The Omicron variant of the Coronavirus, which is ringing alarm bells across the world, was first identified in South Africa through genome surveillance just over a week ago. The first sample containing the mutation was identified in a specimen collected on November 9, according to the World Health Organisation (WHO).

As genomic sequencing continues for the variant to identify all its mutations, Omicron has already spread to over 20 countries. Countries have been imposing restrictions on travellers from South Africa, while some others have also revised travel protocols for countries that have been reporting cases of the Omicron variant.

Nations are using genomic sequencing to see if the S-gene is missing from the SARS CoV-2 sample to ascertain the presence of Omicron.

What is genomic sequencing?

Genomic sequencing is a scientific process through which scientists determine the entire genetic mak-eup of a specific organism or cell type. Through genomic sequencing, the changes in the genetic make-up of the SARS CoV-2 virus can be noted and monitored. Genomic sequencing helps scientists in identifying the parts of the genetic material of the virus that has mutated. It is through this process that Omicron’s over 50 mutations were noticed.

The main parts of the genetic material of the SARS CoV-2 virus include the ORF1a protein, the ORF1b protein, the spike protein, and other smaller gene pieces like the E, N, M and Rd Rp genes.

“Different variants mean that there have been mutations in one or more of the genes. The previous mutants may also have a couple of mutations, but in Omicron a very large number of mutations have occurred -- nearly 50 mutations -- and out of these, nearly 30 are in the spike protein," Dr Naveen Dang, Director of Dr Dangs Lab, was quoted as saying by news agency ANI.

What is the missing S-gene target?

The Omicron variant was first identified in South Africa after scientists found that one of the probes of the RT-PCR tests was failing in a particularly mutated sample, an effect that was replicated in many other samples. This was the Omicron variant. Due to mutation on the spike protein, some of the amino acids (that combine to form protein) were missing on the spike protein of the virus. This deletion would lead to the S-gene target going missing on the virus. While RT-PCR tests would still be effective in identifying cases of COVID-19, the missing S-gene target could be used as a proxy to identify cases of the Omicron variant.

“The S-Gene dropout, or as we say the S-Gene target failure or SGTF, is one of the proxy indicators to (ascertain) whether or not it is the Omicron variant. But this is not necessarily so as the ultimate diagnostic tool is distinct for gene mutation," said Dr Dang.

“So, if there is a patient who is suspected (to be infected) with Omicron, the ultimate diagnosis relies on testing but testing for the mutations that are called gene sequencing," he added.

But the missing S-gene target can only be a proxy for Omicron detection since other variants like the B.1.1.7 or Alpha variant of the virus also have a missing S-gene target. The only way to confirm the presence of the Omicron variant is to test the sample against existing genetic samples.

(Edited by : Thomas Abraham)

First Published:Dec 2, 2021 5:50 PM IST