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New COVID ‘Super Strains’ Could Disrupt Life Again

Jan. 6, 2021 — After 10 months of masks, social distancing, virtual school, fear for vulnerable loved ones, and loneliness, this is the news no one wanted to hear: The virus that causes COVID-19 has changed — once again — in ways that make it more contagious.

At least one new “super strain” of the virus is already in the U.S. Another highly contagious strain from South Africa could be on its way. As bad as things are now, experts believe these new strains are not responsible for the spike in cases seen in many states as people fall ill after holiday travel.

The strains are about 50% more contagious than the virus that has been most widely circulating in the United States, though it doesn’t seem to be more fatal for any one person who catches it.

The danger of the new Covid variant isn’t that it’s more severe, but that it’s more contagious. If more people get infected, this will increase the burden on already-overwhelmed hospitals—and lead to more deaths.

— Dr. Tom Frieden (@DrTomFrieden) January 5, 2021

While that may seem reassuring, it could be disastrous on a wider scale. One public health expert believes the virus is changing itself to adapt and infect more people.

Another, Adam Kucharski, PhD, an associate professor at the London School of Hygiene and Tropical Medicine who specializes in the math of infectious disease outbreaks, says the math shows the infectious strain will be more deadly.

Kucharski recently compared how many people would die after 10,000 new infections over the course of a month. With the current situation, with a virus that sees each patient infect an average of 1.1 others and kills .08% of everyone it infects, you’d predict 129 deaths over a month of spread. With a virus that’s 50% more deadly, you would expect to see about 193 deaths over a month of spread. With a virus that’s 50% more contagious, you end up with 978 more deaths over a month of spread — or five times as many deaths.

This means that unless the U.S. adjusts its response to the pandemic, and adjusts quickly, hospitalizations and deaths could reach terrifying peaks in this country over the next few weeks as the variant strains cause a new wave of infections here.

More Infections, More Deaths

Ashish Jha, MD, dean of the Brown School of Public Health, projected on Tuesday that as the new strains take hold in the U.S., they could cause an additional 10 million new infections by the end of February and as many as 150,000 more deaths.

“Without aggressive action to limit the spread of the virus, bolster health care systems around the country, and accelerate vaccine administration, Los Angeles offers a preview of what many communities are likely to experience over the coming months,” he said in a news release.

Hospitals in Los Angeles are severely constrained. On Monday, Los Angeles EMS crews were told to conserve oxygen, because of a shortage of portable oxygen tanks, and not to transport some patients to crowded hospitals if they could not restore their pulse.

Former FDA Commissioner Scott Gottlieb, MD, predicted Sunday on Face the Nation that the new strain would be responsible for the majority of new infections in this country by March.

“It’s a big deal for a world that’s already stretched trying to keep in control the old variant,” said Marc Lipsitch, PhD, a professor of epidemiology at Harvard’s T.H. Chan School of Public Health in a call with reporters on Tuesday.

“If we don’t change our control measures, once it becomes common, it will accelerate transmission considerably,” he said.

Tracing, Testing, Vaccinating

Lipsitch believes contact tracing efforts in the U.S. — which have been overwhelmed in many places by community spread of the virus — should pivot to focus just on breaking the chains of transmission caused by the new variants.

News of the variants has come as the administration of new vaccines has lagged in the U.S., further raising the worry that these strains will get a foothold before people can be protected against them.

Already, one new “super strain” of the virus is driving an alarming surge of COVID cases in Great Britain. On Monday, Prime Minister Boris Johnson — who had resisted tougher control measures for weeks — reluctantly ordered strict new lockdown measures in that country, following close behind similar moves in Scotland, Wales, and Northern Ireland.

Defending his actions against the economic harm they would cause, he said he had no choice but to lock down again as new cases threatened to overwhelm hospitals.

Once again, most children will stay home for school, and people have been asked not to leave home except to do a very limited number of essential tasks, like seeking health care or going grocery shopping.

A new report from Imperial College London found that a greater proportion of children were infected with the new strain, compared to the older version of the virus. It’s not clear yet if its mutations make it better at infecting children, or if younger people were just more likely to be exposed to it because kids have continued to go to school there, even as many adults have stayed home.

