POST 125. June 9, 2021. CORONAVIRUS. “States are rolling back Covid-19 restrictions as new cases trend down from record highs across the country. But experts warn it might be too much too soon as variants pose an increased risk and the pandemic… is far from over.”

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“Experts who have spent the last year forecasting Covid-19 transmission across the US are now considering scenarios for the spread of new, more infectious strains of the coronavirus.

At the same time, the US continues to lag in surveillance for coronavirus variants, despite having among the most well-developed genomic sequencing infrastructure in the world.

The warnings come as the US appears to have crested a devastating winter wave of infections, which at one time saw more than 300,000 new infections and 4,000 deaths a day. Even though daily infections have more than halved from the peak, with death rates expected to drop soon also, the threat of the more infectious variants has some considering the possibility of a fresh surge.

“It’s a grim projection, unfortunately,” said Ali Mokdad, professor at the Institute for Health Metrics and Evaluation (IHME) at the University of Washington, one of the leading academic forecasters of Covid-19. “I’m concerned about a spike due to the new variant and the relaxation of social distancing,” he said. “People are tired. People are very tired.”

Forecasters still do not consider this the most likely scenario, nor do they see it as the worst-case scenario. But the addition of the model is a recognition of how dangerous new variants can be, even in an environment where hospitalization and death rates are expected to decline.” (A)

“Since May 2020, Jeffrey Milbrandt has had his systems fine-tuned to sequence 1000 coronavirus samples a week. The director of a major sequencing center at Washington University in St. Louis (WashU), Milbrandt knew months ago that the United States urgently needed  to identify and track emerging variants of SARS-CoV-2, the pandemic coronavirus already spreading across the nation.

But to date, fewer than 100 coronavirus samples have made it to his sequencers at the McDonnell Genome Institute, and the United States remains nearly blind to several coronavirus strains that have recently upended the course of the pandemic. “We have it all worked out but there’s not a lot of takers,” Milbrandt says of his center’s sequencing abilities. “We are getting more inquiries from the press than from people who need the information. … Some of us have pipelines available—they are just not being utilized.”

The Centers for Disease Control and Prevention (CDC) plans to rapidly change that by coordinating a national surveillance system for coronavirus variants. Scientists and public health experts welcome the plan.

“The hardware is set up, the people are trained, the infrastructure is in place,” says genome scientist Chris Mason of Weill Cornell Medicine. “It’s just a big question: Who’s gonna pay for it?”…

CDC has also begun to require that state and local public health labs submit, collectively, 750 sequences each week, Walensky noted in late January. But such labs have been both underfunded and swamped during the pandemic. At the Utah Public Health Laboratory—one of the most sophisticated and best equipped of the state labs—a shortage of pipette tips drove sequencing rates down from 600 per week in mid-January to 100 last week, says Kelly Oakeson, the lab’s chief sequencing scientist.

Other scientists say CDC’s goal is too low. “Seven hundred and fifty surveillance strains a week is nothing,” says Lea Starita, a genome scientist at the University of Washington, Seattle, and the Seattle Flu Study. Combined with the 6000 viral genomes CDC expects to receive weekly from the companies, that would allow sequencing of just 0.9% of the current weekly average of nearly 800,000 COVID-19 cases.”  (B)

“The coronavirus variant first detected in the United Kingdom is rapidly becoming the dominant strain in several countries and is doubling every 10 days in the United States, according to new data…

The researchers also found that the transmission rate in the United States of the variant, labeled B.1.1.7, is 30% to 40% higher than that of more common lineages.

The findings lend credence to modelling predictions the CDC released in January. The agency said at the time that the new strain could cause more than half of new infections in this country by March, even as the U.S. races to deploy vaccines.

In the new study, while clinical outcomes initially were thought to be similar to those of other coronavirus variants, early reports suggest that infection with the B.1.1.7 variant may increase death risk by about 30%.

A coauthor of the current work, Kristian Andersen, told The New York Times, “Nothing in this paper is surprising, but people need to see it.”

Andersen, a virologist at the Scripps Research Institute in La Jolla, CA, said, “We should probably prepare for this being the predominant lineage in most places in the United States by March.”

“Our study shows that the US is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality,” the researchers write.

The authors point out that the B.1.1.7 variant became the dominant SARS-CoV-2 strain in the United Kingdom within a couple of months of its detection.

“Since then, the variant has been increasingly observed across many European countries, including Portugal and Ireland, which, like the UK, observed devastating waves of COVID-19 after B.1.1.7 became dominant,” the authors write.

The B.1.1.7 variant has likely been spreading between US states since at least December 2020, they write…

“Because laboratories in the US are only sequencing a small subset of SARS-CoV-2 samples, the true sequence diversity of SARS-CoV-2 in this country is still unknown,” they note.

Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, said the U.S. is facing a “Category 5” storm with the spread of the B.1.1.7 variant as well as the variants first identified in South Africa and Brazil.

“We are going to see something like we have not seen yet in this country,” Osterholm said recently on NBC’s Meet the Press.” (C)

“TWO new COVID-19 variants, one of which has been classified as a “concern”, have been identified in England with some similarities to the South African and Brazilian variants, a government advisory scientific committee said on Tuesday.

One of the new variants, first identified in Bristol, has been designated a “Variant of Concern”, by the New and Emerging Respiratory Virus Threats Advisory Group.

