Following the rise in COVID-19 cases and the wake of the detection of a new variant of interest — JN.1 — in the neighbouring States, all eyes are now set on whole genome sequencing (WGS) of positive samples. However, the laboratory at Bangalore Medical College and Research Institute (BMCRI), the State’s nodal WGS facility, is yet to resume the process of isolating the strain.
This is because the laboratory has neither received the required number of eligible samples — those with a Cycle Threshold (CT) value of less than 30 — nor has the human resources and consumables required for sequencing, in the event of a surge. “We need a minimum of 50 samples for one run. We have been sending whatever samples we get to the National Institute of Virology (NIV), Pune,” said a doctor from the laboratory that is one of the INSACOG (The Indian SARS-CoV-2 Genomics Consortium) approved government facilities.
With hardly any COVID cases being reported in the last eight months, genome sequencing — aimed at hunting new mutant strains of SARS-CoV-2 virus — had come to a standstill in the State. However, now with a new mutant strain being detected in some States, focus is again on genome sequencing.
Human resources
Sources in BMCRI said previously the laboratory was running with contractual staff. “In the absence of COVID cases, the necessity of renewing their contract did not arise. If we have to restart genome sequencing, we need consumables such as sequencing kits and reagents apart from manpower including a research scientist, research assistant, technician and data entry operator. We have submitted a requisition to our Dean and Director,” said a senior doctor from the laboratory.
Confirming that he has received a requisition, Ramesh Krishna K., BMCRI Dean and Director, said that the requirements would be provided at the earliest. “However, if there are an adequate number of eligible samples, sequencing can be done using staff from the Virus Research and Diagnostic Laboratory (VRDL) where RTPCR tests are done,” he said.
Sources said the issue was discussed at Sunday’s Technical Advisory Committee (TAC) meeting following which the requisition has been submitted to BMCRI Dean.
Top priority
V. Ravi, former nodal officer for genomic confirmation of SARS-CoV-2, said WGS is very crucial to identify new circulating strains and check the spread. “Eligible samples will start coming in once testing is ramped up. Even asymptomatic persons can have a low CT value and can be detected through RT-PCR tests,” he said.
Underlining the importance of WGS, U.S. Vishal Rao, member of the State’s Genomic Surveillance Committee and Dean, Centre for Academic Research at HCG Cancer Centre, said genome sequencing needs to be a top priority for Karnataka at this point.
“In case the test positivity rate crosses 5%, we would need to further ramp up genomic surveillance. It is at that time we will be seeing some of the true manifestations of the clinical outcomes which is what other countries have been talking about in terms of severity or death. WGS will help us keep an eye on the changing strains, the clinical symptoms and correlate them better,” he added.
