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What’s up with the BA.2, BA.2.12.1 and BA.4/5 Omicron sub-variants?

  • Find out the latest variant proportions: CA | US | Global
  • The highly infectious BA.2.12.1 sub-variant rapidly increased in California from 15% on April 23 to 44-61% on May 9. So far 6 cases of the immune-evading BA.4/5 sub-variants were detected in California as of May 9.
  • BA.2.12.1 was first identified in New York in mid-April and has increased in proportion in the US at a faster rate than BA.2. BA.2.12.1 appears to be even more transmissible than BA.2 by 23-27%. It appears to have similar disease severity so far. Vaccines, boosters, masks, testing and ventilation all still work to reduce infections and severity from BA.2.12.1.
  • In early May 2022, South African scientists shared that two new Omicron sub-variants, BA.4 and BA.5, are causing a new surge in a population that has about 90% immunity, primarily from prior infections (in the Gauteng, Western Cape and KwaZulu-Natal provinces). A study on neutralizing antibodies also suggests that BA.4/5 reinfect people who had BA.1 infection, especially if they are unvaccinated. This raises the concern that the virus may be evolving further to evade prior immunity.
  • The highly transmissible BA.2 Omicron sub-variant became the dominant variant in the US in late March. The WHO also reported that the BA.2 subvariant has rapidly become the dominant variant worldwide.
  • This is likely due to a combination of BA.2’s increased transmissibility, our waning immunity, and the reduction in masking and other precautions.
  • Transmissibility is higher: Data from Denmark found BA.2 to be about 30% more transmissible than the BA.1 (first) Omicron variant, with a household secondary attack rate of 39% compared to 29% for BA.1.
  • Severity is similar to BA.1: Data from South Africa found that the odds of being admitted to the hospital was similar between the two sub-variants.
  • Immunity from BA.1 and boosters is likely protective against BA.2: A lab study found that vaccinated people infected with Omicron BA.1 had high levels of antibodies that would probably protect against BA.2. Boosters were needed to maintain high enough antibody levels against both BA.1 and BA.2.
  • Dr. Anthony Fauci has emphasized the importance of everyone eligible getting vaccinated and boosted as soon as they can to reduce the risk of another surge in cases from BA.2.
  • Second mRNA vaccine boosters were authorized on March 29 for people ages 50+, adults who’ve gotten 2 doses of the J&J vaccine, and people with immunocompromise ages 12+ at least 4 months after their first booster dose.
  • High-quality masks (N95, KN95, KF94s) still protect you and others from BA.2 and all variants. Click here to get free N95 masks at a pharmacy near you, including many East Bay locations.

How do we prepare for the next variant wave?

  • Get vaccinated and boosted. The more doses your immune system is exposed to, the better it’s able to recognize new variants. Click here for where to get free vaccines.
  • Have a supply of high-quality masks (N95, KN95, KF94s) and be ready to wear them when virus levels increase in your community. Click here to get free N95 masks at a pharmacy near you.
  • Have a supply of rapid home COVID tests ready to use. Get them while supply is plentiful. Click here to order 4 free rapid tests (order up to 2 sets per household).
  • Make a plan to get treatment in case you get infected.
  • Have back-up plans for gatherings and travel if cases increase.
  • Check the amount of virus in your community using the early detection wastewater surveillance US dashboard.

What are variants of concern? Why do they matter?

We have learned that SARS-CoV-2, the coronavirus that causes COVID-19, is a shape-shifting virus. Like all viruses, it mutates randomly when it replicates in someone’s body and creates new variants. When the mutations help the virus spread faster/better and spreads to others, the new variant can cause new outbreaks. These are called variants of concern.

SARS-CoV-2 has infected so many people that it has tons of chances to accumulate mutations, including ones that make it more transmissible and evade our immune systems, especially in the spike protein. We have also learned that this is a hardy virus – able to withstand a lot of mutations and still replicate and spread rapidly. We can’t predict how much new variants will be more transmissible, evade our immunity from vaccines and/or infection, escape detection from tests, remain susceptible to our treatments, or what their disease severity will be.

