From samples to kits, experts explain why genomic sequencing takes time

From samples to kits, experts explain why genomic sequencing takes time

Sunitha.Rao@timesgroup.com

Bengaluru:19.12.2021

Genomic sequencing reports are key to identifying the Omicron variant. But due to several factors, sequencing is taking a minimum of 5-8 days and the delay in results is leaving everyone, including patients and hospitals, on the edge.

This situation was discussed at a recent meeting with chief minister Basavaraj Bommai as most Covid-infected persons are recovering by the time genomic sequencing results are out. STOI takes a look at why the process is slow.

The sequencer requires over 300 samples to initiate the process, but only under 100 are sent in a day. Hence, sequencing is done once in three days. According to virologist Dr V Ravi, state nodal officer and chairman, committee for Covid-19 whole genome sequencing, one needs to understand that the sequencing is not like RT-PCR test and not all Covid-positive samples are suitable for it.

He said only Covid-positive swab samples with Cycle Threshold (CT) value below 25 qualify for genomic sequencing, as the viral load will be more in those with low CT value. The value indicates the number of cycles in RTPCR test needed to amplify viral RNA to reach a detectable level. Currently, with less than 400 cases a day, just about 10-12 samples would have CT value less than 25, he said.

Dr Ravi said the chips used in the process require either 100 samples or over 300 at a time for the sequencing to be done. “The cost of the chip is Rs 2.5 lakh. The cost remains the same whether there are 10 samples or over 300. The situation here is not like that of the UK, where 80,000 persons are turning positive every day,” he said.

Agreeing with Dr Ravi, another technical advisory committee member said genomic sequencing is like running an aircraft. “For an aircraft with a capacity of carrying 300 passengers, the cost remains the same irrespective of whether it has 10 or 300 on board. If there aren’t enough samples, we will have to wait for them to accumulate. The government will only reimburse the cost of samples sequenced and not for running the entire process with fewer samples,” a TAC member explained.

The purpose of sequencing is to detect a new variant, which two labs in Karnataka have been doing successfully, said Dr Ravi. “On November 26, Omicron was declared as a variant of concern. On November 30, Karnataka was the first to detect Omicron (though it was later announced on December 3 after verification),” he added. Stating that the state’s labs were at the forefront in detecting Alpha and Delta variants earlier, Dr Ravi said a resource-intensive method like sequencing should not be used for every sample.

Dr Ravi said irrespective of the variants, the treatment remains the same for Covid patients, but that Omicron cases need to be hospitalised and can be discharged only after they test negative to prevent community spread.

Prof Satyajit Mayor, director, National Centre for Biological Sciences, said sequencing is not a trivial affair. “We have to wait till we have 300 samples. It takes a week’s time to put out the results and we are doing our best,” he said.

Genomic sequencing was temporarily halted for at least a week at Nimhans owing to global shortage of kits. Dr Ravi said the institute lab has procured them now.

According to the health and family welfare department, there is no delay in genomic sequencing. “The reports are available within 5-8 days,” said Randeep D, commissioner of the department.

DOING THE NEEDFUL: A worker collects a swab sample at a bus stand. (Left) Marshals fine those flouting mask rule

The process of sequencing takes 12 hours. After that data is fed into the computer for analysis and this takes three days. One has to manually check the sequence and see that the computer hasn’t made a mistake. This takes a total of five days

Dr V Ravi CHAIRMAN, COMMITTEE FOR COVID-19 WHOLE

GENOME SEQUENCING

The sequencer requires over 300 samples to initiate the process, but only under 100 are sent in a day. Hence, genomic sequencing is done once in three days