‘Stealth’ Omicron raises fear in Telangana

TS reported 90 cases of BA.2, the newly-identified sub-lineage of the variant

Hyderabad: Telangana is among the top four Indian States from where a large number of Covid positive infections with the latest version of the Omicron variant have been reported. Based on the genome sequencing data available with GISAID, the global platform to share genomic data of influenza viruses, between December 27, 2021, and January 5, 2022, a total of 90 samples from individuals had tested positive for BA.2, the newly-identified sub-lineage of the Omicron variant.

During the same time frame, Maharashtra had 155 cases, New Delhi had 129 and Gujarat had 128 cases of BA.2 sub-lineage of the Omicron variant. Although the dominant Omicron variant continues to be BA.1, the fact that Telangana has substantially more infections originating due to the new BA.2 lineage could be a cause for concern, public health officials here fear.

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The BA.2 is a sister lineage of the previous BA.1 and at present both these lineages are defined as the Omicron variant. In the past few months, the genome scientists were able to identify BA.1 lineage of the Omicron variant but were unable to identify BA.2, and that’s why it is often described as the ‘stealth variant’.

The new sub-lineage BA.2 shares all existing 32 mutations of BA.1 and also has 28 unique mutations, a major reason why it has raised a lot of concerns among public health officials and genetic researchers. Based on reports from multiple genetic researchers, the BA.2 is a major Omicron lineage in India and the Philippines and there is enough evidence that it is rising exponentially in Denmark, the United Kingdom and even Germany.

The steady growth of BA.2 in multiple countries could be an indication that it is far more transmissible than the earlier Omicron variant. Senior public health officials here who are closely tracking the genome sequencing of Omicron pointed out that due to the lack of much research, very little is known about the nature of the BA.2 when compared to the earlier BA.1.

Due to the rapid rise of number of patients infected by this particular sub-lineage of the Omicron variant, the UK has declared BA.2 as a variant under investigation. Apart from India, the new variant has also been found in Denmark, Sweden, the Philippines, France, Norway and Singapore.

“BA.2 lineage is a substantial fraction in India and S gene dropout based screening is thus likely to give high false negatives. Tests suitable for PCR based screening applicable to all Omicron lineages have been approved for use. While most Omicron cases so far have been asymptomatic or mild, hospitalisations and ICU cases have been increasing in the current wave,” INSACOG, the Indian SARS-CoV-2, Genomics Consortium (INSACOG), said.

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