Omicron BA.2: What Do We Know So Far?

Paolo Spriano

April 15, 2022

Editor's note: Find the latest COVID-19 news and guidance in Medscape's Coronavirus Resource Center.

This article was originally published in Italian on Univadis.

Since November 2021, the Omicron variant of SARS-CoV-2 has quickly become the most dominant variant worldwide. Early sequencing of Omicron in South Africa alerted researchers to the possibility that Omicron could be a cause for concern due to extensive mutations of the spike protein. Omicron has 30 mutations of the spike protein, compared with the original Wuhan-Hu-1 variant, with 15 mutations of the receptor-binding domain (which are linked to a decrease in antibody binding), mutations at the furin S1/S2 site (which improves furin binding and increases infectiousness), and mutations of the amino terminal domain (which is the main binding site for some of the therapeutic antibodies used to treat COVID-19 infections).

Omicron's Functional Characteristics

Non-peer-reviewed studies have shown a replication of Omicron in pulmonary epithelial cells, which was shown to be less efficient, when compared to Delta and Wuhan-Hu-1. The number of viral copies from an Omicron infection in pulmonary epithelial cells was significantly lower compared to infection with the Delta or Wuhan-Hu-1 variants. The association of these characteristics found an increase in the number of viral copies in human epithelial cells (taken from the nasal airways) infected with Omicron. This supports the understanding that Omicron is more transmissible but results in a less severe manifestation of the disease.

As for the phenotypic expression of the infection, attention has been focused on Omicron's reduced capacity to cause syncytia in pulmonary tissue cultures, information which is relevant to its clinical significance, if we consider that the formation of syncytia has been associated with a more severe manifestation of the disease. Furthermore, it has emerged that Omicron can use different cellular entry routes, with a preference for endosomal fusion over superficial cellular fusion. This characteristic allows Omicron to significantly increase the number of types of cells it can infect.

Omicron BA.2 Evolves

Between November and December 2021, Omicron progressed, evolving into a variant with characteristics similar to those of its predecessors (that is, it underwent a gradual and progressive increase in transmissibility). Early studies on the Omicron variant were mainly based on the BA.1 subvariant. Since the start of January 2022, there has been an unexpected increase in BA.2 in Europe and Asia. Since then, continued surveillance on the evolution of Omicron has shown an increased prevalence of two subvariants: BA.1 with a R346K mutation (BA.1 + R346K) and B.1.1.529.2 (BA.2), with the latter containing eight unique spike mutations and 13 missing spike mutations, compared with those found in BA.1.

From these differences, we cannot presume whether their antigenic properties are similar or different, but they seem to be antigenically equidistant from wild-type SARS-CoV-2, likely jeopardizing in equal measures the efficacy of current COVID-19 vaccines. Furthermore, BA.2 shows significant resistance to 17 out of 19 neutralizing monoclonal antibodies tested in this study, demonstrating that current monoclonal antibody therapy may have significant limitations in terms of adequate coverage for all subvariants of the Omicron variant.

Omicron BA.2 and Reinfection

BA.2 initially represented only 13% of Omicron sequences at a global level, quickly becoming the dominant form in some countries, such as Denmark. At the end of 2021, BA.2 represented around 20% of all Danish cases of SARS-CoV-2. Halfway through January 2022, this had increased to around 45%, data that indicate that BA.2 carries an advantage over BA.1 within the highly vaccinated population of Denmark.

BA.2 is associated with an increased susceptibility of infection for unvaccinated individuals (odds ratio [OR], 2.19; 95% CI, 1.58 - 3.04), fully vaccinated individuals (OR, 2.45; 95% CI, 1.77 - 3.40), and booster-vaccinated individuals (OR, 2.99; 95% CI, 2.11 - 4.24), compared with BA.1. The pattern of increased transmissibility in BA.2 households was not observed for fully vaccinated and booster-vaccinated primary cases, where the OR of transmission was below 1 for BA.2, compared with BA.1. These data confirm the immune-evasive properties of BA.2 that further reduce the protective effect of vaccination against infection, but do not increase its transmissibility from vaccinated individuals with breakthrough infections.

Omicron, BA.2 and Vaccination

The understanding of serum neutralizing activity, in correlation to the efficacy of a vaccine, is a priority of research due to the growing epidemiological significance of BA.2. There is evidence to support the claim that the immune-evasive nature of BA.2 doesn't seem to be as severe as for BA.1, and it is possible that there are other viral or host factors that are enabling the rapid diffusion of BA.2. A study published in Science Immunology investigated humoral and cellular immune responses to Omicron and other variants of concern (VOCs), looking to understand how, and to what degree, vaccinated individuals are protected against Omicron. From the results, a very low level of antibody cross-neutralization of Omicron, or a lack thereof, was seen when compared with wild type, Beta, and Delta variants, which could be partially restored by a third booster vaccination. Furthermore, T lymphocytes were shown to recognize Omicron with the same efficacy as seen for the other VOCs, suggesting that vaccinated individuals maintain T lymphocyte immunity, an element that is capable of providing protection in the absence of neutralizing antibodies, limiting the chance of serious disease.

These results are consistent with those available from a study performed in a population from Qatar made up of 2,239,193 people who had received at least two doses of a BNT162b2 or mRNA-1273 vaccine. The efficacy of the booster against a symptomatic Omicron infection, compared with that from the primary series, was 49.4% (95% CI, 47.1 - 51.6). The efficacy of the booster against hospitalization for COVID-19 and the death rate from Omicron infection, compared with the primary series, was 76.5% (95% CI, 55.9 - 87.5). The efficacy of the BNT162b2 booster against a symptomatic Delta variant infection (or B.1.617.2), compared with the primary series, was 86.1% (95% CI, 67.3 - 94.1).

To summarize, the constant increase in the prevalence of BA.2 in more countries over the world has confirmed the growth advantage that this variant has compared with others. BA.2 reduces the protective effect of vaccination against infection. Omicron antibody cross-neutralization can be partially restored by a third booster vaccination, an aspect that becomes problematic in the context of a low vaccination rate, where peaks of Omicron may increase the likelihood of infection in the elderly and in other groups at a higher risk of severe disease. Omicron BA.2 opens up new evolution channels, but what do the experts think will happen?

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