Omicron Replaces Delta In Odisha: Know About Its 'Stealth' Version Detected In Many States

It is official now. Community transmission of the super spreader variant Omicron is rapidly on in Odisha. The whole-genome sequencing data of only around 3 percent of the 7-day positives in the State during the period Jan 9-16 reveals big.

In just a week's time, the Omicron sequenced genomes in the State have more than doubled. From a mere 67 Omicron positives from the samples collected and sequenced between the period Dec 29 and Jan 9, the tally today shot up by a massive 116 percent to touch 145 Omicron sequenced genomes during the period Jan 10 to 16.

The speed of spread is nailed by the fact that when 67 sequenced genomes were Omicron out of 263 samples sequenced in the Institute of Life Sciences, Bhubaneswar, on Wednesday, out of 249 samples, 147 sequenced genomes nail the Omicron variant.

Simply put, when in December last and January 1st week, 2 in every 10 samples sequenced were Omicron genome, by mid-Jan, nearly 6 (5.8) in every 10 genomes sequenced confirm the super mutant variant.

The above number crunching reveals that in a span of 19-days, Omicron spread nearly 3-times faster in the State. The variant's genome has grown to nearly 6 from a mere 2.5 in the State.

Omicron Dominance  

As per the ILS whole-genome sequencing data, the new variant of concern has replaced the Delta variant in the State. The results released today clearly indicate so.

While Odisha samples have largely displayed the gene of Omicron and its sub-lineage BA.1, the data from Gujarat reveals the presence of 9 percent BA.2 lineage.

The data with INSACOG further reveals that Omicron and its sub-lineages (BA.1 and BA.2) now occupy 67 percent of the genomes sequenced in the country.

What Is BA.1 And BA.2?

Both the sub-lineages carry almost all the spike RBD (Receptor Binding Domain) mutations first noted for Omicron and both furin cleavage adjacent mutations. They both have the NSP6 deletion seen in other Variant Of Concerns.

However, the new sub-lineage BA.2 does not carry the spike 69/70 deletion and will thus not be detectable by SGTF (S-gene target failure). For which, the new lineage is being labelled as “stealth” Omicron by some scientists.

Scientists are yet to reach any confirmative conclusions regarding exactly the impact of unique mutations in BA.2 on its transmissibility and virulence.

Will Omisure Detect BA.2?

With the first lot of 50 k Omicure test kits having reached Odisha, the moot point is while it will in 4-hours time detect whether an individual is Omicron positive or negative, will it nail the "stealth Omicron"?.

Or, whole-genome sequencing is the only way to trace this 'stealthy' sub-lineage.

Will It Duck?

Omisure is basically an RT-PCR kit. It is developed by the Mumbai-based Tata Medical and Diagnostics Ltd (TATA MD) in collaboration with the Indian Council of Medical Research (ICMR). 

As per the kit developers, this new kit is designed to identify the Omicron variant by zeroing on two regions of the S - the spike gene.

RT-PCR tests in the lab target the S, the Enveloped (E), and Nucleocapsid (N) genes to identify the presence of SARS-CoV-2 in human cells. The test usually shows positive for all the above genes when a patient's sample tests positive.

But since Omicron has undergone largescale mutations in the S gene, the RT-PCR miss it out and shows negative. Though based on E and N positive, RTPCR tests declare an individual Covid positive, it still will show S negative (S gene is Unique to SARS-CoV2).

Since Omicron has S-gene mutations and deletions, the S-gene drop out or say SGTF (S-Gene Target Failure) has been labelled as Omicron positive.

However, as far as BA.2 is concerned, RT-PCR reports S-gene positive. The sample then needs genome sequencing to confirm the presence of Omicron.

But as per the claim by the Omisure developers, this kit can nail the 'stealth' version via the S gene mutation amplification.