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k a rl h e nn i ng:
No good: Coronavirus cases in South Africa nearly triple in three days as fears over omicron grow

k a rl h e nn i ng:
‘I don’t think we’re back to square one.’ Beth Israel races to find out how much vaccines protect against Omicron

The hospital’s researchers are part of a global effort to understand the fast-spreading variant.

By Jonathan Saltzman Globe Staff, Updated December 2, 2021, 27 minutes ago

Dr. Dan Barouch’s Thanksgiving morning began with an e-mail that made him shudder.

The message had been sent the night before by a computational biologist at the Los Alamos National Laboratory in New Mexico. She alerted the Beth Israel Deaconess Medical Center immunologist and more than a dozen other US scientists to some worrisome new coronavirus variants she was tracking, especially a highly mutated strain first detected in the African nations of Botswana and South Africa.

“I’m so sorry to send you [news of] horrible variants just before a holiday,” wrote Bette Korber, who studies the evolutionary changes of SARS-CoV-2, the virus that causes COVID-19. “But it seemed important to get the word out, as these are so very different. The potential of these scare (sic) me.”

Barouch runs Beth Israel’s Center for Virology and Vaccine Research, which helped create the Johnson & Johnson vaccine and has studied rival shots from Pfizer-BioNTech and Moderna. Korber’ e-mail was the starting gun for a race by his lab and dozens of others around the world to assess the threat posed by what is now known as Omicron.

Barouch understood her alarm when he looked at the genetic sequence of the variant. It had 32 mutations on the spike protein, which the virus uses to invade human cells. Many were in an area that antibodies latch onto when attacking the virus. That immediately raised concerns that the mutations could diminish the effectiveness of the vaccines.

“It really felt like we have to be on this right away,” he remembered thinking that day as he sat at his computer at home in Newton. “Here we go again.”

Although it was a holiday, lab employees hastily began trying to determine whether the three COVID vaccines cleared for use in the US will protect recipients from the variant. Roughly a third of Barouch’s 60 researchers are designing experiments and starting to synthesize Omicron’s spike protein so they can test it on blood samples taken from people who have received vaccines and boosters.

Researchers in the US and abroad are doing similar work. Others are trying to determine whether the variant is more contagious than the now-dominant Delta strain or causes more severe illness. Unfortunately, in an era when people expect to find answers on the Internet within seconds, researchers say it will likely take at least a couple of weeks to get clarity about Omicron.

That’s particularly frustrating given how fast viruses can spread. Hours after Barouch spoke with a reporter Wednesday, the first case of Omicron in the US was confirmed in a vaccinated traveler who returned to California after a trip to South Africa. The person, who had received two doses of the Moderna shot, but had not been vaccinated long enough to receive a booster, is improving and agreed to remain in quarantine, California officials said. A second case of the Omicron variant was identified in the US on Thursday, detected in a Minnesota man who was fully vaccinated and had received a booster shot and had traveled to New York City for a convention attended by tens of thousands of people.

Although executives from Pfizer’s German partner BioNTech and from Cambridge-based Moderna have publicly expressed hopes that their firms’ vaccines will continue to provide at least some protection against Omicron, Barouch says no one can say anything with certainty until the evidence is in.

“If I were to speculate, I don’t think we’re back to square one,” he said in his 10th-floor office overlooking the Longwood Medical Area. He suspects that the antibodies and immune cells stimulated by vaccines for the coronavirus that emerged in China in late 2019 will still provide some protection, or “cross-reactive immunity,” to Omicron. How much, he said, “is not clear.”

Last Thursday, Barouch and his wife, Dr. Fina Barouch ― an ophthalmologist and former classmate at Harvard Medical School ― and their two school-age daughters were preparing for a Thanksgiving feast featuring a 24-pound turkey when he read the e-mail from Korber. She tracks hundreds of genetic sequences of variants around the world that are entered into a public online database called GISAID. Most variants on the database don’t pose a serious threat. But the one that Korber flagged had several troubling features.

The variant, which had been sequenced by South African health officials after it was detected in coronavirus samples at a private lab in that country, had a startling number of mutations, at least 50. Of those, 32 were on the spike protein.

Barouch showed a reporter the genetic sequence of the Omicron spike protein on his computer screen, which displayed line after line of letters. Most were black, but 32 were red, blue, purple, or yellow. Each colored letter represented a mutation. In contrast, he said, the genetic sequence of the Delta variant would have had only a handful of colored letters, illustrating the profound evolutionary changes in Omicron.

“We haven’t seen this number of mutations before,” he said.

Several other things were troubling. Twelve of the mutations on the spike protein were in the so-called receptor-binding domain, the target of disease-fighting antibodies stimulated by the vaccine or an infection. Scientists recognized several of the mutations from other variants and knew they have the ability to evade antibodies. The combination of features, Barouch said, is “the reason why it caused such a global panic.”

Beginning Friday at 5 a.m., after a delayed Thanksgiving dinner with his family, Barouch began exchanging a torrent of e-mails with top executives of J&J’s pharmaceutical division, Janssen, in the US and the Netherlands. They asked whether he thought J&J’s coronavirus vaccine ― which accounts for less than 4 percent of the more than 461 million COVID vaccine doses administered in the US ― would protect recipients against the new variant. He said he didn’t know, but his lab would start to run experiments on that and the two other vaccines.