Seven States and Countng

One of the new super strains — the so-called U.K. variant — has been detected in six U.S. states, according to the CDC: Colorado, California, Georgia, New York, Florida, and Pennsylvania. One other state is still looking into cases and hasn’t made an announcement, according to Greg Armstrong, MD, director of advanced molecular detection at the CDC’s National Center for Emerging and Zoonotic Infectious Diseases. Armstrong thinks fewer than one in 200 COVID-19 cases in the U.S. are currently caused by mutated UK strain, but there’s some uncertainty around that number because the U.S. has done a limited number of gene tests on samples of the SARS-CoV2 virus.

His estimates are based on results from commercial testing companies Illumina and Helix, which have partnered with the CDC to look for the variant as they process COVID tests. Helix screened more than 2 million COVID tests for signs of the variant. They forwarded 158 samples to Illumina for further testing. Of those, 51 were positive for the UK variant. According to the companies, as of Jan. 6, 54 cases of the UK variant had been identified in the U.S.

Going forward, the plan is for Illumina to sequence the genomes of 1,000 samples per week to look for the UK variant and others.

Many people infected with the new variant have no history of travel, which suggests it is already being passed person-to-person in some areas.

Surging Before Variant

Still, experts believe this variant is not the main reason for the surges of cases in the U.S. The South African variant has not yet been detected in the U.S., though it has been in the U.K.

Commercial labs doing PCR testing for the virus are looking for cases where one of the three probes — or markers — they use to detect proteins in the spike of the virus is negative while the other two probes are positive.

These “s-gene dropouts” can happen with many versions of the virus that are circulating, not just the super strains. Labs then have to follow up with a test that reads all the genes in the virus to look for the signature mutations in the super strains.

The University of Washington is actively doing this genome sequencing to look for the U.K. strain, but it hasn’t found any cases out of 250 positive cases it screened last week, says Alex Greninger, MD, PhD, assistant director of the clinical virology laboratories at the University of Washington Medical Center.

Not All Mutations Are the Same

Viruses mutate all the time. Mutations are errors a virus makes when it copies itself. Coronaviruses mutate more slowly than most others because they have a built-in proofreading mechanism that corrects these errors.

But they can still change in ways that the proofreader doesn’t catch or fix.

Most of the time, these changes don’t make them more harmful. But sometimes a mutation makes for a competitive advantage, something that allows that version to outperform the viruses around it.

Because the new coronavirus has infected so many millions of people around the world, it has had more opportunity to mutate, and it is adapting to become better at infecting people.

“beast mode COVID” a most appropriate title for the variant that could render public health recommendations substantially futile during the winter months and turn the Pandemic into a race between Beast mode COVID and vaccination success.

— Paul A Sobotka, MD, FACC, FAHA (@sobotka_paul) January 5, 2021

Both the U.K. super strain and the super strain found in South Africa have the same mutation on their spike protein — called N501Y. But each strain developed the mutation independently. When you see things like that, Greninger says, it probably didn’t happen by chance. The virus is evolving in ways that make it better at infecting humans.

“To me, the dominant story of the U.K. variant right now, as it stands, is adaptation to humans,” he says.

The mutations on the viruses’ spike protein work together to make the virus more infectious, according to recent research by Rafael Najmanovich, PhD, a professor of systems and structural biology at the University of Montreal.

The spike proteins on the virus rotate between “open” and “closed” positions. They can attach to doors on our cells called ACE2 receptors only when they are in their open positions.

Najmanovich’s modeling shows new gene changes allow the spike proteins to stay open about 40% longer than the older versions of the virus, which means that each individual particle of virus is more likely to be able to infect our cells when we come into contact with it.

In theory, that means fewer copies of the virus — a smaller dose — is needed to make a person sick, though Najmanovich says this still needs to be proved in an experiment. His research has been published in a preprint article that has not yet been peer-reviewed.

Lockdowns, Restrictions Possible

Because the virus is becoming more potent, we will need stricter measures to control its spread.

In recent days, some public health experts, like former CDC Director Tom Frieden, MD, who now leads the nonprofit Resolve to Save Lives, said it might be a good idea for people to wear more protective masks — like surgical masks or N95 respirators, though these still may be in short supply across the country.

Lipsitch, at Harvard, said given the more contagious nature of the new variants, it’s more important than ever to stay home as much as possible, limit contact with those outside your household, and, he said, cut daily contacts by at least a third to slow the pace of new infections and once again flatten the curve.

