Covid: 2 govt labs to start genome sequencing from July to detect mutations

Two genome labs under the Delhi government will start sequencing samples from the first week of July to detect variants or mutations of the Sars-CoV-2 virus that causes Covid-19, said Delhi health minister Satyendar Jain said on Wednesday.

The labs will be set up at the Lok Nayak (LN) Hospital and the Institute of Liver and Biliary Sciences (ILBS) as part of the Delhi government’s preparations to tackle a possible third wave of the Covid-19 pandemic, the minister said.

“We are preparing two genome sequencing labs at LN hospital and ILBS to study the mutating coronavirus. It will take about a week for these labs to start functioning. Earlier, such samples were sent to the central government (labs) for study. Now, Delhi has the technique and (sequencing) will be performed at the two Delhi government hospitals,” said Jain in a press briefing on Wednesday.

Currently, all Sars-CoV-2 genomes are sequenced by a group of laboratories across the country called Indian SARS-CoV-2 Genomic Consortia (INSACOG). In view of variants of concern such as alpha (B1.117) and delta (B1.617.2) causing a surge in cases in Delhi in April-May, experts have highlighted a need for increasing sequencing.

“A third wave might happen only if a new variant emerges, which is more transmissible than the delta variant or completely circumvents the immunity. So, we need to remain alert and sequence more samples to ensure that we detect mutations. At the same time, we need to ensure that masking and social distancing norms are followed; whatever the variant, these steps can prevent transmission,” said Dr T Jacob John, former head of the department of virology, Christian Medical College, Vellore.

Two central government laboratories -- National Centre for Disease Control and Institute of Genomics and Integrative Biology -- in Delhi, which are part of INSACOG, are already sequencing Sars-CoV-2 genomes.

Lok Nayak hospital sources said the sequencing machine, which has been imported, has already been installed and is currently being calibrated. “It will take another four days or so to start sequencing the virus,” a hospital official said, asking not to be named. The lab will have a capacity to sequence 40 to 50 viral genomes a day, the official further said.

Earlier this month, chief minister Arvind Kejriwal had said that Delhi will set up two genome sequencing laboratories in Lok Nayak Hospital and ILBS within three months.

The lab at ILBS is already equipped to sequence samples and has two sequencing machines in place. “We have two machines and are waiting for the Delhi government to approve the budget, for kits and consumables needed for the sequencing process. Once that is done, we will be able to start sequencing Sars-CoV-2 genomes,” said a senior doctor from the hospital, also asking not to be named.

The laboratory will be able to sequence 300 to 400 samples a week with the existing staff strength. “We have also asked for additional manpower. If we get more hands, then we will be able to sequence more genomes,” the doctor said.

The Union government had earlier set a target of sequencing 5% of all positive samples, but it later altered its sequencing strategy to sentinel surveillance, wherein states have to identify five laboratories and five tertiary care hospitals as sentinel sites for sending samples to designated regional laboratories.

Each of the sentinel sites is sending 15 samples routinely for whole genome sequencing to the designated laboratories. In addition, event-based surveillance will be conducted for special and unusual events such as large clusters, unusual clinical presentation, vaccine breakthrough and suspected reinfections.