New 'Super COVID' Strains Could Upend Life Again in the US

Brenda Goodman, MA

January 06, 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 here, though it doesn't seem to be more fatal for any one person who catches it. 

While that may seem reassuring, it is potentially 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, adds that 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, and 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 5 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.

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 additional 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 overcrowded 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, a professor of epidemiology at Harvard' TH 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," Lipsitch said.

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 escalating 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 lockdown 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 seek health care or go 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. 

One of the new super strains — the so-called U.K. variant -- has been detected in 6 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 1 in 200 COVID cases in the U.S. are currently caused by mutated strains. 

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. 

The CDC plans to double the number of coronavirus genomes being sequenced to look for new COVID-19 mutations in the U.S. over the next 2 weeks, according to CNN.

The U.S. is doing genome sequencing tests on 3,000 samples per week, and the CDC hopes to increase that to about 6,500 samples per week.

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

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 so-called "s-gene dropouts" can happen with many different versions of the virus that are circulating, not just the super strains. Labs then have to follow up with an additional 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 hasn't found any cases out of 250 positive cases they screened last week, said Alex Greninger, MD, PhD, assistant director of the clinical virology laboratories at the University of Washington Medical Center.

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 confers 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 for mutations to develop, and it is adapting to become better at infecting people.

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 dominate story of the UK variant right now, as it stands, is adaptation to humans," he said.

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

The spike proteins on the virus rotate between 'open' and 'closed' positions. They can only attach to doors on our cells called ACE2 receptors 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 proven in an experiment. His research has been published in a preprint article that has not yet been peer reviewed.

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 U.K. has decided to close schools and I think we might find ourselves there in not too long," he said.


Adam Kucharski, PhD, an associate professor, department of infectious disease epidemiology, at the London School of Hygiene and Tropical Medicine, in London, UK

Ashish Jha, MD, dean, School of Public Health, Brown University, in Providence, RI

Scott Gottlieb, MD, "Face the Nation," January 3, 2021

Marc Lipsitch, PhD, professor of epidemiology, TH Chan School of Public Health, Harvard University, DeCambridge, MA

Alex Greninger, MD, PhD, assistant director of the clinical virology laboratories at the University of Washington Medical Center, Seattle, WA

Rafael Najmanovich, PhD, a professor of systems and structural biology at the University of Montreal in Canada

Greg Armstrong, MD, director of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, Atlanta, GA

Report 42, MRC Center for Infectious Disease Analysis, Imperial College London, Dec. 31, 2020

Press release, Illumina, Jan. 5, 2020

CNN: "CDC hopes to double the number of coronavirus samples checked for new mutations."