Pvt labs try to procure RT-PCR kits which can spot Omicron variant

Pvt labs try to procure RT-PCR kits which can spot Omicron variant

Sunitha.Rao@timesgroup.com

Bengaluru:05.12.2021

Private labs in the city have been trying to procure RT-PCR test kits targeting the S gene, following concerns over the Omicron variant.

Currently available RTPCR kits can detect Covid-19 positivity in a person, but can’t specifically say if it is Omicron or some other variant, say experts.

Testing kits look for specific genes to confirm the presence of SARS-Co-V2 in a sample. While N gene points to the presence or absence of the nucleocapsid protein of SARS-Co-V2 in a given swab sample, the ORF1 gene searches for the polyprotein. Mutations in the latest variant — B.1.1529 — have occurred in the S gene that encodes the spike glycoprotein. If a sample is negative for S gene, then it is an indicative marker of the presence of Omicron variant, which needs to be further confirmed through genomic sequencing.

Dr Sujay Prasad, medical director, Neuberg Diagnostics, said conventional Covid RT-PCR test kits in use at present have reagents that detect the presence of N and ORF1 genes, but not the S gene.

“It is now established that the Omicron variant escapes the S gene. But RT-PCR testing kits that we have now don’t contain the reagent for S gene. If the test shows negative for the presence of S gene in a given sample, it is an indicator that the person may have been infected by the Omicron variant,” said Dr Prasad.

“We need to find out if a given sample shows negative or positive for S gene. If negative, such samples must be immediately sent for genomic sequencing,” said Prasad.

Dr HM Venkatappa, chairman of Bangalore Diagnostics Centres’ Association, said labs will now have to procure test kits with S gene. “We are in the process of finding out test kits that help us in early identification of the Omicron variant. But if we use the new kits, the government’s price cap of Rs 800 at private labs and hospitals can’t be adhered to...,” he said.

‘Genomic sequencing can point to specific strain’

Dr CN Manjunath, nodal officer for Covid testing, said the currently available kits are good enough to detect viral positivity in a patient and it is genomic sequencing that can point to the specific variant.

Only one testing kit produced by Thermo Fisher has a Covid-19 diagnostic product with S gene detection, which is being highly sought after by private laboratories now.

Some of the government laboratories in Karnataka are using the kit, where swab samples of vulnerable persons from clusters and those of international passengers are being tested.

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A marketing gimmick: Virologist

Dr V Ravi, virologist and member, Technical Advisory Committee, said all RT-PCR test kits are spike-gene independent and variantproof. “We have been detecting Delta, which has so many mutations in the spike protein. Nobody raised these issues then. It’s more of a marketing gimmick. Indian kits are not missing Omicron. However, if any cluster shows the variant, we should think of replacing the testing kits. Ultimate proof will come from genomic sequencing,” he said.