What doctors wish patients knew about the BA.2 Omicron subvariant

With the rolling back of mask requirements and physical distancing, many people have been on a search for a new normal. But there is still reason to be cautious. The highly transmissible and contagious BA.2 Omicron subvariant—dubbed “stealth” Omicron—is now the dominant strain in the United States, causing more than 85% of all COVID-19 cases, according to the Centers for Disease Control and Prevention (CDC). This has led to more questions.

Based on the CDC’s genomic surveillance, the BA.2 or stealth Omicron subvariant is responsible for most new SARS-CoV-2 infections in the U.S. BA.2 is a subvariant of the original SARS-CoV-2 Omicron variant (B.1.1.529), along with BA.1.1 and BA.3.

The BA.2 subvariant has been referred to as stealth Omicron because it contains genetic mutations that can make it harder to distinguish from the Delta variant using PCR tests compared to the original Omicron variant. That means that while the test can detect a BA.2 infection, it looks like it is the Delta variant instead.

The AMA’s What Doctors Wish Patients Knew™ series provides physicians with a platform to share what they want patients to understand about today’s health care headlines, especially throughout the COVID-19 pandemic.

In this installment, AMA member Nancy Crum, MD, an infectious disease specialist at Avita Health System in Galion, Ohio, discusses what patients need to know about the BA.2 Omicron subvariant. Dr. Crum is also an alternate delegate in the AMA House of Delegates for the Infectious Diseases Society of America.

“As we've hit year three of the pandemic, the virus … has mutated and changed over time,” said Dr. Crum. “The major variants are named according to the Greek alphabet—Alpha, Beta, Delta and now Omicron.”

“If it’s a more minor shift in the genetic sequencing, then it becomes a subvariant,” she said, noting that “Omicron BA.1 was the major variant that supplanted Delta and that happened over the winter months.

“And now we have BA.2, which is a modified version of the BA.1 that's becoming the most prevalent in the United States,” Dr. Crum added.

“The concern is that even though our COVID-19 rates are super low right now—at least where I work—could this variant or the variant after this one take off and cause increasing numbers of cases, hospitalizations and deaths again?” said Dr. Crum. That’s because the BA.2 subvariant of Omicron is “more transmissible.”

Dr. Crum noted that most experts “say it’s 30% to 60% more transmissible, so it’s a risk—especially if it gets into a nonimmune population—to be able to skyrocket in terms of the number of cases.  However, fortunately this variant is not more virulent in terms of causing more severe disease,” she said.

“People are really concerned because: one—yes, it's here in the United States, and two—yes, it's caused outbreaks in other countries. So what this is going to mean for us is really the big question,” Dr. Crum said. “Is it just going to be there at low levels causing a few cases or are we going to see an upsurge of cases over the next several weeks?

“And then the other question is, will we get yet another variant that’s going to supplant BA.2 that’s going to start up in the future and how impactful will these future variants be?” she added. “The concern is that people are discontinuing mask wearing, opening up venues and getting rid of a lot of the COVID-19 precautions, which may provide a foothold for this and future variants then to take off.” 

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“We've been seeing a lot more of sore throat and pharyngitis that we didn't really see before,” said Dr. Crum. Some of the other symptoms experienced are “very similar to the other coronaviruses such as febrile illness and respiratory symptoms.”

“Patients can also have gastrointestinal symptoms such as diarrhea, and loss of taste or loss of smell, although I’ve seen that a lot less with the newer variants,” she said, noting that symptoms for BA.2 may also include muscle or body aches, headache, nausea or vomiting, and congestion.

“We’re seeing very low rates of positivity for coronavirus right now and we’re actually seeing more influenza,” said Dr. Crum. That’s why “everyone coming in with any of those symptoms gets both a COVID test and an influenza test at the same time.”

“If there’s a question, you should test because it’s SARS-CoV-2 is a virus that we have treatment for and we know in this particular variant is very contagious,” she said, emphasizing that it is important to know that “it’s not just your allergies and you can go to your party tonight. It may be coronavirus BA.2 and you really need to stay in and quarantine for public health reasons.”

“The good news is that many places in the United States continue to report decreased or very low rates of cases and hospitalizations,” Dr. Crum said. “So, we really haven't seen this variant take off.

“But we do need to be careful because we still have quite a few unvaccinated people in the United States and if we’re going to take away masks and other preventive strategies, we’ve got to be cautious,” she added.

