Fearing that Coronavirus is changing variants fast and may become uncontrollable, several States Have expedited setting up their own genome sequence facility to speedily detect the mutation and take steps accordingly to tackle the impending Covid-19 third wave.
The move comes amid concerns that central genome labs, 28 in number, are too few and overburdened. They are taking more than two to three months to detect mutations in Sars-CoV-2 virus.
“The process of sending samples to other institutions is time-consuming. At this time when the virus is mutating, it becomes important to carry sequencing every now and then,” said Prof Jagat Ram, Director of the Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh which is setting up genome lab within the institute in wake of rapid increase in Delta variant of concern (VOC) in the region.
Genome sequencing is a crucial tool to detect pathogens like variants of the coronavirus and can serve as an early warning system to guide the public-health response.
States like Maharashtra, Tamil Nadu, Madhya Pradesh, Kerala, Punjab, Gujarat, Andhra Pradesh, Odisha, Rajasthan, Jammu, Karnataka and Haryana are in the process of setting up the facilities for cutting edge technology.
The spread of the Delta Plus variant, categorised as a ‘Variant of Concern’ by the Union Health Ministry, is currently under scrutiny in the country with as many as 51 Delta Plus cases reported in the country. “The genome sequencing is an effective arsenal in the current fight against Covid-19. Delay in results of the samples means delay in treatment and preventive measures to contain the virus from spreading.,” said a senior official from Delhi Health Department.
In the national capital, two genome sequencing labs to detect variants of the coronavirus are coming up at Lok Nayak Hospital in the first week of July while the Institute of Liver and Biliary Sciences (ILBS) is ready to begin sequencing a small number of samples.
Dr Suresh Kumar, Medical Director of Lok Nayak Hospital informed that training personnel for conducting genome sequencing at the hospital is underway while the lab is expected to operationalise soon. “The gene sequencing machine has been imported from Singapore and training is ongoing on using it. We already have several ICMR projects on molecular work happening in the hospital, and PhD students, so we have personnel to conduct the sequencing,” he said.
ILBS Director Dr SK Sarin said, “The most important thing will be genome surveillance because the virus is likely to mutate at a very fast rate. ILBS is one of the regional labs of INSACOG (Indian SARS-CoV-2 Genomic Consortia), which is monitoring genome sequencing in India and will also be doing it for the Delhi government. “
Rajasthan, which reported a Delta plus variant has already started the facility for Genome Sequencing in the SMS Medical College in Jaipur with State Health Minister Dr Raghu Sharma stating that the facility of genome sequencing has been made available in the state to prevent the Covid-19 spread.
“ Till now the samples from the state were being sent to the IGIB lab in Delhi set up for Rajasthan by the Central Government's Indian Council of Medical Research (ICMR). As per the fixed limit, 10 samples per day, that is 300 samples in a month were sent, but their reports were not being received on time.”
Now, the machine installed at the SMS Medical College can check 20 samples per day and soon its capacity will be increased to check 80 samples per day, he said.
Similarly, Tamil Nadu will soon have its first laboratory for genome sequencing analysis of coronavirus, at the Tamil Nadu Dr MGR Medical University campus, said State Health Minister Ma Subramanian. The state has logged in nine cases of the Delta Plus variant, including one death.
As of now, coronavirus samples are sent to InSTEM, Bengaluru for genome sequencing. Epidemiologist Dr Chandrakant Lahariya saids that all large institutes need to have in-house genomic sequencing capacity. “We should aim for 2 per cent of daily cases as well as all samples of those who died and a reasonable proportion from cases in children and that of moderate to severe cases. More important is to have representative samples from all states of the country.”
Brihanmumbai Municipal Corporation (BMC) in Maharashtra too will no longer have to send samples outside the city, mainly to the NIV in Pune and IGIB in Delhi. It will soon have its own WGS in the public health setup while Haryana Government has given orders for the setting up of a laboratory for genome sequencing at the Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences in Rohtak.
Thus far, genome sequencing has failed to make inroads in India mainly because of the high costs, lack of infrastructure for data systems, and limited availability of public health experts trained in genomics, pointed out Dr Rahul Bhargava, Director-Bone Marrow Transplant Programme, Fortis Memorial Research Institute, Gurugram.
He said, ”it is not just Delta Plus, but also other potential variants of the virus that may become a cause for concern or other pathogens can be detected.” Setting up this cutting-edge technology is a long term investment, Dr Bhargava pointed out.
