Only 137 Covid-19 samples from Karnataka received for sequencing: Union Health Minister Harsh Vardhan in Lok Sabha

Centre has received only 137 Covid-19 samples from Karnataka for genome sequencing till March 10, although the combined capacity of the two labs in Bengaluru, NIMHANS and NCBS-InStem, which are part of INSACOG (Indian SARS-CoV-2 Genomics Consortium) are testing 2,400 samples per month.

This is as per the data tabled by Union Health Minister Harsh Vardhan in the Lok Sabha, in reply to a question, on March 19.

As per the guidance document of the Union health ministry for INSACOG, NIMHANS' capacity to sequence total Covid-19 samples is 1,200, but the total number of samples sequenced from January to March 18, 2021, is 122 as per the National Centre for Disease Control.

Similarly, though NCBS-InStem's capacity to sequence samples per month is 1,200, only 183 have been sequenced so far as per the institute. This despite the two labs tasked with sequencing not just Karnataka's samples, but those from Tamil Nadu and Puducherry too.

Also read: India sees over 62,000 Covid-19 cases for second straight day in the highest daily spike so far this year

From Puducherry, five samples were received for sequencing and from Tamil Nadu 102, till March 10, as per Harsh Vardhan's reply. The reply makes it clear that the labs are still running on their own funds. No money has been received from the Ministry of Science and Technology yet.

As per the guidance document, the plan was to start sentinel surveillance, where 5% of samples testing positive every day was supposed to be sequenced. But the state is far from it.

For example, on Wednesday, 2,298 coronavirus cases were reported in the state (5% of this is 115 samples). Bengaluru's 11,520 active Covid-19 cases have put it on the list of 10 districts in India with the most number of active cases. Nine of the districts are from Maharashtra.

Eminent virologist Dr Shahid Jameel, chair of INSACOG, told DH, "One of the bottlenecks is that all the reagents required for sequencing have to be imported. The stock is not as much as we expect. Everything requires money and logistics."

On the under-utilisation of the labs' capacity, he said, "Not enough samples are being sent to the labs. There is no backlog at the labs. Many times, officers on the ground don't send samples or don't send samples with the suitable Ct values," he said.

"The required funds have already been sanctioned by the Department of Biotechnology. The final approval is expected from the Science Ministry any time now," he said.

Prof Satyajit Mayor, Director of National Centre for Biological Sciences (NCBS), Bengaluru, echoed the statement and said importing reagents was a problem.

Rs 10,000 per sample

"It costs Rs.10,000 to sequence a sample," he said, adding that the institutional funds are currently being used for sequencing.

Dr Uma Ramakrishnan, a professor at NCBS, said, "If we get more samples, we can sequence more. We are sequencing samples of international travellers and not prioritising clusters. We have sequenced the high-priority samples that we have received so far. We are working with other labs that have a high load so that they can redirect the samples to us when necessary."