15 Mar What is the BA.2 or “stealth” Omicron sub-variant?
The omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for coronavirus disease 2019 (Covid-19), has spread rapidly around the world and has already become the predominant variant circulating in many countries.
As of February 2022, omicron variants have been divided into four distinct sublineages: BA.1, BA.1.1, BA.2, and BA.3.1.
Most circulating omicron variants belong to sublineage BA.1; however sublineage BA.2 is now becoming dominant in many counties with this highly probable in Australia.
The subvariant BA.2 has been referred to as “stealth” Omicron because it has genetic mutations that could make it harder to distinguish from the Delta variant using PCR tests as compared to the original version of Omicron.
This Omicron subvariant BA.2, is 1.5 times more transmissible than the original Omicron strain. While there is currently no evidence that the BA.2 lineage is more severe than the BA.1 lineage it is likely BA.2 will extend the current pandemic.
Viruses like SARS-CoV-2 are continuously evolving as changes in the genetic code (genetic mutations) occur during replication of the genome.
These genetic differences between viruses identify the variants and how they relate to each other.
Key Definitions
Mutation: A mutation refers to a single change in a virus’s genome (genetic code). Mutations happen frequently, but only sometimes change the characteristics of the virus.
Lineage: A lineage is a group of closely related viruses with a common ancestor. SARS-CoV-2 has many lineages; all cause COVID-19.
Variant: A variant is a viral genome that may contain one or more mutations. In some cases, a group of variants with similar genetic changes, such as a lineage or group of lineages, may be designated by public health organizations as a Variant of Concern (VOC) or a Variant of Interest (VOI) due to shared attributes and characteristics that may require public health action.
Key Points
- Genetic lineages of SARS-CoV-2 have been emerging and circulating around the world since the beginning of the COVID-19 pandemic.
- SARS-CoV-2 genetic lineages are routinely monitored through epidemiological investigations, virus genetic sequence-based surveillance, and laboratory studies
On November 30, 2021, the U.S. SARS-CoV-2 Interagency Group (SIG) classified Omicron as a Variant of Concern (VOC). This classification was based on the following:
- Detection of cases attributed to Omicron in multiple countries, including among those without travel history
- Transmission and replacement of the Delta variant in South Africa
- The number and locations of substitutions in the spike protein
- Available data for other variants with fewer substitutions in the spike protein that indicate a reduction in neutralization by sera from vaccinated or convalescent individuals
The SIG Variant classification scheme defines four classes of SARS-CoV-2 variants:
Variant Being Monitored (VBM)
Variants designated as VBM include those where data indicates there is a potential or clear impact on approved medical countermeasures or have been associated with more severe disease or increased transmission but are no longer detected, or are circulating at very low levels. These variants do not pose a significant and imminent risk to public health.
- Alpha (B.1.1.7 and Q lineages) Beta (B.1.351 and descendent lineages)
- Gamma (P.1 and descendent lineages) Epsilon (B.1.427 and B.1.429)
- Eta (B.1.525) Iota (B.1.526)
- Kappa (B.1.617.1) 617.3
- Mu (B.1.621, B.1.621.1) Zeta (P.2)
Variant of Interest (VOI) : Currently, no SARS-CoV-2 variants are designated as VOI
Variant of Concern (VOC)
A variant for which there is evidence of an increase in transmissibility, more severe disease (eg increased hospitalizations, deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.
Attributes of a variant of concern:
- Evidence of impact on diagnostics, treatments, or vaccines
- Widespread interference with diagnostic test targets
- Evidence of substantially decreased susceptibility to one or more class of therapies
- Evidence of significantly decreased neutralization by antibodies generated during previous infection or vaccination
- Evidence of reduced vaccine-induced protection from severe disease
- Evidence of increased transmissibility
- Evidence of increased disease severity
Variants of concern typically require one or more public health actions including local and state efforts to control spread, increased testing, plus research to determine the effectiveness of vaccines and treatments against the variant.
Current variants of concern that are being closely monitored and characterized are listed below.
- Delta (B.1.617.2 and AY lineages)
- Omicron (B.1.1.529 and BA lineages)
As of February 2022, omicron variants have been divided into four distinct sublineages: BA.1, BA.1.1, BA.2, and BA.3.
Variant of High Consequence (VOHC) : Currently no variants of high consequence have been identified as VOHC
To help protect yourself and your patients against COVID-19 the following remains recommended:
- Get a COVID-19 vaccine and/or booster.
- Wear a mask.
- Stay 6 feet apart from others.
- Avoid crowds and poorly ventilated indoor spaces.
- Test to prevent spread to others.
- Wash hands often with soap and water. Use hand sanitizer if soap and water not available.
Looking Ahead: Winter’s Twindemic
Australia will soon enter what is potentially the most dangerous phase of the pandemic to date. The coming months will bring a triple respiratory virus threat: Delta, Omicron, and seasonal influenza.
In the northern hemisphere there have been outbreaks of influenza A (H3N2).
For unvaccinated individuals, the winter months represents increased risk for severe illness and death.
For vaccinated persons and especially for those who have been boosted, infections are more likely to be mild and not require medical attention.
Who is being given a fourth vaccine dose?
Most countries offering a fourth vaccine are prioritising people who are immunocompromised. The rationale for these policies is supported by a range of evidence, including from the UK based Octave (Observational Cohort Trial T Cells Antibodies and Vaccine Efficacy in SARS-CoV-2) study, which found that four in 10 people who were clinically vulnerable generated lower concentrations of antibodies than healthy recipients after two doses of a covid-19 vaccine.
Study data from UK, USA and France indicate ~50% patients who had no antibody response after two doses had some kind of response after three doses. This indicates ~25% immunosuppressed patients had no responses after three doses.
What is the evidence for giving four doses?
Israeli studies have noted that antibody concentrations increased fivefold a week after a fourth dose, suggestive of significantly increased protection against infection, hospital admission, and severe symptoms. These findings were based on a small unpublished study of 154 hospital employees who had received a fourth dose of Pfizer’s vaccine.
Similar studies are underway in the UK [Imperial College, London] including the Melody (Mass Evaluation of Lateral Flow Immunoassays in Detecting Antibodies to SARS-CoV-2) study. This is investigating the proportion of immunosuppressed patients who have detectable antibodies after three and four doses of vaccine and assessing whether a lack of an antibody response correlates with the subsequent risk of SARS-CoV-2 infection and severity of disease.
It remains unclear whether a fourth dose may be necessary for people who aren’t immunocompromised. This group are currently being studied for any evidence of additional clinical efficacy eg infection rates , hospital admissions and deaths.