The Truth About the ‘Stealth’ Variant

US officials had predicted that Omicron would be the variant to end the pandemic. However, varying degrees of pandemic lockdown measures are still being carried out in recent weeks, while the new variant in the Omicron family–BA.2 has continued to spread to more than 110 countries based on data from outbreak.info.

To differentiate them better, BA.1 is used as a name to describe the original Omicron. 

What is the pathogenicity and transmissibility of BA.2, and how do Covid vaccines and natural immunity hold up against this subvariant? To get clear answers, we turned to Dr. Yuhong Dong, expert in infectious diseases and antiviral drug development. 

Where Is BA.2?

Covid cases began to decline early February, and rise again slightly in the week of March 14. These infection waves took place largely in Asia, Europe, and the Pacific. In Europe, there were no large spikes, but increases mainly in France, United Kingdom, and Italy. The largest outbreaks were in China, Hong Kong, South Korea, and New Zealand—these places saw increases in infections and deaths, and the cases were largely of Omicron subvariant BA.2. 

In the United States, the CDC stated this week that the majority of Covid cases are now due to the Omicron BA.2 subvariant, which has in recent weeks displaced other variants of the virus.

BA.2 is significantly different from Omicron subvariant BA.1, so much so that Japanese virologists recommended it be treated as a new variant of concern (VOC) entirely. 

There are three major differences between these two subvariants BA.1 and BA.2, Dr. Dong explained, regarding the traceability of the subvariant, the transmissibility, and the protections offered by natural immunity and vaccines. 

“The New England Journal of Medicine published a study from Harvard University (chart here) which showed that BA.2 has eight new mutations in the spike protein compared to BA.1,” Dr. Dong said. “The mutations in BA.2 are what make it difficult to detect, and that is why it’s referred to as the ‘stealth variant.'”

‘Invisible’

“The BA.1 subvariant included a specific mutation, a deletion mutation at positions 69-70. This can lead to false negatives when using PCR tests, which test for the virus spike protein,” Dr. Dong explained. Thus a lot of people will take negative PCR test results as a positive for Omicron BA.1. 

“By contrast, BA.2 does not have this deletion mutation and therefore no false negatives in PCR tests. Yet, BA.2 cannot be rapidly detected with existing PCR tests, and require more complex whole-genome sequencing to confirm. These lab tests are not nearly as quick, taking about 10 days to complete, so BA.2 has also been referred to as the “invisible variant.” 

Higher Transmissibility 

These eight new mutations also make it so that the transmissibility of BA.2 has significantly increased, about 30 to 40 percent from the transmission rate of BA.1. 

“A recent Danish study found that people infected with BA.2 were more likely to infect neighbors than those with BA.1, regardless of whether they had Covid vaccinations,” Dr. Dong said. 

The researchers looked at the transmissibility of BA.2 in populations with different vaccination status, compared to those with BA.1:

• 2.29-fold increase in transmission risk from unvaccinated persons to people living in the same household
• 2.45-fold increase in transmission risk from persons who received two-dose vaccines to people living in the same household
• 2.99-fold increase in transmission risk from persons who had received a third (booster) dose to people living in the same household

“People infected with BA.2 are more likely to transmit the BA.2 to people in the same household than those with BA.1, regardless of whether they have received Covid vaccines or not. This explains the sharp outbreak in Hong Kong, where a study estimated the number of new cases caused by the BA.2 variant doubled roughly every 1.28 days,” Dr. Dong said. 

Past Immune Is Protection Reduced

Similarly, protection against infection of the BA.2 variant has declined, whether you’re talking about natural immunity or vaccines.

“The Harvard study also looked at 24 subjects and observed their immunity to the BA.2 variant,” Dr. Dong said. 

“Immunity to the old virus was relatively high for those who had received two doses of the vaccine, but the protection it afforded against BA.1 and BA.2 was more than 20 times lower,” Dr. Dong said. “Six months after two doses of the vaccine, the vaccine protection against the old virus drops significantly, but protection against BA.1 and BA.2 drops to almost undetectable levels.”

“After the third booster shot, the protective power again increases—but against BA.1 and BA.2, the protection is 6.1 and 8.4 times weaker, respectively, than against the old virus,” Dr. Dong said. 

It’s worth noting, Dr. Dong pointed out, that the study only analyzed the two-dose mRNA vaccines. Most of the vaccines used in China, where there are massive outbreaks and inhumane lockdowns, are inactivated vaccines which have not been analyzed and researched. 

“The researchers also looked at immunity to BA.2 in a group of people who had been vaccinated and then later had Omicron BA.1 infections and now had acquired immunity,” Dr. Dong said. “They had antibodies, T-cell and B-cell immunity, and other levels of immunity. However, their protection against BA.2 was still 1.3 times weaker than against BA.1.”

Reduced Disease Severity? 

According to the Nextstrain database, BA.1 cases at one point accounted for 99 percent of global infections. Many of these are asymptomatic and mild infections, and in all cases afford some protection against new BA.2 infection induced diseases. 

“Countries that have experienced a peak in BA.1 infections may have established immunity that protects them from severe BA.2 infections,” Dr. Dong said. “So even if you are in an area where BA.2 infections have risen sharply, you don’t need to panic. If you have been infected with BA.1 or BA.2, the natural immunity of the antibodies produced will afford a high level of protection against severe disease.

“Many countries are currently studying the morbidity rate of BA.2. A study looking at infections in South Africa did not find an increase in rate of hospitalization or severe illness compared to BA.1. A study in the UK found similar results,” Dr. Dong said. 

And now that most people have received two or three doses of Covid vaccines, what is the chance of becoming seriously ill with BA.2? 

“A study from Denmark analyzed more than 16,000 BA.1 cases and more than 2,600 BA.2 cases, assessing probability of hospitalization 14 days after infection, and tracking vaccination status. There was no increase in risk of hospitalization in those with BA.2 infections compared to those with BA.1,” Dr. Dong said. 

Smiling in the Face of Ever-Changing Variants

Antibodies are the key focus of the current anti-COVID strategies. A common limitation of most current studies is that they mainly focus on serum antibodies.

Due to technical restrictions, very few studies have taken a decent look at a broader scope of immunity from mucosal immunity, functions of macrophages, or expression levels of interferons in epithelium cells. 

Vaccinated persons may despair at the findings of lowered protection against BA.2, but Dr. Dong has good news.

“Antibodies are not everything, but only a second line of defense in the human battle against viruses. We should not forget about our God-given natural immunity existing in the tonsils, mucous layer, defending against all different viruses or bacteria independent of their genes,” she said.  

“Natural immunity reacts first and continues to work as one comes in contact with the virus, up through the first week of virus infection. Having incomplete innate immunity against SARS-CoV-2 would likely result in persistent replication inside our bodies upon infection, so one would eventually show clinical symptoms,” Dr. Dong said. 

“A wise strategy for us would be focusing our attention in ways to strengthen our natural immunities. For example, enjoying regular sunshine, setting an alarm to go to bed and get up on time everyday, taking a deep breath or walking outside when feeling stressed, and meeting inevitable changes with a positive mindset or a smile. 

“These are not trivial. Our behavior and mindset have implications on our natural immunity. It’s like cultivating a plant with water and sunlight. If we often remember to take care of it, it would be strong enough to fight against viruses without breaking a sweat.”