The second wave is yet to trough and there are signs that a third wave may be round the corner, but India’s efforts to sequence genomes to track for emerging variants plummeted after April.
Data from the National SARS-CoV-2 Genome Consortium (INSACOG), a network of 28 labs across the country equipped to sequence genomes of the coronavirus for emerging variants, shows that in July, only 184 genomes were sequenced. In June, 4,381 samples were sequenced, which is itself a stark decline from May (13,142 samples) and April (15,546 samples). The latter two months were when India bore the brunt of the second wave that saw daily cases grow to as many as 400,000.
As of July 30, INSACOG had sequenced 58,240 genomes, of which 46,124 samples had been analysed and their lineages (variant history) ascertained and submitted to the National Centre for Disease Control (NCDC), according to the response to a question in the Lok Sabha.
However, INSACOG data visible on a website maintained by the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, one of the key INSACOG labs, shows 49,770 genomes as having been analysed and assigned to 232 lineages. These numbers include genomes sequenced by Kerala and Maharashtra, which have their own genome surveillance programmes. In absolute numbers, Maharashtra accounts for a fifth of the national genomes surveyed and Kerala about a tenth.
Renu Swarup, Secretary, Department of Biotechnology, which coordinates INSACOG, said that the numbers available on the public website weren’t the latest for June and July. “This is not the complete data for June or July. So this gives you data only of sequences analysed and this is not real-time. We now have a real-time portal and soon its link will be available,” she told The Hindu .
A scientist from one of the INSACOG labs said that there was always a lag in when the samples from a region, from any month, were analysed, and that there would an increase in July samples in the coming weeks. However, there are challenges in the programme. The INSACOG initiative was originally planned for three months, and because the project has only recently been extended, the funds available to labs for carrying out sequencing were delayed. The other reason, this source said, was that many States were not sending samples: “The National Centre for Disease Control has specified that at least 300 samples should be sent from each State per month. Very few States are actually complying with this directive.”
The Health Ministry said in the Lok Sabha last week that the existing guidelines were to sequence 15 samples from every sentinel site in every 15 days from each State so that districts are represented from an epidemiological point of view. Every State is expected to have 10 such sentinel sites, which are notified laboratories and tertiary care hospitals. “This is a more diverse sampling strategy as against a random 5% sample sequencing,” the Ministry noted.
The INSACOG database has the contribution of 28 States and Union Territories. Thus, ideally, there ought to be 8,400 samples a month, which as the numbers for June and July suggest, are far below the requirement.
The dominant variant across India continues to be the Delta variant but limited sequencing means that it will be impossible to track if new variants may be driving surges. Currently, Kerala reports about half the daily caseload, and rising trajectories are seen in several northeastern States. Meghalaya, Mizoram, Assam andTripura have each contributed less than 200 samples for genome sequencing, according to the INSACOG database.
Though the month of July has the least number of samples, the proportion of Delta variant samples has fallen to 73% from being over 85% of the analysed samples in May and June.
