POST 131. February 17, 2021. CORONAVIRUS. “It really is right now – a race between how quickly new variants, particularly the U.K. variant, can spread in the United States and how quickly we can get people vaccinated”

New coronavirus variants are throwing yet another wrench at the idea of reaching herd immunity.

As the virus spread across the world, infecting over 100 million people, it had the opportunity to mutate. Not every change was important, but now, several variants are circulating that pose additional challenges to controlling the pandemic.

Three variants in particular have sparked concerns: one first found in the U.K., one discovered in South Africa and another that appeared in travelers from Brazil. The variants are referred to as B.1.1.7, B.1.351 and P.1, respectively.

The first variant has shown signs of being more transmissible and possibly more deadly than the original strain. The Centers for Disease Control and Prevention has said it could become the main strain spreading in the U.S. in March.

Preliminary data shows the second variant, B.1.351, has reduced vaccine efficacy in small studies and reinfected trial participants in South Africa who previously had the coronavirus.

Like B.1.351, the third variant has also sparked concerns about reinfections after the Brazilian city of Manaus saw a recent surge in the virus despite beliefs that three-fourths of the population was previously infected.

The data suggests that neither previous infection nor vaccination grants a free pass from getting the virus in the future. The developments don’t change the long-standing strategies for controlling the pandemic, experts say. They do, however, make things more complicated at a time when the public is growing tired of uncertainty.

It also muddles the elusive goal of reaching herd immunity – the idea that a certain percentage of the population needs to be protected from the virus through either vaccines or previous infections so that it can no longer spread effectively – anytime soon.

“It’s very hard for us to say it, but we don’t see it in any near future,” Ali Mokdad, a professor of health metrics sciences at the University of Washington, says of reaching herd immunity.

Mokdad says that he has discussed with other public health professionals the possibility that the virus will stick around in a way that is similar to the flu season. He says it is “the conclusion we are going towards, unfortunately.”

“It will be with us for a long time, and every year we have to get a new vaccine” to stay ahead of the variants that are circulating, Mokdad says….” (A)

“The spread of highly contagious coronavirus variants is accelerating in Europe, outpacing an already-slow vaccine rollout and forcing governments to extend and possibly tighten restrictions on civil society and businesses to prevent a new surge in infections before the end of the region’s winter.

A shortage of vaccines in the European Union—only 4.8% of Europeans have been vaccinated since late December—means the continent hasn’t even started the race against virus mutations that many experts say will define health policy in coming months and years…

The three variants now circulating in Europe are believed to be more easily transmitted, and potentially more dangerous, than the original pathogen that still makes up the majority of cases in Europe. There is also mounting evidence that some strains might be less susceptible to the vaccines currently authorized in the region, according to the European Center for Disease Prevention and Control.

The variant first identified in Britain accounted for 96% of viral samples examined at three major laboratories in England by early February, compared with just over a third at the beginning of December, according to the U.K. government.” (B)

“Covid hospitalization rates are falling nationwide, but experts talk in dire terms about what will happen if variants of the virus are allowed to surge this spring.

“I’m very worried we’re letting our foot off the brakes,” said Atul Gawande, a surgeon at Brigham and Women’s Hospital and a professor at the Harvard T.H. Chan School of Public Health.

The U.S. saw a spike in cases last spring, mainly in the Northeast, last summer in the South, and November through January pretty much everywhere. As the nation’s death toll from COVID-19 approaches half a million people, public health experts said they dread the possibility of a fourth wave.

“We are done with it, but it is not done with us,” added Dr. Luciana Borio, former acting chief scientist of the Food and Drug Administration.

Three state legislatures lifted mask mandates in recent days, and New York and Massachusetts eased restrictions on restaurant seating in time for Valentine’s Day.

“It’s like we’re trying our best to help the virus rather than stopping it,” said Theodora Hatziioannou, a virologist and research associate professor at the Rockefeller University in New York City.

More contagious variants of the virus have raced across Europe, South Africa and Latin America. They have all arrived in the U.S., and one first identified in the United Kingdom is likely to be dominant here by the end of next month, according to the U.S. Centers for Disease Control and Prevention.

Dr. Peter Hotez, dean for the National School of Tropical Medicine at Baylor College of Medicine in Houston, said that if the infectiousness and case fatality rate for the variant known as B.1.1.7, turns out to be the same in the U.S. as it is in the U.K., “I worry we could reach a staggering death toll by the summer and fall.”

Another variant, which originated in Southern California, has been spreading rapidly across the U.S., according to a study, although it’s not clear whether it’s more contagious or more dangerous. Many more may be here, too, according to one early review, though again, the significance of all these variants isn’t clear.

The two vaccines available, one by Pfizer-BioNTech and the other by Moderna, appear to be effective against these variants, said Hatziioannou, who published a study on the subject.