It’s still not known whether the mutations will affect how well the approved vaccines work, but experts believe that because vaccines generate a big immune response in the body that acts against the virus in different ways, the new shots will probably still work, though pharmaceutical companies are running tests now to make sure.

Still, the vaccines won’t help if they aren’t made more widely available, more quickly.

Ultimately, the new strains could send kids back to virtual learning, just as schools in many areas were getting ready to reopen.

“If we’re not going to close other kinds of activities, we shouldn’t close schools, because schools are more important than almost anything else that we do in terms of what they produce and what they allow the rest of society to do,” Lipsitch said, but the virus many not give us a choice.

The new variants could prove to be disastrous on a wider scale. One public health expert believes the virus is changing itself to adapt and infect more people.

Another New Covid-19 Variant Discovered In L.A. Might Be Vaccine Resistant, Researcher Says; Strain First Identified In Denmark

Tom Tapp

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Two days after the Los Angeles Public Health Department announced that the much-talked-about UK variant of Covid-19, known as B.1.1.7, had been identified in the region, the California Department of Public Health revealed that another lesser-known strain had been circulating in the county as well.

Known as L452R, the newly announced arrival was first identified in Denmark in March. It showed up in California as early as May.

Dr. Charles Chiu, a virologist and professor of laboratory medicine at UCSF who, in concert with state authorities, has been genetically sequencing test samples to identify new variants said early indications are the L452R might be less susceptible to the currently approved vaccines, but more investigation is needed.

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“This variant carries three mutations, including L452R, in the spike protein, which the virus uses to attach to and enter cells, and is the target of the two vaccines that are currently available in the United States,” said Dr. Chiu. A spike protein mutation could, then, interfere with the vaccine’s efficacy.

According to the California Department of Public Health, Santa Clara County has sequenced a large number of positive specimens collected from community testing sites and outbreaks in the county. The L452R was present in specimens from the community and from several large outbreaks, including outbreaks where very high numbers of people exposed contracted the virus.

“This variant was identified in several large outbreaks in our county,” said Santa Clara County Health Officer Dr. Sara Cody. She called that correlation “a red flag and must be investigated further.”

The new variant also has been detected in Los Angeles, Mono, Monterey, Orange, Riverside, San Francisco, San Bernardino, San Diego, San Luis Obispo, Humboldt and Lake counties. Because genomic sequencing is sparse, it is currently unknown how prevalent L452 is statewide, nationally or globally.

Dr. Chiu said L452R grew from about 3.8% of the samples he tested in late November 2020 through early December to more than 25.2% in late December through early January 2021.

And there might be another issue with vaccine efficacy.

California’s State Epidemiologist Dr. Erica Pan said on Sunday that a “higher than usual” number of people had apparent allergic reactions to a batch of Moderna’s vaccine at a San Diego-area clinic.

“Out of an extreme abundance of caution,” Pan recommended that clinics should stop using doses from that specific batch until it is investigated.

California received about 330,000 doses from the lot in question. That equates to approximately 10% of all vaccine distributed to date across the state.

On Monday, the state’s numbers were mostly down, which is good. There were just over 30,000 new cases, 201 new deaths, 20,968 virus patients hospitalized and 1,113 ICU beds available. That last figure is the lowest number of ICU beds available during the pandemic, which is worrying.

There is also the potentially more contagious UK variant, B.1.1.7., on the horizon. Los Angeles Public Health officials confirmed the first case of that strain in the area over the weekend.

Though Saturday may mark the strain’s first identified appearance in Los Angeles County, health officials said in recent weeks that it was very likely already circulating in L.A. B.1.1.7 had previously made its way through San Diego and San Bernardino Counties. Before that, the strain had been found in Colorado, where it made its U.S. landfall.

The CDC warned that the presence of B.1.1.7 may mark a new phase of “exponential growth” in total Covid-19 cases.

“Current projections by the experts predict that if left unchecked, this variant could dominate locally by March,” Los Angeles Public Health director Barbara Ferrer said on Friday.

We can now add to that the threat of a potentially vaccine-resistant strain, L452R, as well.

As a result, L.A. County officials have been discussing the possibility of new restrictions for the shutdown-weary county.

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Known as L452R, the newly-announced strain was first identified in Denmark and now might account for up to 25% of the cases in California.