10 Things to Know About the New COVID Strains
Mutations from across the world (and a few homegrown U.S. variants) remind us we aren’t out of the pandemic woods yet.
Eighteen months into the pandemic—can you believe it's summer again?—and, thankfully, there is new hope in the form of vaccines. But there are also some pressing new problems. The coronavirus continues to ravage the world as mutating strains emerge, some of them more transmissable and deadly. Which means this crisis is by no means behind us.
Multiple variants of COVID-19—some from across the globe and some originating in the U.S.—are spreading rapidly and causing concern in the scientific community. Originally named for their place of origin and assigned a corresponding number, new strains are now named after Greek letters—Alpha, Beta, etc.—to make them easier to distinguish, and to avoid maligning a specific country or people, a decision made by the World Health Organization on May 31. We have a lot of questions about these variants, so we turned to two epidemiologists for answers. Here’s everything you need to know about the new strains of COVID and what makes them worth paying attention to.
1. Alpha, first documented in the UK last fall, is now the dominant strain in the U.S.
This COVID variant, called B.1.1.7 or Alpha, was first discovered by scientists through genetic sequencing—a procedure used to track how viruses change and mutate—in September 2020 in southeast England. As of April 2021, it has been found in all 50 U.S. states and has become the predominant strain in this country, as well as many other places throughout the world. Science suggests that the Alpha variant is 50% more transmissible than previous strains of COVID-19, leading to more cases and hospitalizations overall.
2. Beta emerged in South Africa around the holidays, and Gamma was found in Brazil.
On December 18, 2020, after news had come out about the UK strain, South Africa announced that it was dealing with a similar new variant of COVID-19, called B.1.351 or Beta. And, a different strain from Brazil, called P.1 or Gamma, was discovered on January 12 after having circulated in that country since at least December.
In theory, these fast-evolving viral mutations aren't all that surprising. “Viral mutations are quite common and expected,” says Saskia Popescu, Ph.D., infection prevention epidemiologist in Phoenix and member of the Federation of American Scientists COVID-19 task force. As a living organism, a virus naturally adapts and changes—just like the flu mutates each year. In fact, COVID variants have already existed for months, helping scientists track the spread of the virus across the world.
The reason these strains are garnering widespread interest is because they appear to be spreading more due to "changes on the spike protein that binds to the human respiratory cell,” explains Shira Doron, M.D., infectious disease physician and hospital epidemiologist at Tufts Medical Center in Boston. “That’s worrisome. It binds more tightly than other normal variants, suggesting that it has an easier time entering the cell.”
3. More recently, Delta, a new variant from India, has been spreading rapidly. EEK, a spike mutation, is causing concern in Japan.
B.1.617.2 (aka Delta) is a strain that has newly emerged in India during the country's spring 2021 COVID outbreak. It has been dubbed a double mutant variant, meaning it contains at least two mutations of the spike protein on the original SARS-CoV-2 virus. (It actually contains 13 mutations in total.)
As of June 9, the Delta variant has been reported in 60 countries, including the U.S. It has replaced the Alpha strain as the predominant COVID variant in the UK, and it accounts for about 6% of U.S. COVID infections. One thing that makes Delta unique is its prevalence in younger people—peak transmission occurs among those aged 12 to 20 years old. The latest research shows that vaccines do protect against the Delta variant, but one dose of an mRNA vax may not be protective enough on its own. (All the more reason to get your teens fully vaccinated ASAP.)
In Japan, the spike mutation E484K (nicknamed "EEK") raised alarm bells after it was identified in almost 70% of COVID patients in one Tokyo hospital. This is not a variant in itself, but is a mutation present in variants in Japan, the UK, South Africa, Brazil, and New York. Dubbed an “escape mutation,” it helps the virus get past our immune defenses and may potentially evade our current monoclonal antibody treatment options.
4. All of these new strains might be more deadly, but for different reasons.
Mutations of the S protein make these new COVID strains more transmissible, and the math alone tells you that more hospitalizations may very well equal an uptick of deaths, overall. A March 15 study in Nature found that the Alpha variant is associated with a 61% increased risk of death compared to previous forms of COVID, due to a combination of higher infection rates and more severe disease.
