Omicron variant: Kerala prioritizes genome sequencing of international travellers' samples


Representational image | Photo: AP

Kozhikode: Amid reports on Omicron variant of Covid-19, health department in the state has prioritized genome sequencing and analysis of samples of international travellers, from high-risk countries, who turn positive for Covid-19. Sequencing and analysis help in identifying mutations and variants.

According to a top official at Directorate of Health Services, the sentinel samples of international travellers from high-risk countries who turn positive for Covid-19 in the 11 selected labs will be sent to Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, as part of sentinel surveillance.

“Genome sequencing and analysing is an ongoing process. We are doing it since a long time. There are 11 selected labs in the state which sent sentinel samples of Covid-19 positive cases to RGCB for analysis and sequencing. Each lab will send 30 samples in a month. In the wake of reports on Omicron variant, we have directed those labs to prioritize the samples of international travellers from high risk countries who turn positive for Covid-19,” said the official. Apart from that, labs conducting RT-PCR tests in the state are sending 100 Covid-19 samples to Council of Scientific and Industrial Research–Institute of Genomics and Integrative Biology (CSIR–IGIB), New Delhi, added the official.

However, the official pointed out that only those positive cases in which Ct value* is less than 25, will be sent to RGCB. (*Ct value or cycle threshold is the number of cycles required to detect the virus. Lower Ct value suggests higher viral load).

Meanwhile, according to Dr T Jacob John, an eminent virologist and former director of the ICMR’s Centre of Advanced Research in Virology, the decision to prioritize genome sequencing and analysis of Covid-19 positive cases among international travellers from high-risk countries is a good choice for quickly identifying the presence of new variant. But he pointed out that it would be better to sequence all positive cases to rule out the probable chance of the variant presence in general population.

“Whether we have to take a chance is the question. Omicron variant was first confirmed based on the specimen collected on November 9 in South Africa. It was reported to WHO on November 24. WHO announced it as a variant of concern on November 26. We can see that there was a huge gap for the virus to spread globally in that period between November 9 and November 26 itself. Or even before that. So it would be better to sequence and analyse all Covid-19 positive cases for at least 5 to 10 days in the state. I am aware of the practical difficulty. And it will be a policy level matter. Not just in Kerala, all states should take that call. Otherwise we cannot rule out variant without confidence and it would take another community spread to identify the variant. Even then it will not be easy to identify the source which in turn make containment difficult,” he said.

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