But these variants are likely to make targeted drugs such as monoclonal antibodies less effective. They will continue to change and eventually will evade vaccines and diagnostic tests if they keep spreading, she said.

Now is the time, she and others said, to double-down on precautions, to avoid a deadly fourth wave and finally bring the virus under control.

“The best way to mitigate the threat of the strains is to control the virus,” Borio said. And the best way to control the virus is through the public health tools we have,” like mask-wearing, hand-washing, avoiding crowds, and vaccination…

A fourth wave would be far less likely, he said, if people get vaccinated when they become eligible and carefully follow public health measures such as mask-wearing and avoiding crowds” (C)

“Two variants of the SARS-CoV-2 coronavirus that causes covid-19 have combined their genomes to form a heavily mutated hybrid version of the virus. The “recombination” event was discovered in a virus sample in California, provoking warnings that we may be poised to enter a new phase of the pandemic.

The hybrid virus is the result of recombination of the highly transmissible B.1.1.7 variant discovered in the UK and the B.1.429 variant that originated in California and which may be responsible for a recent wave of cases in Los Angeles because it carries a mutation making it resistant to some antibodies.

The recombinant was discovered by Bette Korber at the Los Alamos National Laboratory in New Mexico, who told a meeting organised by the New York Academy of Sciences on 2 February that she had seen “pretty clear” evidence of it in her database of US viral genomes.

If confirmed, the recombinant would be the first to be detected in this pandemic. In December and January, two research groups independently reported that they hadn’t seen any evidence of recombination, even though it has long been expected as it is common in coronaviruses.

Unlike regular mutation, where changes accumulate one at a time, which is how variants such as B.1.1.7 arose, recombination can bring together multiple mutations in one go. Most of the time, these don’t confer any advantage to the virus, but occasionally they do.

Recombination can be of major evolutionary importance, according to François Balloux at University College London. It is considered by many to be how SARS-CoV-2 originated.

Recombination could lead to the emergence of new and even more dangerous variants, although it isn’t yet clear how much of a threat this first recombination event might pose.

Korber has only seen a single recombinant genome among thousands of sequences and it isn’t clear whether the virus is being transmitted from person to person or is just a one-off.” (D)

“The Centers for Disease Control and Prevention is in discussions with at least 13 labs to expand its efforts to sequence the genomes of coronavirus samples as the U.S. races against time to track new variants.

More than 40 states have reported cases of the three major coronavirus strains, first spotted overseas; all are more contagious than older versions of the virus, and at least one is more virulent. By sequencing genetic material from virus samples collected around the country, health officials can track where and how these strains are spreading — and use the information to help contain hotspots and guide vaccination efforts.

So far, though, the federal effort is lagging. CDC expects to increase the number of coronavirus samples analyzed each week by the agency and its partners from more than 4,500 now to 7,000 by the end of February. But that would still be less than one percent of all positive samples identified through testing nationwide. It’s also well below the 5 to 10 percent that public health experts say is needed…

Information gleaned from sequencing is crucial for policymakers trying to figure out whether to relax coronavirus precautions, such as limits on indoor dining and gyms or school closures. The United States’ limited sequencing capacity hearkens back to the first months of the pandemic when diagnostic testing was limited, making it hard for health officials to track where the virus was spreading and take appropriate action. With more contagious variants spreading, those same officials need sequencing data to understand how to modify their pandemic playbook.

“A lot of people are getting a little whiplash going in and out of social distancing, we see that people are getting fatigued of it,” said Phil Febbo, chief medical officer of Illumina, one of the companies contributing to the federal sequencing program. “The more that public health officials, governors, mayors have the best information about the variants and the impact on their communities, the less likely they’re going to have to over rotate one way or the other. And they can set appropriate expectations as we try to move toward ending the pandemic.”.. (E)

“As Americans anxiously watch the spread of coronavirus variants that were first identified in Britain and South Africa, scientists are finding a number of new variants that seem to have originated in the United States — and many of them may pose the same kind of extra-contagious threat.

In a study posted on Sunday, a team of researchers reported seven growing lineages of the coronavirus, spotted in states across the country. All have gained a mutation at the exact same spot in their genes…

It’s not unusual for different genetic lineages to independently evolve in the same direction. Charles Darwin recognized convergent evolution in animals. Virologists have found that it happens with viruses, too. As the coronavirus branches into new variants, researchers are observing Darwin’s theory of evolution in action every day.

It’s difficult to answer even basic questions about how prevalent the new variants are in the United States because the country sequences genomes from less than 1 percent of coronavirus test samples. The researchers found examples scattered across much of the country, but they can’t tell where they first arose.