There is also evidence that both the Beta and Gamma variants, as well as the EEK spike mutation, may be more deadly because they appear not to respond well to our available treatment options. (Find out why below in question #8.)
5. There have also been a few U.S-based strains recently identified.
Several homegrown COVID mutations are causing particular concern in the scientific community.
Epsilon (also called CAL.20C or B.1.429/B.1.427) is a variant from California that emerged around November 2020. As of early spring, it accounted for at least one-third of COVID cases in the state, and it has spread into other parts of the country, as well. This mutation has officially been classified by the CDC as a "variant of concern" because it's 20% more transmissible and also demonstrates resistance to antibody or vaccine therapies.
Another variant, this one originating in the New York City region last November, is called Iota (or B.1.526). It now accounts for at least 25% of coronavirus cases in that area and potentially more. The CDC lists this one as "variant of interest" (one step down from "variant of concern"), citing potential resistance to available treatment options. This variant has similar characteristics to the South African and Brazilian strains (along with the dreaded EEK mutation), so scientists are concerned that it may be more deadly and potentially render vaccines less effective, although more research needs to be done to confirm this.
Yet another pair of variants (COH.20G/501Y and COH.20G/677H) were discovered in Ohio on January 19, though the CDC hasn't bumped them up to priority status. No specifics are yet known about these variants, but their genetic makeup is similar to the UK and South Africa strains, meaning they also may be extra contagious.
6. You wouldn’t necessarily know if you had a new strain or an older form of COVID.
Most, but not all, of the existing rapid and point-of-care (PCR) tests work at detecting the newer strains. (On January 8, the FDA released an alert about three different brands of PCR tests that might give a false negative in the case of the UK variant.) But not all can tell the difference between the new variants and older strains of COVID—they might just provide a positive result.
Dr. Doron explains that sometimes PCR tests can provide a clue as to whether someone has a new variant, based on the specific parts of the genetic code they are built to detect. But to know for sure which strain you had, scientists would need to do genetic testing. For most of us, not an option.
7. Evidence suggests that some variants may make our current crop of vaccines less effective...
Here's the good news: Pfizer and Moderna have both reported (and increasing evidence has shown) that their mRNA vaccines will protect against all existing forms of COVID, including variants containing the EEK spike protein mutation.
A February 8 study in Nature found that the Pfizer vaccine protects against the Alpha and Beta strains of COVID-19, and a February 17 report from the New England Journal of Medicine confirmed the Pfizer vax protects against the Gamma variant. But a more recent study from Israel has brought this initial data into question, finding that Pfizer's vaccine might not be quite as effective against the Beta variant as previously thought (this study has yet to be peer reviewed). Still, the CDC asserts that vaccination is still the best way to protect yourself against all these new COVID mutations.
Johnson & Johnson's single-shot adenovirus vaccine, which was approved by the FDA on February 27 (then briefly paused and reinstated in April as U.S. officials looked into rare reports of blood clotting following vaccination), has shown a range of efficacy results against moderate and severe disease in different countries, the company announced, ranging from 72% in the U.S. to 66% in Latin America and 57% in South Africa. Experts suspect that the dominance of the new strains in Brazil (Gamma) and South Africa (Beta) may be responsible for lower efficacy of the vax in those countries. And, despite the reduced efficacy of the J&J vaccine in South Africa, that country is now choosing it over AstraZeneca's candidate, which appears to provide even less protection against the South African strain, according to mid-February reports.
AstraZeneca's candidate is a two-dose viral vector vaccine. It was approved in the UK in January but has not gotten the green light in the U.S. According to U.S. clinical trial data released on March 22, this vaccine is 79% effective at preventing symptomatic COVID-19 and 100% effective against severe disease and hospitalization. It also appears to reduce transmission of COVID-19 by 67%, something that had not yet been proven in any other COVID vaccine research. (Emerging evidence suggests this will hold true for all vaccines.)