Scientists at Pfizer, BioNTech, and Moderna are running the same types of tests. All of the makers of the three vaccines have said that they are prepared to roll out booster shots to target Omicron, if necessary. But it could be months before companies would be able to get them in people’s arms if the firms have to develop shots tailor-made to the variant, test them on volunteers, and get them cleared by regulators.

The Pfizer and Moderna vaccines use messenger RNA to instruct cells to create a harmless protein similar to the spike protein on the surface of the coronavirus and stimulate an immune response. The J&J vaccine does the same thing by using a virus that causes colds to deliver part of the spike proteins into cells.

Barouch also exchanged e-mails with hundreds of scientists at the World Health Organization, the National Institutes of Health, the Harvard-affiliated Massachusetts Consortium on Pathogen Readiness and universities around the world.

Researchers at his lab also scrambled on the holiday weekend in response to the news.

Katherine McMahan, a research assistant, was driving back to Boston from Pittsburgh on Thanksgiving when she began exchanging texts with Catherine Jacob-Dolan, a PhD student in the lab who was visiting her parents in Arlington.

“Are you working on this?” McMahan recalled asking. “What do you know?”

Jacob-Dolan was indeed working on it and had begun ordering reagents from suppliers. Reagants are used in the lab for chemical reactions in experiments.

John Ventura, a post-doctoral fellow at the lab, said he was at the Boston Museum of Science on Friday, looking at the full-size Tyrannosaurus rex model with his 5-year-old son, Teddy, when he saw an e-mail about Omicron. He quickly brought his son home so he could head to the lab.

“He said, ‘Daddy, why do we have to leave the museum?’” Ventura recalled. “I said, ‘Well, I have to go be with the viruses.’”

Although everyone wants to know whether existing vaccines protect against Omicron, Barouch said that even when researchers across the globe begin to report initial results of studies, it will take time to confirm the findings.

“In the next days to weeks, data will just pour out from hundreds of labs around the world,” he said. “Even when the first pieces of data come out, they’re not definitive until they’ve been reproduced by many people.”

k a rl h e nn i ng:
Even in Mass. the unvaccinated remain "a significant minority."

‘Not good at all’: Spike in Massachusetts COVID-19 infections show pandemic isn’t over, experts say

By Sahar Fatima and Felice J. Freyer Globe Staff, Updated December 2, 2021, 11:18 a.m.

Massachusetts reported the highest number of COVID-19 infections and hospitalization rates in months on Wednesday, and specialists say it’s a grim reminder that the pandemic is far from over.

“It’s a reminder that COVID is far from gone,” said Dr. Paul Edward Sax, clinical director of the infectious disease clinic at Brigham and Women’s Hospital. “People who are unvaccinated [a significant minority] and people with underlying immune deficits remain at significant risk.”

He said some of the positive cases involve unvaccinated children, who have a much lower immunization rate than adults.

“We’ve been watching the case numbers and the hospitalizations closely, and this very closely parallels what we saw last year,” Sax said.

The Thanksgiving holiday likely contributed to the increase, Dr. David Hamer, a Boston University professor of global health and medicine, said Wednesday. “We saw this last year ... After each holiday there was an increase in cases.”

On Wednesday, the seven-day proportion of COVID tests that returned positive was 5.14 percent, a level not seen since last January.

“This is not good at all,” said William Hanage, associate professor of epidemiology and codirector of the Center for Communicable Disease Dynamics at the Harvard T.H. Chan School of Public Health. “The positivity rate should be driven down by Thanksgiving testing, because low-risk people are getting tests to fly.”

He said the increase in cases, amplified by the holiday, may not be overly worrying given Massachusetts’ high vaccination rates. As of Wednesday, 70.7 percent of the population was fully vaccinated.

“However, the potential for transmission of Omicron should be a concern,” Hanage said. On Wednesday, the United States reported its first case of the new strain of the virus in a California resident who had traveled back from South Africa on Nov. 22. Another case was announced in Minnesota on Thursday in a vaccinated man who had recently traveled to New York City for an anime convention.

Scientists around the world are racing to understand whether the mutated version of the coronavirus is more dangerous and spreads more quickly.

Reactions to Massachusetts’ high numbers on Wednesday poured in online.

Some people said they’d seen anecdotal evidence of a spike in cases in their own social circle.

Before the state released the latest numbers, the city of Chelsea instated an indoor mask mandate on Wednesday. The order goes into effect on Friday and will apply to all public spaces within private businesses as well as inside public buildings.

Pohjolas Daughter:
Sadly, I'm not surprised to see a rise in a number of cases in the US post-Thanksgiving.

I just ran across this article on the BBC's website which was heartbreaking to read.  Due to a lack of volunteers at a pharmacy, about 1,000 people had to be turned away from receiving their shots.  This was in ONE day:

https://www.bbc.com/news/uk-england-cambridgeshire-59510206

Not certain if they were all booster shots or a mixture.

PD

k a rl h e nn i ng:
Most coronavirus vaccines work as boosters, with higher antibody levels from Pfizer and Moderna, study finds

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