It’s also hard to say whether the variants are spreading now because they are more contagious, or for some other reason, like holiday travel or superspreader events.

Scientists say the mutation could plausibly affect how easily the virus gets into human cells. But Jason McLellan, a structural biologist at the University of Texas at Austin who was not involved in the study, cautioned that the way that the coronavirus unleashes its harpoons was still fairly mysterious.

“It’s tough to know what these substitutions are doing,” he said of the mutations. “It really needs to be followed up with some additional experimental data.”” (F)

“British government scientists are increasingly finding the coronavirus variant first detected in Britain to be linked to a higher risk of death than other versions of the virus, a devastating trend that highlights the serious risks and considerable uncertainties of this new phase of the pandemic.

The scientists said last month that there was a “realistic possibility” that the variant was not only more contagious than others, but also more lethal. Now, they say in a new document that it is “likely” that the variant is linked to an increased risk of hospitalization and death…

The reasons for an elevated death rate are not entirely clear. Some evidence suggests that people infected with the variant may have higher viral loads, a feature that could not only make the virus more contagious but also potentially undermine the effectiveness of certain treatments.

But scientists are also trying to understand how much of the increased risk of death may stem from the propensity of the variant to spread very easily through settings like nursing homes, where people are already vulnerable.

No matter the explanation, scientific advisers to the British government said on Saturday, the new findings laid bare the dangers of countries easing restrictions as the variant takes hold.” (G)

“As lawmakers push for billions of dollars to fund the nation’s efforts to track coronavirus variants, the Biden administration announced on Wednesday a new effort to ramp up this work, pledging nearly $200 million to better identify the emerging threats.

Calling it a “down payment,” the White House said that the investment would result in a significant increase in the number of positive virus samples that labs could sequence. Public health laboratories, universities and programs run by the Centers for Disease Control and Prevention sequenced more than 9,000 genomes last week, according to the database GISAID. The agency hopes to increase its own contribution to 25,000 genomes a week.

“When we will get to 25,000 depends on the resources that we have at our fingertips and how quickly we can mobilize our partners,” Dr. Rochelle Walensky, the C.D.C. director, said at a White House news conference on Wednesday. “I don’t think this is going to be a light switch. I think it’s going to be a dial.”

The program is the administration’s most significant effort to date to address the looming danger of more contagious variants of the virus. A concerning variant first identified in Britain has infected at least 1,277 people in 42 states, although scientists suspect the true number is vastly higher.

Doubling about every 10 days, the B.1.1.7 variant that emerged in Britain threatens to slow or reverse the rapid drop of new coronavirus cases. From a peak of almost 260,000 new cases a day, the seven-day average daily rate has fallen to below 82,000, still well above the high point of last summer’s surge, according to a New York Times database.

What’s more, Dr. Walensky said that the nation had seen its first case of B.1.1.7 that had gained a particularly worrying mutation that has been shown in South Africa to blunt the effectiveness of vaccines.

Other worrisome variants have also cropped up in the United States, including one that was first found in South Africa and weakens vaccines.

The F.D.A. is preparing for a potential redesign of vaccines to better protect against the new variants, but those efforts will take months. In the short term, experts say, it is critical to increase sequencing efforts, which are too small and uncoordinated to adequately track where variants are spreading, and how quickly.” (H)

“Though coronavirus vaccinations continue and the state’s number of cases and hospitalizations improve, Gov. Phil Murphy said plans to further lift safety restrictions in New Jersey are being held up by uncertainty over how more contagious variants of COVID-19 of will affect the state.

“But for the variant, I think we would be planning right now a much more … fulsome series of steps to reopen over the next few weeks,” Murphy said during his latest coronavirus briefing in Trenton. “The variants sort of hang over our head.”

“If we continue to see especially hospitalizations continue to drop, there’s no question we’ll take more steps to open up,” Murphy said. “But I think we will be more cautious than we otherwise would have been absent the variants.”

State officials so far have identified only one variant in New Jersey — the B.1.1.7 strain discovered in the United Kingdom — though at least seven new coronavirus variants have been found in the United States recently. New Jersey has seen 50 cases of the U.K. variant as of Wednesday, state Health Commissioner Judith Persichilli said.

But Murphy said “the assumption” is that other variants are “already in the state.”

Health officials say it’s common for viruses to mutate and vaccinations appear to be effective against the U.K. coronavirus variant.

Still, the variant is between 30% and 70% more transmissible than the typical COVID-19 strain and could become the dominant strain in the U.S. by March, according to the federal Centers for Disease Control…

Dr. Eddy Bresnitz, a coronavirus consultant to the state Department of Health, said officials are “not really seeing that the vaccine is less effective” against the variant.

But Bresnitz noted the difficulty is “making policy decisions when you don’t really know what’s coming.” (I)


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