Sub-variants of Omicron replacing Delta in India: Report

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The highly transmissible Omicron with three sub-variants is likely replacing the previously dominant Delta strain in India, pushing the daily tally of Covid-19 cases in the country.

According to the World Health Organization (WHO), the Omicron variant (parent Pango lineage B.1.1.529) includes three descendent lineages (BA.1, BA.2 and BA.3). While BA.1 and BA.3 have the 69-70 deletion in the spike protein, BA.2 does not.

Among the three sub-lineages, scientists at Department of Biotechnology’s Indian SARS-CoV-2 Genomics Consortium (INSACOG) in India have noted the significant presence of both BA.1 and BA.2 in genone tests conducted in the country. BA.1, in particular, has been co-circulating with Delta and also replacing it in Maharashtra and several other states. BA.3 has not been detected so far in the country, media reports said.

First detected in South Africa and Botswana in late November 2021, Omicron has been discovered in more than 100 countries and across all seven continents, as per the open access data sharing platform GISAID.

The unique mix of spike amino acid changes in Omicron (clade GRA, lineage B.1.1.529 and descendants BA.1 and BA.2) comprises several that were previously identified to affect receptor binding and antibody escape.

As the BA.1 and BA.2 sub-variants with and without a deletion in spike and a few other changes respectively are co-circulating, they also complicate the use of PCR tests to diagnose Omicron based on “S-gene target failure” – a marker suggestive of Omicron..

It is because the presence of the 69-70 deletion in the spike protein of BA.1 causes a negative signal for the S gene target in certain PCR assays.

Thus, sequencing for at least a subset of samples, is necessary as this deletion is also found in Alpha and subsets of Gamma and Delta), the WHO has said.

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