Virus Variants: What Do You Need To Know Now?

[This article was originally published Feb. 18, 2021 and was last updated on June 22, 2021.]

Note: Information in this article was accurate at the time of original publication. Because information about COVID-19 changes rapidly, we encourage you to visit the websites of the Centers for Disease Control & Prevention (CDC), World Health Organization (WHO), and your state and local government for the latest information.

For some of us, relief that more and more people are fully vaccinated against  COVID-19 is now tempered with continued media reports about mutations to the virus (SARS-CoV-2) that causes it.

Are vaccinations effective against them? Do these new variants allow the virus to spread more easily? What are the variants we should be worried about?  

In short, emerging data shows that the current vaccines used in the United States are effective against variants, but enhanced vaccination efforts—globally—are imperative to keep this the case, says Nathan Grubaugh, PhD, a Yale School of Public Health epidemiologist.

“Back in March, I was very concerned when we were lifting restrictions and we were seeing a rise in cases, the vast majority of which were Alpha [the variant first detected in the United Kingdom],” he says. “I thought that it was too soon, but thankfully, we were rescued by the vaccines. As long as we continue to increase vaccination across all age groups, we should be protected.” 

Grubaugh says he is optimistic about this summer, but “worried that we may see a rise in cases this fall and winter when transmission is enhanced with cool, dry weather and people gathering more indoors. But at least we now have a good system for monitoring variants, which is important, too.” 

We talked with Grubaugh and other Yale experts about why variant surveillance matters—and other issues, including the importance of vaccination and why viruses mutate. Below are their answers.

Mutations are a normal part of a viral life cycle, explains Akiko Iwasaki, PhD, a Yale immunobiologist and leading COVID-19 researcher. “Viruses mutate all the time, and that’s how they survive various environments,” she says. 

Not only that but mutation is actually key to how viruses spread, notes Grubaugh. “Viruses mutate during each infection; what I’m worried about is ‘selection,’” he says. “Basically, selection is when mutations that help the virus survive get passed on to another host. Sometimes, selected mutations can help to make viruses more transmissible or evade immune responses.” 

According to the Centers for Disease Control and Prevention (CDC), new variants sometimes disappear; other times, they persist and become dominant. Multiple variants of the virus that causes COVID-19 have been documented in the United States and around the world since the pandemic began. 

“This pandemic has gone on for over a year. It's caused millions of infections, which means there have been so many different opportunities for selection to happen,” says Grubaugh. “As a result, some viruses now contain constellations of unique mutations, which are called variants.” 

Currently, several SARS-CoV-2 variants are causing concern—including Alpha; Gamma, one first detected in Brazil; and Beta, one first detected in South Africa. 

Plus, a variant that has devastated India, Delta, is thought to be more transmissible than the variant responsible for Britain’s COVID-19 surge last winter. The variant has arrived in the U.S. but so far is at low levels and it’s not likely to cause much harm here thanks to our high vaccination rates, Grubaugh says.

“Delta is causing a lot of panic right now because of what is happening in India and the data coming out of the U.K. It appears to be outcompeting Alpha, which up to now was thought to be the most transmissible of the variants,” Grubaugh says. “But from what we know so far, the vaccines are effective against it.”

As COVID-19 continues to spread, more variants are likely to appear. “We might be talking about three mutations, or we might be talking about 20 mutations that collectively change the behavior of the virus,” Grubaugh says. “They can make the viruses more transmissible, or they can make them more likely to evade our immune response, whether it’s naturally occurring or from a vaccine.”

Although new information is being released as doctors and researchers learn more, so far experts believe that the current vaccines will provide coverage—in some capacity—to the emergent variants. 

In early May, the Pfizer-BioNTech vaccine was found to be more than 95% effective against severe disease or death from Alpha and Beta in two studies based on real-world use. Johnson & Johnson’s vaccine has been shown to offer protection against the Alpha variant. According to the analyses the FDA released in late February, there was 64% overall efficacy and 82% efficacy against Beta. 

In mid-May, a study in England showed that the Pfizer vaccine was 88% effective against symptomatic disease from Delta variant two weeks after a second dose, compared with 93% effectiveness against Alpha.

As for Moderna’s vaccine, some research has suggested it may provide protection against Alpha and Beta, but it is still being studied. 

Grubaugh says updated vaccines may be needed in the future as more mutations occur.  

But it’s important to note that slowing transmission, through vaccination and other control measures, is key, he adds. 

“Globally, we're playing a game of whack-a-mole—if we're trying to suppress transmission in one place to decrease variants, new ones will keep popping up,” says Grubaugh. “So, this really is a global problem and we all need to work together. We don’t live in a vacuum. A problem in one location can soon be a problem in another. What is ultimately needed is equitable vaccine distribution around the world.” 

No, unfortunately, says Richard Martinello, MD, a Yale Medicine infectious disease specialist, explaining that standard COVID-19 tests in the U.S. do not include genetic sequencing, which is the only way to gather information about mutations. Only a small percentage of positive COVID tests are brought to laboratories for genetic sequencing, he says. 

“When the virus is sequenced, they compare it to other sequences of the virus from the past,” he explains. “They determine a genotype based on the genetic sequence and can then measure what proportion of the virus [of the samples taken within a community] is this variant,” he says. Dr. Martinello adds that in 2020 the United Kingdom, known for its outstanding public health program, sequenced 10% of viruses, compared to about 0.3% here in the U.S. 

But since December of 2020, the CDC has significantly increased the number of virus specimens that undergo sequencing, as well as increased support to states for this testing, says Dr. Martinello. 

Surveillance, Grubaugh explains, is our “flashlight.” 

“Without it, we don’t know what is there. Across the country, public health programs are drastically ramping up their virus genomic surveillance programs to shed light on where these new variants are spreading,” he says. 

In Connecticut, the Yale Schools of Public Health and Medicine have formed a partnership with the Department of Public Health and Jackson Laboratories and diagnostic labs throughout the state to increase variant surveillance. They obtain COVID-19 samples to screen for variants using simple molecular assays and confirm them via sequencing. This program found the first cases of the Alpha variants in Connecticut and is helping to track the spread of new introductions. (Click here for to see COVIDTrackerCT for more details.)

“We now have one of the best genomic tracking programs at the state level in the country. We are sequencing between 5 and 10 percent of cases consistently. In New Haven County and at Yale New Haven Hospital, we are sequencing nearly every case, which is easier to do when there aren’t as many cases,” Grubaugh says. “It gives us a really good picture of what is circulating locally. Before, it was a lot of guesses. Now, we aren’t caught off guard when we see a rise in certain variants.” 

Nationally, there have been improvements, too, he adds. “We have now sequenced more samples than any other country, but in terms of percent of cases, we still aren’t as good as the U.K., Denmark, and Australia, but we are so much bigger and have had more cases so it’s hard to set up these technologies for the whole country,” he says. “But the CDC, along with state and academic labs, has done a good job of stepping up across the country. In the most recent COVID relief bill, the CDC was granted $1.7 billion for sequencing.” 

In the end, Grubaugh says that we have all the tools needed to stop the spread of variants.

“We know what works. And we have the ultimate tool now in vaccines. We know that they are very effective and safe and it’s now a lot easier for people get an appointment,” Grubaugh says. “We need to aid the world in suppressing transmission or else we will have new variants here.” 

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