“Data suggests the vaccines are protective against BA.1 and BA.2. I haven't seen data to suggest that vaccines would not be helpful for the current circulating variants,” said Dr. Crum. “We're still recommending people get their primary series and their booster vaccines accordingly.”

“The question I'm getting now is do we need a second booster? And the answer's going to be, yes,” she said. “If you’re 50 or older and it’s been at least four months since your last booster,” or if you have a compromised immune system, you are eligible for another mRNA booster to increase protection against severe disease from COVID-19.

Additionally, adults who received a primary vaccine and booster dose of Johnson & Johnson’s Janssen COVID-19 vaccine at least four months ago may now receive a second booster dose with an mRNA vaccine.

“These days, we still just recommend people get the vaccine if you haven't because there is protection against the current circulating virus,” said Dr. Crum.

“One of the things that's amazing about this virus is the different problems people have come in with,” Dr. Crum said. “It’s not just simply a short-term illness with a sore throat or a cough, rather up to 30% of people are having long COVID—defined as four weeks or more of symptoms—with all kinds of issues from shortness of breath to fatigue to hearing problems to dizziness to ocular symptoms.”

“What this new variant is going to look like as far as its propensity to cause long COVID, we don’t know, but I would expect for us to see more people with long term issues,” she said. That is why it’s important “to have people protected not just for the short-term illness, but from the issues that people can have for months and maybe even years after having COVID-19.”

“For me, one of the scariest things is that it's not just the people who are hospitalized and have severe COVID that are developing long COVID,” said Dr. Crum. “In fact, a lot of the data that's emerging is that it's more common in patients who have mild COVID to develop long COVID.

“It's very common to see young, previously healthy people that now can't go back to work or now are having all these issues,” she added. “It’s not the old people or the people with severe disease. It’s really hitting people at the prime of their life and people who never were hospitalized for COVID that just can’t shake the symptoms that go on and on.”

“Sometimes people say, ‘Oh, if I get COVID, no big deal,’ but that’s a very naïve because many of these patients then will develop long term symptoms, which is really horrible and often life-altering” Dr. Crum said.

“There are patients that don’t meet the definition of long COVID, but they’re certainly having symptoms longer than just a few days or a week,” said Dr. Crum.  While some are referring to this as “medium COVID,” there isn’t a scientific name for it just yet.

Whether it is medium COVID or some other term, “we’ve really seen the whole gamut from one day of symptoms from COVID-19 and then everything is well to one year or more of symptoms and things are still really bad,” she said.

“Certainly, if you've had a COVID infection, let's say with BA.1, you would likely have some protection via natural immunity against BA.2,” said Dr. Crum.  But “vaccination is better than getting the infection and assuming protection, meaning even if you've had previous coronavirus infections, there's still a clear benefit for vaccination in terms of the immunity that you'll have against future variants,” she said.

“There's certainly cause for concern, mainly because it's so transmissible,” Dr. Crum said. “What will happen with this in the next few weeks? None of us know.

“My sense is that we’re not going to have a major outbreak that’s going to return us to where we were a few months ago in terms of our case counts,” she said. “But for some people, they will get infected with this new subvariant. It’ll be highlight transmissible to their family and friends and we should keep our guard up.”

“We need to pay careful attention to see if rates will start to go up, and if so, we may need to go back to some of the mandates,” Dr. Crum said. “I know nobody wants to hear that, but that’s really the reality of where things are.”

“A lot of those populations, especially the very immunosuppressed, will not have great immune responses to the vaccine or to having COVID infection in the past,” said Dr. Crum. “They're a population that we have to be especially concerned about.

“We have prophylactic monoclonal antibodies that have been developed and could be considered in those patients who we really think do not have good immunity against the virus,” she added. “But the reality is that traditional prevention strategies of masking and hand hygiene remain important for these groups.”

“The best thing we could do is all be immune against coronavirus so that these variants could slowly fade away,” Dr. Crum said. “That means vaccination, having COVID or both. If you've had a COVID infection, we still want people to get vaccinated to provide them with even more protection against the variants that circulate. Studies have clearly shown the benefit of vaccination despite prior COVID infection.”

The AMA has developed frequently-asked-questions documents on COVID-19 vaccination covering safety, allocation and distribution, administration and more. There are two FAQs, one designed to answer patients’ questions (PDF), and another to address physicians’ COVID-19 vaccine questions (PDF).