COVID-19: All eyes on genome sequencing of positive samples

With the government deciding to do genome sequencing of samples of U.K. returnees who test positive for COVID-19, all eyes are now set on this process aimed at hunting the mutant strain of SARS-CoV-2 virus.

According to virologists from NIMHANS where the genetic sequencing is being done, it will take a maximum of four days for the sequencing and subsequent analysis of the samples. In this context, the results of the 10 positive cases are likely to be known by Monday.

Explaining the process of the sequencing, V. Ravi, former professor and head of the department of neurovirology at NIMHANS, who is also part of the State’s COVID-19 Technical Advisory Committee (TAC), said that it is a technique used to break down genetic code of any DNA.

“Genomic sequencing involves extracting and isolating the RNA from the sample, converting it into a DNA sequence and amplifying to a large enough size to start analysis,” he said.

“After extracting the RNA of the SARS-CoV-2 virus , it is converted into cDNA (complementary DNA synthesised from a single-stranded RNA template). Then multiple Polymerase Chain Reactions (PCR) are done on the cDNA. PCR is a method used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail. This is unlike a diagnostic PCR,” he explained.

Following this procedure, the product is cleaned up and put into a chip that will do the sequencing. This will take anywhere between 12 hours to 48 hours depending on how much material was there in the original specimen.

Also, the cycle threshold (CT) value, which indicates the number of cycles needed in the RT-PCR test to amplify viral RNA, of the sample should be less than 30 for successful sequencing. Otherwise, the process may take a longer time or sequencing may not be successful, Dr. Ravi said.

“After the sequencing, we need to analyse the data and subject it to comparison with the global SARS-CoV-2 database. This may take another 48 hours. Sometimes, we can get data in a short span of time when a specimen has lots of RNA and no other genetic material,” he said.

The approximate cost of a genome sequencing test can vary between ₹20,000 and ₹25,000. This if the sample is processed using Nanopore sequencing, where a total of 12 samples are loaded. “However, if the Illumina sequencing process is used, we can test 50 samples at a time, and the cost will also be less,” said Dr. Ravi.

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Sagar Biswas

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