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With original omicron nearly gone, these are the BA.2 subvariant's key differences

All versions of the omicron variant seem to cause similar coldlike symptoms among vaccinated and boosted people. A runny nose is the most common.
A woman takes a PCR COVID-19 test
Lyndsey Marko takes a free PCR Covid-19 test in Echo Park, Calif., on Jan. 18.Myung J. Chun / Los Angeles Times via Getty Images file

The omicron variant of the coronavirus has been dominant in the U.S. since December, but the version of omicron that drove the major infection surge during the winter now accounts for less than 2 percent of new cases.

A more transmissible subvariant, BA.2, accounts for around three-fifths of cases. And BA.2, in turn, has spawned its own sublineage, BA.2.12.1, which has been gaining steam: It rose from 7 percent of cases in early April to 36 percent by the end of the month.

Together, these subvariants are driving a surge in U.S. Covid cases — new daily cases have risen 45 percent, on average, over the last two weeks, according to NBC News' tally.

So far, the key difference between the newer versions of omicron and the one that previously rocketed through the U.S. is transmissibility. The White House’s chief medical adviser, Dr. Anthony Fauci, has estimated that BA.2 is 50 percent more transmissible than the original omicron lineage. The recent gains BA.2.12.1 has made suggest it has a further advantage over its predecessor.

But the coldlike symptoms vaccinated and boosted people feel as a result of an omicron infection are mostly the same regardless of the subvariant.

"The omicron symptoms have been pretty consistent. There's less incidence of people losing their sense of taste and smell. In a lot of ways, it's a bad cold, a lot of respiratory symptoms, stuffy nose, coughing, body aches and fatigue," said Dr. Dennis Cunningham, the system medical director of infection control and prevention at Henry Ford Health in Detroit.

Symptoms of the BA.2 subvariant

The Zoe COVID Symptom Study in the U.K. has enabled hundreds of thousands of people to self-report their symptoms through smartphone apps.

One of the apps’ co-founders, Tim Spector, a professor of genetic epidemiology at King's College London, said that based on Zoe data, a runny nose is still the most common symptom of omicron, followed by fatigue, sore throat, sneezing, headache, cough and hoarse voice.

"The changes from BA.1 to BA.2 have been quite subtle — perhaps runny nose and fatigue [are] going up," he said.

Spector said 84 percent of people in the U.K. who logged symptoms lately said they had runny noses, compared to around 73 percent in early January. Seventy-two percent said they had fatigue, up from 68 percent during the first omicron wave.

But it's hard to attribute those changes directly to a subvariant, Spector said, because there are many confounding factors.

What are the chances of reinfection?

BA.1 and BA.2 are about as genetically similar as delta was to alpha, experts said. In general, the chances of getting Covid after a prior infection increase with time, but Dr. Amesh Adalja, a senior scholar at the Johns Hopkins Center for Health Security, said people who recovered from an omicron infection in the winter are likely to have protection against BA.2 for at least several months.

"If they share enough of the mutations to be classified as an omicron variant, there’s likely going to be a lot of cross-protection. But over time, we know with all coronaviruses that reinfection becomes common as antibody levels fall," he said.

Your level of protection could also depend on how sick you got before. Montefiori said immunity from an omicron infection might last anywhere from a month for people who were asymptomatic to a year for those who got seriously ill.

"When we look at the immunity that’s built up from infection, the milder the infection was, the less immunity you get from it," he said.

But Adalja said that even for those who got mild cases, "it’s unlikely to see erosion of protection against severe disease, which I think is what really matters."

Differences between virus lineages and subvariants can also influence the effectiveness of monoclonal antibody treatments.

"We know even with BA.1 and BA.2, which are both subtypes of omicron, that different monoclonal antibodies work for one but don’t work for the other," Adalja said.

What should we make of all these new omicron sublineages?

BA.2 and BA.2.12.1 aren't the only omicron subvariants health leaders are watching. In South Africa, two others — BA.4 and BA.5 — have spurred a major case surge. Those two sublineages have been detected in at least 13 U.S. states and Washington D.C. as well.

A small preprint study by South African scientists, posted online last month, suggested people previously infected with the original omicron variant may not have much protection against BA.4 and BA.5.

"It’s as though the virus is trying to find a way to punch a hole through the immunity that’s built up in the population," said David Montefiori, a professor at the Human Vaccine Institute at Duke University Medical Center.

Still, he said, the public shouldn’t worry too much about the emergence of each omicron subvariant.

"At some point, you just can’t get nervous every time there's a new variant, because there’s always going to be a new variant," Montefiori said. "We've been through multiple waves of variants that really mattered a lot, but we might be coming out of that because there's so much immunity built up in the population."

What about those who haven't yet gotten Covid?

Vaccinations, masks, testing and social distancing can help control the spread of the prevailing omicron strains, experts said.

Although scientists are still studying how vaccination protection fares in the face of the new subvariants, Adalja said, young, healthy people probably won't need a fourth shot.

"With these first-generation mRNA vaccines, it’s hard to get anything more than protection against severe disease over a longer period of time because of the evolution of variants like omicron," he said.

Rapid tests, meanwhile, easily pick up BA.2, although they're generally less sensitive to omicron than they were to delta. Data from the Zoe COVID Symptom Study showed that at-home tests were 85 percent sensitive to delta and 80 percent sensitive to omicron.

"These home tests are still doing pretty well to get 80 percent accuracy," Spector said. "They're not giving false positives, either."