The Karnataka government will send samples of all COVID-19 patients with a cycle threshold (Ct) value less than 25, for genome sequence to detect the presence of the Omicron variant of the coronavirus. Cycle threshold (Ct) value indicates the viral load in a patient infected with SARS-CoV-2. A low Ct value means that it took fewer cycles of the test to detect the virus, which, in turn, means that there is a high amount of the virus present in the sample. "All samples with a Ct value less than 25 are being sent for genome sequencing from this week. Our daily caseload is around 200-300 cases and we want to send 80% of these cases for genome sequencing," Randeep D, Commissioner, Health and Family Welfare Department, told TNM.
Previously, samples of international travellers from 'high-risk countries' and samples from known clusters of COVID-19 cases were prioritised for genome sequencing and detecting the presence of the Omicron variant of the virus. The decision to expand the testing to detect the Omicron variant in Karnataka was taken since the state has detected 19 cases of the Omicron variant so far. It was also observed that the testing is usually done in large batches of up to 384 samples at once.
According to health experts, genome sequencing is currently the only way to detect if a COVID-19 patient contracted the disease from the Omicron variant. It is both a resource-intensive and expensive form of testing.
Dr V Ravi, retired head of virology from NIMHANS, Bengaluru and the present member of the INSACOG (Indian SARS-CoV-2 Genomics Consortium) Steering Committee as a representative of the Ministry of Health and Family Welfare (MoHFW), had earlier told TNM that genome sequencing is done in batches of 24, 96 or 384 and that it costs relatively lesser to do it in larger batches. The process of genome sequencing itself takes up to 12 hours, while the analysis and confirmation of the variant take at least three to four days. With practical delays considered, this process could take up to a week.
In Karnataka, when the Omicron variant was confirmed in a cluster of cases in a residential school in Bantwal, Dakshina Kannada, on December 18, it was detected almost a month after the cases were reported on November 22. This was because the samples were sent for genome sequencing only in the first week of December as the patients, who were school-going girls aged between 13 and 14, had no known history of international travel.
The children reported symptoms of fever and loss of taste and smell, something that was not observed previously among patients with the Omicron variant. District officials were initially worried about the cluster of cases, especially given that they were all unvaccinated. But they now say that the patients have now made a full recovery from the virus. "All of the students who tested positive have recovered. We have also not found any more COVID-19 cases after testing everyone at the school," says Dr Jagdish, district surveillance officer, Dakshina Kannada.
The cases were detected when health officials in Dakshina Kannada found a number of students in the school showing symptoms of the coronavirus in the third week of November, just days after they had returned to school on November 8. "A number of students were showing symptoms so we tested the students. We detected 13 COVID-19 cases in the school on November 22 itself but it was only in the first week of December that these samples were sent for genome sequencing," says Dr Jagdish.
This was one of two clusters with Omicron variant cases that were detected in educational institutions in Dakshina Kannada, with the other being in a college in Mangaluru.
The Omicron variant of the virus has been detected in six districts in the state so far — Bengaluru (8), Dakshina Kannada (6), Udupi (2), Belagavi, Shivamogga, Dharwad (one each). Only five cases in Bengaluru and the lone case in Belagavi had a history of international travel while the other cases detected in the state had no history of international travel or known contact with foreign-returned persons.
The Karnataka government has also decided to restrict New Year's eve celebrations in the state in the wake of the cases of the Omicron variant. Restaurants, bars and clubs will operate at 50% capacity while mass gatherings and special events like parties will be prohibited from December 30 to January 2, Karnataka Chief Minister Basavaraj Bommai said on Tuesday, December 21.
Meanwhile, health officials in the state say that there are now efforts to speed up the genome sequencing process and it is now expected to take 4-7 days to detect the presence of the Omicron variant. "We are now seeing a turnaround time of 4-7 days for the detection of Omicron variant cases. The time gap for this is improving," added Randeep D, Health Commissioner.