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The stealth Omicron variant: BA.2

28 Jan 2022

  By Prof. Suranjith L Seneviratne and Buddhika Samaraweera So far the World Health organisation (WHO) has identified four lineages of the Omicron SARS-CoV-2 variant. These are B.1.1.529, BA.1, BA.2 and BA.3 respectively. What is BA.2? BA.2 is a sub-variant of the original Omicron strain and was first classified in the Pangolin database on 06th December 2022. The two omicron sub lineages BA.1 and BA.2 are sister clades. BA.2 differs from BA.1 by around 20 mutations. They split from each other several months ago and one is not derived from the other. BA.2 has been designated as a variant under investigation (VUI) by the UK Health Security Agency (UKHSA). The WHO has so far not given any special variant designation to it. BA.2 has been referred to as the stealth Omicron variant. Some SARS-CoV-2 variants of concern (such as Alpha and Omicron - B.1.1.529) produce a negative S-gene result in some multiplex Real time Polymerase chain reaction (RT-PCR) assays (such as the Thermo Fisher TaqPath assay). This phenomenon is called S-gene target failure (SGTF). This characteristic has been used as a screening method to identify the BA.1 and Alpha variants of SARS-CoV-2. The failure of the S-gene target is caused by a deletion of amino acids 69 and 70 within the spike (S) gene of SARS-CoV-2. The BA.2 sub-variant does not carry the 69-70 deletion and would thus not be identified by SGTF assays. Although, there is SGTF in BA.1, this is not seen with BA.2. Thus, the SGTF short cut cannot be used with BA.2. However, it needs to be remembered that BA.2 samples would still test positive on SARS-CoV-2 PCR testing, but would need genetic sequencing to be further identified as the BA.2 sub-variant. Where is it found? The first sequence of the BA.2 sub-variant was submitted to a global coronavirus data sharing platform by the Philippines in November 2021. Since then, over 15,000 sequences of BA.2 have been uploaded and currently it has been detected in over 40 countries. Denmark has so far recorded the highest number. We need to remember that Denmark has a high rate of viral genome sequencing and this may account for the high numbers noted here. Presently, BA.2 has become the dominant SARS-CoV-2 stain in Denmark. Some of the other countries with BA.2 includes: India, Norway, Sweden, Singapore, the UK and USA. In the UK, between 08th and 15th January 2021, the proportion of BA.2 cases increased from 0.2 to 0.8 percent and the majority of cases were from London and the South East. What are its effects? There are many ongoing studies comparing the characteristics of BA.2 and BA.1 with regards its transmissibility, virulence and immune escape. There is some indication that it is more transmissible. This is especially so for unvaccinated individuals. According to initial information from Denmark, there is no difference in rates of hospitalisation between BA.2 and BA.1. It is still expected that vaccines have a protective effect against severe illness from BA.2. Those infected with one of the sub-lineages should have good immunity against the others. Conclusions It is a characteristic of viruses to evolve and mutate. Thus the expectation is that new variants would continue to emerge. The detection of SARS-CoV-2 sub-variants is not new. The Delta variant also had several sub-variants, but all of them were referred to as Delta. BA.2 earned its own designation due to the detection of high numbers across several countries. At the present time, it remains unclear if BA.2 would behave differently to BA.1. However, early indicators point to many similarities. Further clarity would be possible as more cases are reported from the affected countries.

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