The other, first identified in Liverpool, has been designated as a “Variant under Investigation” by the group.” (D)

“South Africa has put its rollout of the Oxford-AstraZeneca vaccine on hold after a study showed “disappointing” results against its new Covid variant.

Scientists say the variant accounts for 90% of new Covid cases in South Africa.

The trial, involving some 2,000 people, found that the vaccine offered “minimal protection” against mild and moderate cases.

But experts are hopeful that the vaccine will still be effective at preventing severe cases.

South Africa has recorded almost 1.5 million coronavirus cases and more than 46,000 deaths since the pandemic began – a higher toll than any other country on the continent.

The country has received one million doses of the Oxford-AstraZeneca jab and was preparing to start vaccinating people.

Dr Katherine O’Brien, the WHO’s director of immunisation, said it was very plausible that the Oxford-AstraZeneca vaccine would still have a meaningful impact on the South African variant, especially when it came to preventing hospitalisations and death.” (E)

“The coronavirus variant that emerged from the United Kingdom is spreading quicker in Florida than in any other state.

Florida currently has 201 recorded cases Monday, with that number expected to rise, so we looked at how that moves our herd immunity goal posts.

“Cases have continued to decline over the last four weeks,” said Dr. Rochelle Walensky publicly, the new director of the CDC under the Biden administration. “New COVID-19 hospitalizations continue to decline.”

“Florida’s growing pretty significantly right now,” said Dr. Scott Gotlieb during an interview on Face The Nation, the former FDA commissioner. “Between [5%] and 10% of the infections in Florida, B.1.1.7, that UK variant, the more contagious variant and that’s centered in Southern Florida.”

Florida has more cases of the UK variant than anywhere else in the United States at this time, and research finds these cases can double in about a week, spilling out beyond our borders sooner rather than later.

“The projection is that the 117 lineage will likely become dominant in the United States by the end of March,” Dr. Anthony Fauci said.

That’s only in reference to the UK variant.

Epidemiologist Dr. Stanley Weiss, a professor at Rutgers School of Public Health, says there’s already community spread of the South African and the Brazilian variants.

“Unless you have virtually everyone in the population get the vaccine or have gotten infected already, you’re not going to get to herd immunity,” Weiss told WINK News. “A survey last week said that still 24% of us adults didn’t want to get the vaccine. Well, if they don’t, we can’t reach herd immunity. We might have been close before we had this UK variant.” (F)

“A lab study has found the vaccine effective against UK and South Africa variants. German Health Minister Jens Spahn has voiced his confidence in the EU’s three approved vaccines.

The peer review has confirmed that the BioNTech-Pfizer vaccine is effective against two variants of the coronavirus, the companies announced on Monday.

The review, which was published in the journal Nature Medicine, backed the results of a study completed by Pfizer and the University of Texas in late January.

When the study was originally released, BioNTech and Pfizer said its finding suggested that no new vaccine would be necessary to fight coronavirus mutations first discovered in the United Kingdom and South Africa.

Nevertheless, the continuous transformation of the deadly virus makes clinical data and constant observation imperative. Experts say that it is not a foregone conclusion that vaccines currently in use will remain effective against possible new variants of the virus in the future.” (G)

“Researchers in the United States have conducted a study showing that the Moderna mRNA-1273 vaccine effectively protects against recently emerged variants of severe acute respiratory syndrome coronavirus 2 – the agent that causes coronavirus disease 2019 (COVID-19).

The team compared the neutralization activity of blood taken from infected and vaccinated individuals against a panel of SARS-CoV-2 variants, including the B.1.1.7 that emerged in the UK.

The team – from Emory University School of Medicine in Atlanta, the University of Texas Medical Branch, and the COVID-19 Neutralization Study Group – found that antibodies generated by both infected and vaccinated individuals effectively neutralized all of the variants.

“These findings support the notion that in the context of the UK variant, vaccine-induced immunity can provide protection against COVID-19,” says Mehul Suthar and colleagues.

However, as further variants continue to emerge, it will be essential to assess their impact on the potency of neutralizing responses following both infection and vaccination, warns the team.” (H)

“States are rolling back Covid-19 restrictions as new cases trend down from record highs across the country. But experts warn it might be too much too soon as variants pose an increased risk and the pandemic — almost at the one year mark in the U.S. — is far from over.

In Iowa, Gov. Kim Reynolds, a Republican, lifted the state’s partial mask mandate on Friday. She also said businesses no longer have to limit the number of customers or enforce social distancing, and no limits remain on the size of public gatherings. The Des Moines Register’s editorial board called the move “inexplicable and irresponsible.”

Reynolds isn’t acting alone. Democratic and Republican governors alike have been loosening restrictions. In New York, Gov. Andrew Cuomo, a Democrat, announced Monday that New York City will allow indoor dining beginning on Friday, a few days earlier than originally planned, and middle schools will reopen for in-person instruction on Feb 25. In Massachusetts, Gov. Charlie Baker, a Republican, said restaurants are allowed to operate at 40 percent capacity as of Monday, citing a decline in hospitalizations as part of his reasoning…

“I have some concern it’s premature” to loosen restrictions, said Dr. Justin Lessler, an infectious disease epidemiologist at the Johns Hopkins Bloomberg School of Public Health.

Lessler said the very restrictions in place are what is allowing Covid-19 infection rates to decline.

“When we remove interventions, we frequently see resurgences,” he said, advising caution if states want to see continued decline. “When new variants come along, the stepping back that may have been OK before is not OK anymore because of the more transmissible variants.””  (I)

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