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‘Presume all RT-PCR-positive cases are Omicron’

Genome sequencing reports delayed because sequencing is done in batches of 24, 96, or 384 samples

Recently, four girls from a cluster of 14 cases at a residential school in Dakshina Kannada were found to have been infected with Omicron. While the cluster was identified in November, the variant of infection being Omicron was confirmed about a month later, when all the four girls had recovered.

Similarly, the 46-year-old government doctor without any travel history, India’s second Omicron case, was detected with Omicron ten days after he tested positive for COVID. His three colleagues, who were his primary contacts, left the dedicated Omicron facility at Bowring and Lady Curzon Medical College and Research Institute in desperation as although they had tested negative twice their genome reports had not arrived.

With genome sequencing reports – that are key to identifying the Omicron variant – getting delayed invariably, experts said that every positive case should be presumed as Omicron and appropriate precautions should be taken.

C.N. Manjunath, nodal officer for labs and testing in the State’s COVID-19 task force, said irrespective of the variant the infection is COVID-19. “In the wake of the high transmissibility of Omicron, it is important that every positive case should be presumed as Omicron and appropriate precautions should be taken from the public perspective,” he said.

“Although institutional quarantine is mandatory for all Omicron cases, those who test RT-PCR positive for COVID-19 should be immediately isolated and their contacts should be tested without any delay. If their genome sequencing reports return positive, they can be shifted to a hospital if required,” he said.

M.K. Sudarshan, chairman of the State’s COVID-19 Technical Advisory Committee (TAC), said all international travellers, especially from high-risk countries, who test RT-PCR positive should be presumed as suspected Omicron cases and isolated and treated, pending genomic confirmation. “Even if their genome reports get delayed, the risk of transmission is cut because they were isolated immediately. As the treatment protocols for COVID-19 of any variant remain the same, early isolation and intervention will help in quick recovery too,” he said.

“Besides, all positive cases from clusters who present classical COVID-19 symptoms and CT values of less than 25 should also be presumed as suspected Omicron cases and treated,” he said.

He said the TAC has recommended that the State should start using S-gene target failure (SGTF) test kits at the Bowring Hospital for probable diagnosis of Omicron.

“The TaqPath ‘S’ gene COVID-19 diagnostic kit by Thermo Fisher should be procured in this hospital that has been designated as a dedicated Omicron facility. The Thermo Fisher TaqPath assay can be used as a proxy test for detecting the new variant, pending confirmation by genome sequencing,” Dr Sudarshan said.

Why the delay?

V. Ravi, nodal officer for genomic confirmation of SARS-CoV-2 in Karnataka who also heads the State Genomic Surveillance committee, said genome sequencing reports are delayed because sequencing has to be done in batches of 24, 96, or 384 samples. “Genome sequencing is highly resource-intensive and expensive. This is why you cannot test every single sample as and when each comes. Testing 384 samples on one sequencing chip costs around ₹10,000 per sample. The cost is higher when the number of samples is lower,” he said.

“We have to wait for enough samples to be collected to do the sequencing. Further, only samples with a CT value less than 25 can be used for genome sequencing. If the value is higher, it is tougher to get the full gene sequence, which compromises the accuracy of results. While the process of gene sequencing takes up to 12 hours, the subsequent analysis and manual confirmation takes 3-4 days,” he explained.

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