To manage future outbreaks from new variants, we need to keep a close watch on genomic sequencing of circulating SARS-CoV-2 strains, wastewater and case/hospitalization trends, and be ready at the earliest signs of an outbreak to rapidly implement the precautions we know that work: masking, distancing, rapid testing and isolation, and rapid access to vaccine updates and antivirals.

Click to learn more about variants in California state, the US and worldwide


Is Omicron highly transmissible? Yes, Omicron is very contagious.

  • The Omicron BA2.12.1 sub-variant is estimated to be 25% more transmissible than BA.2, which was 30%+ more transmissible than Omicron BA.1, which was 50% more transmissible than Delta, which was 80-90% more transmissible than Alpha, which was 30-50% more transmissible than the original strain.
  • The original Omicron variant (BA1) is estimated to have an R0 of 4-8, which means each person who is infected with the BA1 variant is estimated to transmit the virus to 4-8 more people.
  • Omicron has spread 2-3x more rapidly than Delta, as shown in data from the UK and South Africa, with cases doubling every 2-3 days, leading to explosive outbreaks.
  • Omicron’s high transmissibility likely due to a combination of immune evasion, shorter incubation time (~2-3 days instead of 4 days for Delta and 5 days for older variants), and rapid replication in the upper airways (70x faster in one study).
  • A CDC study found that household transmission for Omicron was 53%. Secondary attack rates were lower for people who were boosted (43%), people had their primary vaccine series (44%), compared to people who were unvaccinated (64%). People with infection who wore masks had lower transmission rates (40%) compared to those who didn’t wear masks (69%). Those who isolated also had lower transmission rates (41%) compared to those who didn’t isolate (68%). 

Does Omicron evade immunity? Yes, partially.

Do vaccines still work? Yes! Especially with boosters (third doses for all; fourth doses for all immunocompromised people and maybe all older people).

  • Vaccines, including two doses, still work well against severe illness though not so well against infection. Boosters significantly increase protection. Prior infection provides less reliable immunity against Omicron compared to vaccinations and especially boosters.
  • The more immunity we have built up over time, the better we are able to protect ourselves against Omicron and future variants. It’s safest and most reliable to do this with multiple vaccine doses. Infection will also add a layer of immunity, though as Omicron and Delta have shown us, a less reliable one.
  • The Omicron variant has so many mutation in the spike protein that it is much better able to escape antibody immunity in the nose and mouth compared to earlier variants, including Delta. B-cell and T-cell immunity is still effective in protecting us from severe disease, but they don’t activate until after the virus enters the body, so we are more likely to get upper airway infections with Omicron compared to earlier variants.
  • Data from the US shows that vaccine efficacy against hospitalization during the Omicron surge was 90% after an mRNA booster, 81% within 6 months of getting a second mRNA dose, and 57% 6+ months after a second mRNA dose. This compares to 94%, 90% and 81% respectively during the Delta surge, suggesting that the Omicron variant has mutations that confer significant immune evasion.
  • A study on vaccine efficacy across 10 US states including Northern California through January 22, 2022 found that mRNA vaccine efficacy against hospitalization during the Omicron surge was 91% during the first 2 months after the booster/third dose and 78% by the 4th month.
  • A large UK cohort study found that boosters gave the best protection against hospital admission from Omicron (aHR 0.22) compared to past infection alone (aHR 0.55).
  • Data from the UK up to January 13, 2022 shows vaccine efficacy against hospitalizations with the Omicron variant for all brands they use (Pfizer, Moderna, Astra-Zeneca) to be 64% in the first 6 months after a second dose, 44% after 6 months of the second dose, and 92% in the first month after a booster, waning to 83% when it’s been more than 2.5 months after a booster. (Compared to 95-99% booster efficacy against hospitalization with the Delta variant.)
  • A large study from New York State in January 2022 found that while the Pfizer vaccine for children 5-11 was still protective against hospitalizations with Omicron (48%), protection against infections declined rapidly (from 56% in the first 2 weeks after the 2nd dose to 12% after 2 weeks). For children aged 12, who received the higher 30 mcg dose, protection against infections was 67% (compared to 11% for children aged 11). The authors conclude: “These results highlight the potential need to study alternative vaccine dosing for children and the continued importance layered protections, including mask wearing, to prevent infection and transmission.”
  • South African epidemiologists have reported more reinfections with Omicron compared to earlier variants.

