NEW DELHI: The genome sequencing by the Indian SARS-CoV-2 Genetics Consortium helped in detection of ‘variants of concern’ in real-time and it was also shared with states, the Union health ministry said on Tuesday, highlighting that the turnaround time was 10 to 15 days.
The ministry said that the effect of known ‘variants of concern’ (VoCs) on disease transmission and severity is already established.
But for new mutations or variants under investigation, and for correlation of genomic mutations with epidemiological scenarios and clinical perspective, it is important to monitor epidemiological trends of cases, clinical severity and proportions of samples with genomic variants, it said.
These have to be done over a few weeks to generate scientifically valid evidence, the ministry said.
The health ministry also referred to some media reports which alleged low quantum of sequencing in the country and significant lag between sample collection and sequence submission into the database for pattern detection and actionable alerts to governments.
“It is clarified that a sampling strategy is based on the country’s objectives, scientific principles and WHO (World Health Organisation) guidance documents. Accordingly, the strategy has been reviewed and revised from time to time,” it said.
The Indian SARS-CoV-2 Genetics Consortium (INSACOG) was set up by the government on December 25 last year to study and monitor genome sequencing and virus variation of circulating strains of COVID-19 in India.
In the initial phase, sampling was done with the objective of identifying international travellers who could be carrying the variant strains and to find out if the variant or variants are already present in the population.
Accordingly, a two-pronged strategy was adopted — international passengers arriving from selected countries and their contacts were targeted for whole genome sequencing (WGS), and community-based sampling of five per cent of the RT-PCR positive cases was done from each state.
It is important to note that the five per cent norm was selected based on the then daily caseload (approximately 10,000–15,000 per day) and the sequencing capacity of the Regional Genome Sequencing Laboratories (RGSLs) at that time, the ministry said.
Both the objectives were met when it was conclusively established that international passengers were carrying variants and the transmission of these had also been established in the community in a few states, it said.
Subsequently, in line with the global sequencing strategy and WHO guidance document, the sampling strategy has been revised by INSACOG with the objective to detect emerging genomic variants or mutations by prospective sampling and to detect the VoCs and genomic variants in special and unusual events like large clusters, unusual clinical presentation, vaccine breakthrough, suspected reinfections, among others, the ministry said.
It said that accordingly, a strategy has been adopted in view of the increase in the number of new COVID-19 cases, existing capacity of RGSLs and timely detection of VoCs, including other genomic variants being detected in the country and elsewhere. The strategy was revised on April 12 to the ‘Sentinel Surveillance’, the ministry said.
This was also endorsed by the WHO which had issued similar guidance, it said.
Under the present sentinel surveillance strategy, states have identified five laboratories and five tertiary care hospitals each as sentinel sites for sending samples to designated RGSLs and each of the sentinel sites is sending 15 samples routinely for WGS to the designated laboratories, the ministry said.
In addition to the sentinel surveillance, an additional event-based surveillance for special and unusual events to detect, investigate and respond to these was also approved,it said.
The details of the epidemiological investigations, study methodology, number of samples to be collected for WGS depends on the situation or event.
“As far as the turnaround time is concerned, INSACOG sequencing has helped in detection of VOCs in real time and this was also shared with the relevant states. The present turnaround time for VOCs is only 10 to 15 days,” the ministry said.
Regarding enhancing the number and capacity of existing genome sequencing labs, it is informed that in addition to existing 10 labs, 18 other labs have also been approved for incorporation in the INSACOG network, the ministry added.