Genome sequencing: As Covid-19 cases rise, can Delhi keep up?

The high number of cases in Delhi could be owing to two factors — high traffic of international travellers at Delhi airport and the government sequencing all positive RT-PCR samples with “enough” viral load. Genomic sequencing is a highly sophisticated test that can map out the whole genetic makeup of the virus from a patient sample and assign it a category.

With the threat of the omicron variant, the government made genomic sequencing mandatory for all international travellers who test positive for Covid-19. As for community-level surveillance, for nearly four months, the government has been sequencing the samples of all those who test positive on RT-PCR and have a Ct value of less than 25.

The Ct value or cycle threshold is the number of cycles of amplification a patient sample has to go through for the virus to be detected. A high Ct value is indicative of a low viral load. Any sample where the virus is detected in more than 35 cycles is considered to be negative, and could likely be from contamination.

“It is difficult to sequence a sample that has a very low viral load, so as per the instructions of the National Centre for Disease Control, we send all samples with Ct value of more than 25 for sequencing to the three designated laboratories,” said a Delhi government official. Both government officials as well as Delhi labs confirmed that they have been sending all positive samples for sequencing.

This, however, discounts those who test positive on the rapid antigen test, even though they are likely to have a higher viral load. Rapid antigen tests detect the virus without amplification and hence people test positive only when the viral load is high.

Over the last one month, almost 90% of the Covid-19 testing has been conducted using the more accurate RT-PCR method, which means samples of almost all those who tested positive for Covid-19 were sequenced.

However, with cases of Covid-19 sharply increasing in the capital, it would be difficult for genomic sequencing efforts to keep up.

How many samples can Delhi labs sequence?

All samples from Delhi are sent to three genome sequencing labs – the National Centre of Disease Control, and the two state-run satellite labs under INSACOG (Indian SARS-CoV-2 Genomics Consortium). The INSACOG consists of 10 central laboratories and at least 28 satellite laboratories.

The laboratory at Lok Nayak hospital, which is the only government centre designated for the treatment of Omicron variant, has a capacity of 100 tests in each cycle.

Every batch of samples has to undergo a series of processes that take about three days before being put into the sequencer for a day, according to virologists working in genomic sequencing labs.

The laboratory at the Institute of Liver and Biliary Sciences has two sequencers – one that can process 96 samples in a batch and the other that can process 380 samples. The lab is currently using only one machine with the capacity of 380 samples because there is a shortage of smaller reagent kits in the market. Each day, the lab receives around 80 samples that are processed and stored at -80 degrees Celsius and run together in the sequencer every fourth or fifth day.

At present, the turnaround time for genomic sequencing at the two labs is between five and eight days.

The National Centre for Disease Control, which comes under the Central government, can sequence up to 3,000 viral genomes in a month. However, along with Delhi, this capacity is shared by east Madhya Pradesh, Uttarakhand, Chandigarh, Haryana, Himachal Pradesh, Ladakh, Jammu and Kashmir, and Punjab.

“Yes, it would not be possible to sequence all samples once the cases have increased. But this is a matter of policy decision. So far, we have instructions to send all samples for sequencing,” said an official from Delhi’s health department.

The official said that the government is likely to take a decision on the sampling for genome sequencing in a “couple of days”. “The government is likely to revert to the old sampling method,” the official said.

Initially, when the INSACOG started working in January this year, the objective was to sequence nearly 5% of the total positive cases. The sampling method was later changed to sentinel surveillance, wherein positive samples from selected sites – representative of the country’s geography – were to be sequenced in addition to samples from any cluster of infections or infections where the symptoms were not typical.

Other than not having the capacity to conduct the test, and the time-consuming, expertise-intensive nature of sequencing, it also costs a lot of money. Its reagents and consumables cost nearly Rs 3,000 to Rs 4,000 per test even at a government centre. For setting up a new lab, the cost for machines for genomic sequencing goes into crores, unlike RT-PCR for which the machine costs about Rs 15-20 lakh and can be used to diagnose other diseases. This is the reason for the rapid increase in the number of RT-PCR labs across the country.

Can private players sequence Sars-CoV-2 genomes?

In September this year, the government had agreed to allow private sector laboratories to conduct genomic sequencing, wherein anonymised samples will be sent to them. Detailed standard operating procedures for the involvement of the private sector were also released to that effect. However, no private laboratory across the country has been inducted into the INSACOG yet.

There are at least eight to ten laboratories across the country that can conduct genome sequencing and add significant capacity to the government’s effort. “With our current machines, we have a capacity to sequence 1,500 viral genomes a week, which can be doubled by increasing manpower. We are willing to join the government’s genome sequencing effort, especially in the light of the new omicron variant,” said Dr Harsh Mahajan, founder and chief radiologist, Mahajan Imaging, which also conducts Covid-19 RT-PCR tests.