Do rapid tests detect Omicron infections? Yes!

  • The Unidos en Salud group in the SF Mission found that rapid antigen tests still pick up 95% of people with viral loads that are most associated with infectiousness.
  • Most importantly, rapid tests will give you crucial results within 15-30 minutes of testing so you have a good idea of whether someone is currently infectious or not.
  • While PCR tests are more sensitive, by the time you get the result, the person’s most infectious period may be over.
  • Omicron appears to results in symptoms sooner, about a day or two after exposure, so it’s important to start isolating and test as soon as you feel symptoms.
  • Omicron also appears to replicate rapidly first in the throat before the nose, so some countries (like the UK) and some people have been swabbing their throats before swabbing their noses for the rapid antigen tests (though this has not been authorized by the FDA/CDC yet). Only use the swabs that come in kits and are intended for rapid testing. Q-tips and other cotton swabs will interfere with test results.

Is Omicron less virulent (cause less severe, “milder” disease)? Maybe, depending on your vaccine status, immunity, demographics and comorbidities. Early studies suggested that Omicron caused less severe disease, but a later study that controlled for vaccination status, demographics and comorbidities showed that the Omicron wave was just as deadly as the Delta and Alpha waves. Kids too young to get vaccines had similar or higher hospitalization rates with Omicron compared to Delta.

  • How mild/severe Omicron infection is depends on an individual’s immune status and underlying health conditions.
  • A pre-print study posted in May 2022 comparing the hospitalizations and deaths in Massachusetts during the Omicron wave found that after adjusting outcomes for vaccination status, demographics and comorbidities, hospitalization and mortality risk was similar during the Omicron wave compared to the Delta and Alpha waves.
  • A nationwide study found that Omicron causes less severe illness, especially among people who are vaccinated/immune (9 deaths/1,000 cases during Omicron vs. 13 deaths/1,000 cases during Delta). COVID-19 hospital stays were shorter, with fewer hospitalized people needing ICU stays, thanks to people getting vaccinated. However, case rates were 5x higher and hospitalization rates were 1.8x higher during the Omicron surge compared to the Delta surge, leading to more overall hospitalizations.
  • Among adults in the US ages 65+, those who were unvaccinated were 49 times more likely to be hospitalized for COVID-19 compared to those who were boosted as of January 19, 2022.
  • A large UK cohort study found that hospitalization and death rates for Omicron were much lower compared to Delta for people ages 11+ vaccinated and unvaccinated (aHR 0.41 overall for hospital admission and aHR 0.31 for death from Omicron; aHR 1.1 for kids <11 for hospital admission).
  • How severe an infection depends on a person’s underlying level of immunity (how many vaccine doses, prior infection, time since vaccination or infection, etc.) and health status.
  • Infection is less severe if you have a certain level of immunity, especially from vaccination and boosters.
  • People who are unvaccinated and/or only have immunity from infection from an earlier variant are at higher risk for severe illness from Omicron.
  • Omicron appears to stay more in the upper airways and cause less pneumonia.
  • The fact that Omicron infects many more people and there are still so many unvaccinated people led to hospitals across the US still getting overwhelmed with cases during the winter surge of 2021-2022.

Is there effective treatment or PrEP for Omicron infections? Yes!

  • If you have COVID and are at risk for serious illness, ask your medical provider if/where you can get treatment or PrEP.
  • Treatment is available. When treatment is in short supply, it is prioritized for people at highest risk for severe disease.
  • Much more treatment availability is anticipated in April 2022 and after.
  • Read more here.

The emergence and rapid spread of the Omicron variant reminds us of how crucial it is to get vaccines, boosters, testing, high-quality masks and good ventilation to everyone around the globe.