No genomic sequencing in state after June despite new Covid variants

Karnataka has not conducted any genomic sequencing of Covid cases in July and August, despite concerns being raised globally about newer variants.

On Monday, the Centre instructed states to ramp up both testing and whole genomic sequencing (WGS) in view of the Omicron sub-variants EG.5 and BA.2.86, that WHO has respectively declared as a ‘variant of interest’ and ‘variant under monitoring’.

Data on these variants is still only emerging, but they are noted for high transmissibility, but lesser likelihood of hospitalisation. Without WGS, it is won’t be clear, if these are circulating in Karnataka.

Currently, most government and private hospitals are not testing patients for Covid.

“There are no guidelines for testing ILI/SARI patients now. We test only those who are very sick or who have tested negative for flu,” says Dr Rajat Athreya, pediatrician at a private hospital and member of the state’s Covid Technical Adivsory Committee.

A paediatrician at Bangalore Medical College says they were not suggesting Covid tests as treatment course would be the same in all fever cases, and that testing in complicated cases had also stopped.

Dr Shariff, deputy director, National Vector Borne Disease Control Programme), says WGS was not done as only 10-15 samples fit for sequencing (with CT value below 25) were identified since July.

“As per central government’s guidelines, WGS should be done when there are at least 50 samples,” he says. “We have been doing close to 2,000 tests per day, but positive cases are in single digits, and samples fit for WGS are even fewer.”

As per the department’s bulletin of August 21, the state had only 15 positive cases over the previous week, all of which were from Bengaluru Urban district.

Health commissioner D Randeep acknowledges that reduced testing was a reason for fewer samples being available for genomic sequencing.

“With the spike in respiratory infections over the past couple of months, our testing should have been higher. Around 500 of the 2,000 daily tests are being done in Bengaluru Urban and Rural alone. Some districts are testing in single digits only, and we have asked the district health officers to increase the numbers.”

For example, on August 21, Kodagu and Vijayanagara districts had conducted zero tests, and Raichur and Chikkamagaluru had conducted one test each. Except five districts, all others had done fewer than 100 tests. Randeep says the target is to touch 5,000 daily tests next week, and 8,000-10,000 later.