But, again, AstraZeneca appears to be less effective in protecting against the Beta strain. This vaccine has also hit a few roadblocks: Several European countries suspended distribution of the AstraZeneca vaccine in mid-March after 37 cases of dangerous blood clots were reported out of 17 million people who had received the shot. The vaccine was swiftly reinstated after an investigation showed it to be safe for widespread use.
In addition, another vax in the running (but not yet FDA-approved) from Novavax has shown 89.3% efficacy for protecting people from the disease yet is only 49.4% effective in South Africa, the company reported, with nearly all the infections it analyzed there involving the Beta variant.
8. …and antibody treatments may not work against some of the new variants.
Concerningly, research suggests that monoclonal antibody treatments (laboratory-produced proteins that mimic the immune system to help fight off harmful antigens, including viruses) may not work as well against some of these newer mutations. A January 13 study in Cell Host & Microbe suggests that the Beta variant may be able to evade detection by the antibodies in the immune system, due to its specific mutation in the spike protein that binds to the respiratory cell.
According to CDC data, both the Beta and Gamma variants reduce susceptibility to one specific combination of antibodies: bamlanivimab and etesevimab. The Alpha variant does not affect antibody treatments, and the other mutations affect antibody treatments to varying and unknown degrees.
Bottom line? Many of these new variants appear to be able to resist antibody treatments, though we don't know the full extent of the danger this poses. Scientists are still working hard to find out.
9. These strains likely won’t change our vaccination schedule.
Some public health experts have floated the idea of vaccinating everyone one time, rather than holding back enough existing shots for people to get second doses of Pfizer or Moderna. (Now that J&J's single-shot vax is approved and most Americans have access to vaccination, perhaps fewer will push for it.) The thought behind this is that some level of immunity might be conferred to a large swath of the public this way, thereby potentially thwarting the spread of newer strains. But Dr. Doron warns that this goes against the way clinical trials were developed and conducted. “We didn’t study the effect of one dose,” she says. “We don’t know how much infection it prevents, and we don’t know how long [immunity] lasts.” After months of promises by health experts and drug companies that these vaccines would go through every level of vetting, she thinks it is simply too risky to deviate from the approach that was studied, saying, “We could never support that as experts.”
10. The same strategies can be used to protect yourself against the new strains.
“The routes of transmission haven't changed, so our intervention strategies are still effective and needed now more than ever,” Popescu says. Until you are fully vaccinated, continue to wear a mask at all times and maintain six feet of distance from others. (Though it should be noted, on March 19 the CDC announced that three feet of social distancing was sufficient for masked students inside school settings only.) The Pfizer and Moderna vaccines aren't fully effective until two weeks after the second dose, and the Johnson & Johnson vaccine takes 28 days to confer full immunity.
Though these variants may be more transmissible, they are not transmitted any differently than other existing strains of the virus. “It doesn’t change how your respiratory secretions travel through the air, [and] it doesn’t change how likely your spit is to go through a mask,” Dr. Doron says. “It’s just, when you come into contact with virus, how much is needed or how likely is it that that virus is going to make you sick?” To prevent infection, now is the time to keep doing what we’ve all been doing for months now: quarantining, limiting contact with others, and avoiding non-essential travel, at least until you've reached fully vaccinated status.
With or without these new variants, we are still neck-deep in this pandemic, and we all need to keep doing our part. “We’re losing thousands of people a day—we absolutely need to put an enormous amount of effort and prioritization on vaccinating as many people as possible,” Dr. Doron says. “This is time to do more than you’ve ever done before to prevent the spread of infection.”
