It seemed like everything was getting better — and then the mutants arrived.

Yes, the horror story that is our lives a year into the coronavirus pandemic had already challenged us with plenty of just-when-you-let-your-guard-down twists and turns. And here we are, with case rates and deaths plummeting, businesses reopening and millions of people getting vaccinated in every corner of the country. Things are looking up. But now health officials and infectious disease experts are keeping an eye on something that threatens all this progress: the COVID-19 mutations.

You’ve probably heard of these variants by now: the UK, South Africa and Brazilian varieties. There’s even a California and New York version popping up now.

What are they? Will the vaccines protect us from them? And how big of a threat are they to our recovery?

Those are the key questions as scientists and medical providers race to stop their spread and end the pandemic.

Like other viruses, the coronavirus has mutated over time. Its crown-like spikes can change as it spreads. That’s not at all unusual and it’s not always cause for alarm — in fact, tracking mutations helps scientists trace the spread of the virus from place to place. But several variants are causing concern across the U.S.

In general, “they spread faster, they are highly transmissible, they can cause more disease and they can evade the immune response,” said Melanie Ott, director of the Gladstone Institute of Virology in San Francisco.

That’s not necessarily true of every variant, and scientists themselves disagree over whether some of the new strains, such as one first detected in South Africa, make people more sick than the original.

“We don’t know yet,” said Benjamin Pinsky, medical director of the Clinical Virology Laboratory at Stanford.

Even the naming of the variants themselves is controversial and incredibly convoluted. Different researchers are using different names for the same virus. Some draw on the date a variant was first identified, while others have to do with which particular part of the virus has changed. All of it has led people to identify variants geographically. That in turn has raised concerns about residents of those places being unduly stigmatized, but so far there is no clear, standardized alternative.

Here is a quick roundup of the variants of concern in the U.S.:

The UK strain

Also known in the scientific community as B.1.1.7, this variant was identified in the UK last fall. It appears to be about 50% more infectious than the original virus, scientists say. In January, experts in the UK said it also appeared more deadly than the original strain. It was first detected in the U.S. in December 2020 and is now becoming widespread here. According to the Centers for Disease Control and Prevention, there have been more than 2,600 cases reported across at least 47 states and Puerto Rico. California has recorded more than 200 cases. The CDC has said this could become the dominant variant in the U.S. by this spring.

The good news: Researchers like Pinsky are less concerned about the UK variant than some others because vaccines appear to be very effective at keeping people exposed to this variant from getting sick.

The South Africa strain

Also called B.1.351, this variant was identified in South Africa in October and made its way to the U.S. by January. It seems to be better at evading antibodies produced by the body’s immune system, raising some concerns about whether this variant reduces the effectiveness of available coronavirus vaccines. For example, clinical trials overseas on vaccines from Novavax and AstraZeneca PLC showed they were less effective in South Africa than elsewhere.

The U.S. has recorded more than 68 cases of the South African variant in 17 states, including several cases in California. The CDC says there isn’t evidence to suggest the variant has any impact on disease severity, but South Africa’s health minister said it seemed to affect young people more than earlier versions of the coronavirus. (This observation also coincided with a large number of graduation parties where young people gathered.)

The Brazilian strain

Known as P.1, this variant was identified in January when Brazilian travelers arrived in Japan. As with the South Africa variant, scientists are concerned the Brazilian strain may be better at tricking antibodies, meaning vaccines may be less effective.

There is also evidence that people who had already recovered from COVID-19 could be reinfected by the Brazilian strain. That appears to be happening in the Brazilian city of Manaus, which was hit so hard last spring with a different variant that some scientists speculated the city might have achieved herd immunity, where a large percentage of the population has become immune and the virus begins to have trouble spreading. But then P.1 struck earlier this year, infecting people who had already been sick.

So far, at least 13 cases have been reported in at least seven U.S. states. Stanford scientists have found another Brazilian variant, known as P.2, in the Bay Area, and Los Angeles County’s public health director Barbara Ferrer said Wednesday that officials also identified a case there. It’s different from the P.1 variant causing widespread concern but has not been identified yet in California, according to the CDC.

California and New York

There is also another variant of concern in California, what appears to be a homegrown variant known as B.1.427 and B.1.429. This variant is now spreading widely in California, and research out of UCSF suggests it may make people sicker and it may be more contagious than the earlier coronavirus.

On Wednesday, Gov. Gavin Newsom said a variant spreading in New York and the East Coast — B.1.526, which also appears capable of evading some of the body’s defenses — had been identified in Southern California.

Most COVID-19 tests determine only whether or not someone is infected, so it can be hard to say exactly which patients have which variant. But Pinsky said, doing more sophisticated lab tests to figure out which variants are spreading in any given community is helpful because then doctors can tweak treatment plans. For instance, people infected with certain variants respond well to monoclonal antibody treatments. But for other variants, such as the California variant, a combination antibody treatment may make more sense.

In recent weeks, researchers like Charles Chiu, an infectious disease expert at UCSF, have been tracking the California variant in the Bay Area, focusing on San Francisco’s Mission District, where COVID-19 has hit a largely Latinx community hard. As with other variants, experts are tracking how they respond to what are known as neutralizing antibodies — looking at whether the virus resists — and studying transmissibility by looking at how quickly the virus spreads, within individual households and beyond.

Health experts’ understanding is changing on a daily, sometimes hourly basis. But they do know that even though vaccines may be slightly less effective against certain variants, all three approved in the U.S. — Pfizer, Moderna and Johnson & Johnson — have shown to be 100% effective at preventing coronavirus-related deaths and hospitalizations regardless of the variant.

In other words, “even if you get infected and vaccinated, you will not die and you will not go to the hospital,” Ott said.

As far as medicine goes, that’s a minor miracle.

And the drug companies that make the vaccines are already studying ways to make the shots more effective at warding off the variants, potentially through booster shots.

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