Barring a few, States are yet to develop a robust mechanism to collect Covid-19 samples systematically and dispatch them for genomic analysis, according to experts.

For RNA viruses like SARS-CoV2, mutation is a normal process. It happens often when they replicate themselves in the cells. Sometimes, such mutations around the spike protein region — which the virus uses to gain entry into the human cells — can be a concern. So, there is a need to regularly monitor such mutations, say experts.

Thus, proper collection and genomic sequencing of these samples are important for detecting the emergence of variants that have potential to set off another wave of the pandemic, they said.

Called Indian SARS-CoV2 Genomics Sequencing Consortium (INSACOG), this network of 28 national laboratories — jointly set up by the Health Ministry, the Department of Biotechnology (DBT), the Council of Scientific and Industrial Research (CSIR) and the Indian Council of Medical Research — has been sequencing samples collected from all over the country since the emergence of alpha variant (B.1.1.7) in the UK. Through INSACOG and other similar genomic sequencing efforts, around 52,000 samples have been analysed in the country.

Bigger states fail

The number of samples analysed from most other States, including Bihar and Uttar Pradesh, runs to only a few hundreds, the expert rued. “Most worrying are the north-eastern States, which are reporting double-digit test positivity rates. But only a few samples have been collected from these States and sequenced,” the expert said.

Gyaneshwer Chaubey, professor at the Banaras Hindu University, said the genomic sequencing effort leaves much to be desired. “Even some of our small neighbours are doing it more systematically,” he said. The government, however, now plans to improve this. It recently announced setting up 277 sentinel sites. These sites — about 10 each per State — would collect 15 samples every fortnight and send them to one of the INSACOG labs for genomic analysis.

Besides this, another major sequencing effort is being planned in four major cities that have reported a large number of cases— Bengaluru, Delhi, Hyderabad and Pune. Funded by the Rockefeller Foundation, the plan is to sequence around 10,000 samples from each cluster over the next three years.

“We would probably extend this to Mumbai and Chennai as well,” said Rakesh Mishra, former Director, Centre for Cellular and Molecular Biology, who is coordinating this effort.

According to Chandni Sajeevan, a professor at Government Medical College in Kozhikode in Kerala, her district first started sending samples for genomic analysis as early as June last year.

“ Currently, over 100 samples are collected from each of 14 districts every month and sent for analysis to CSIR-IGIB,” she said.