New COVID Variants: Centers for Disease Control and Prevention. (2021.) “New COVID Variants.” cdc.gov/coronavirus/2019-ncov/transmission/variant.html
U.S. Map of Variant Cases: Centers for Disease Control and Prevention. (2021.) “Variant Cases.” cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html
UK Strain, Scientific Brief: Centers for Disease Control and Prevention. (2020.) “Interim: Implications of the Emerging SARS-CoV-2 Variant VOC 202012/01.” cdc.gov/coronavirus/2019-ncov/more/scientific-brief-emerging-variant.html
UK Strain, Boris Johnson Statement: 10 Downing Street on YouTube. (2021.) “Coronavirus press conference (22 January 2021).” youtube.com/watch?v=iCrHEK_00Gk
Brazil Strain of COVID: Virological. (2021.) “Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings.” virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586
Newly Identified U.S. Strain of COVID: bioRxiv. (2021.) “Emergence and Evolution of a Prevalent New SARS-CoV-2 Variant in the United States.” biorxiv.org/content/10.1101/2021.01.11.426287v1
Ohio Strains of COVID: bioRxiv. (2021.) “Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio.” biorxiv.org/content/10.1101/2021.01.12.426407v2
California Strain of COVID: medRxiv. (2021.) “Emergence of a novel SARS-CoV-2 strain in Southern California, USA.” medrxiv.org/content/10.1101/2021.01.18.21249786v1
Ohio Strains of COVID: bioRxiv. (2021.) “Distinct Patterns of Emergence of SARS‐CoV‐2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio.” biorxiv.org/content/10.1101/2021.01.12.426407v1.full.pdf
New York Strain of COVID: bioRxiv. (2021.) “SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape.” biorxiv.org/content/10.1101/2021.02.14.431043v2.full.pdf
New York Strain of COVID: medRxiv. (2021.) “A Novel SARS-CoV-2 Variant of Concern, B.1.526, Identified in New York.” medrxiv.org/content/10.1101/2021.02.23.21252259v1
Pfizer Vaccine Efficacy Against Mutations: Nature. (2021.) “Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera.” nature.com/articles/s41591-021-01270-4
Moderna Vaccine Efficacy Against Mutations: Moderna. (2021.) “Moderna COVID-19 Vaccine Retains Neutralizing Activity Against Emerging Variants First Identified in the U.K. and the Republic of South Africa.” investors.modernatx.com/news-releases/news-release-details/moderna-covid-19-vaccine-retains-neutralizing-activity-against
AstraZeneca Efficacy Data: University of Oxford. (2021.) “Oxford coronavirus vaccine shows sustained protection of 76% during the 3-month interval until the second dose.” ox.ac.uk/news/2021-02-02-oxford-coronavirus-vaccine-shows-sustained-protection-76-during-3-month-interval
FDA Warning About False Negatives: Food and Drug Administration. (2021.) “FDA Issues Alert Regarding SARS-CoV-2 Viral Mutation to Health Care Providers and Clinical Laboratory Staff.” fda.gov/news-events/press-announcements/fda-issues-alert-regarding-sars-cov-2-viral-mutation-health-care-providers-and-clinical-laboratory
South Africa Variant, Antibody Treatment: Cell Host & Microbe. (2021.) “Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition.” sciencedirect.com/science/article/pii/S1931312820306247
FDA EUA: Food and Drug Administration. (2021). “FDA Issues Emergency Use Authorization for Third COVID-19 Vaccine.” fda.gov/news-events/press-announcements/fda-issues-emergency-use-authorization-third-covid-19-vaccine
J&J Efficacy Data: Johnson & Johnson. (2021). “Johnson & Johnson Announces Single-Shot Janssen COVID-19 Vaccine Candidate Met Primary Endpoints in Interim Analysis of its Phase 3 ENSEMBLE Trial.” jnj.com/johnson-johnson-announces-single-shot-janssen-covid-19-vaccine-candidate-met-primary-endpoints-in-interim-analysis-of-its-phase-3-ensemble-trial
J&J Distribution Plan: Johnson & Johnson. (2021). “Johnson & Johnson Announces Submission of Application to the U.S. FDA for Emergency Use Authorization of its Investigational Single-Shot Janssen COVID-19 Vaccine Candidate.” jnj.com/johnson-johnson-announces-submission-of-application-to-the-u-s-fda-for-emergency-use-authorization-of-its-investigational-single-shot-janssen-covid-19-vaccine-candidate