 days and showing a 120% growth advantage over the original Omicron clade, known as BA.1, said Katelyn Jetelina, PhD, MPH, an epidemiologist at UT Health Science Center at Houston.

Other countries, including Denmark, Norway, Sweden, and India, have seen similar growth for BA.2, Jetelina reported in her Substack email. Still, she said, it's "likely nothing like the huge transmissibility jump we saw from Delta to Omicron," which was a 500% growth advantage.

So far some 8,000 cases of BA.2 have been detected in 40 countries, according to news reports.

BA.2 is not a new sublineage. It was first detected in December and made headlines then as the "stealth" Omicron variant because it did not have the same s-gene target failure on PCR testing that BA.1 did. That's because it lacks the spike deletions 69-70 in BA.1, so s-gene targets still turn up positive.

That means BA.2 doesn't have a special signal that tells labs it's Omicron, so labs now must go to genetic sequencing to identify variants, Jetelina said.

She added that while it has many of the same mutations as BA.1, it has a lot of differences too. While BA.1 had about 60 mutations, BA.2 has about 85 mutations.

While it appears to have a transmission advantage, it's not clear what the additional mutations mean for severity, immune evasion, and other parameters.

"It may have a slight growth advantage but [there's] no evidence at all yet that it can evade Omicron (BA.1) immunity or be different to Omicron in any meaningful way," tweeted Meaghan Kall, a PhD student at the U.K.'s Health Security Agency. "Variants will continue to emerge, but not all variants will be a problem."

She noted that while the growth advantage for BA.2 looks "more than slight," it's still "too early to say with so few samples. This happens every time a variant emerges first couple weeks, some sort of founder effect. I'll trust growth estimates next week more."

"Only having a transmissibility advantage at this stage of the game (with population immunity so high) isn't a total showstopper," Kall added.

In Denmark, BA.2 now accounts for nearly half of all cases detected there. Early data, however, indicate that it has not been associated with an increase in hospitalizations there. Health authorities there also said there's likely to be a minimal difference in vaccine effectiveness between BA.1 and BA.2.

Norway reported a rapid increase in BA.2 infections, rising from seven cases detected on Jan. 4 to 611 cases detected on Jan. 19, the majority occurring in Oslo. Norwegian authorities also concurred that BA.2 is likely more contagious than BA.1.

Still, there are no data yet on the key question of whether those who were infected with the "original" Omicron can get re-infected with BA.2.

Omicron is not the first variant to have a "plus" version. Last year, the Delta Plus variant made headlines, but never gained much ground over the original Delta variant.

https://www.medpagetoday.com/special-reports/exclusives/96833