Dr.Sujeet Kumar Singh, director of the National Centre for Disease Control, announced in the weekly press conference that the country is witnessing a surge of BA.2 variant cases of COVID-19 in the samples that were sequenced. A subtype of the currently predominant Omicron, the subtype has 20 additional mutations and can also spread easily. It is being identified as 'stealth Omicron'.
The INSACOG- a consortium of 38 laboratories that are conducting the sequencing have found that the number of samples of BA.2 are now increasing steadily across the country. The World Health Organisation also agrees with this finding that BA.2- one of the three sub-lineages of the Omicron virus, is now replacing its predecessor BA.1 across Europe and Asia.
According to India's genomic data updated on GISAID, a global genome sequence repository, the BA.2 sub-lineage prevalent across Delhi, Gujarat, Uttarakhand, and Karnataka is rapidly replacing Delta and BA.1 as the most transmissible variant of SARS-CoV-2. In fact, Delta is only being found circulating in pockets of Maharashtra, Dr. Sujeet Kumar Singh shared in the press conference on Thursday, January 27.
While Omicron has been classified as a variant of concern by the WHO, the sub-lineage that is slowly increasing in number has received its own unique classification. On January 21, The United Kingdom classified BA.2 as a variant of interest as its numbers have been rising within the country.
Maria Van Kerkove, the COVID-19 technical head at the WHO also tweeted about the WHO being aware of all the three sub-lineages of Omicron- BA.1, BA.2, and BA.3 circulating across the world. She mentioned that as of January 24th, BA.1 continued to be a variant of concern, but independent studies would need to be prioritised to understand the transmissibility of BA.2 as well as observe whether it escapes immunity driven by the existing vaccines. She also noted that this variant was spreading faster in different countries.
Why Is BA.2 Called Stealth Omicron?
A sub-lineage of Omicron, BA.2 has the mutations seen in the predominantly prevalent BA.1 predecessor but also has its own set of unique variants. Additionally, the BA.1 sub-type could be identified through the RT-PCR tests.
While testing, if a person's positive sample did not code for a specific S gene, it was a preliminary deduction that the person was suffering from Omicron without necessarily needing the sample to undergo genomic sequencing. However, that is not the case with the BA.2 variant.
The S- gene is not dropped in a positive sample of BA.2, making it difficult to distinguish whether the person is infected with the Omicron variant or any of the other existing variants. BA.2 can only be deduced through genomic sequencing.
Currently, the BA.2 sub-type is seen in over 44 countries. Denmark has the highest number of BA.2 sequenced cases followed by India. Hong Kong that had managed to keep the delta variant dormant and under control has now reported an outbreak of 200 cases of BA.2.
Dr. T. Jacob John, eminent virologist, told BOOM that the source of this new sub-lineage is most likely humans. "The omicron variant most likely emerged from a non-human source or an immunocompromised person. If it entered from a non-human source, it is bound to further mutate. The BA.2 sub-lineage is assisting in driving the wave."