Indian scientists have launched a multi-city project to track the emergence of various SARS-CoV2 variants in the country in the past with a $9.5-million funding from Rockefeller Foundation.

The insights gained from the three-year project, launched in four cities – Bengaluru, Delhi, Hyderabad and Pune – are expected to help the country develop better capabilities for real-time surveillance and epidemiology.

“The project is to understand how various variants have fared in different parts of the country. We will have samples for four cities, maybe six cities, with proper metadata from hospitals. Sequencing them may help us how the variants have evolved,” said Rakesh Mishra, former director of the Centre for Cellular and Molecular Biology (CSIR-CCMB), a Council Scientific and Industrial Research lab based in Hyderabad.

Top scientists involved

Mishra, currently an advisor at CSIR-CCMB, will spearhead the project with a few other top scientists in other cities. Apart from Mishra, who will lead the efforts in the Hyderabad cluster, Satyajit Mayor, Director of Bengaluru-based National Centre for Biological Sciences; LS Shashidhara of Indian Institute of Science Education and Research, Pune; and Anurag Agrawal of Institute of Genomics and Integrative Biology (CSIR-IGIB) in New Delhi, will be in charge of respective clusters.

“We have around 40,000 sequences in mind, but it may go up to 60,000 a year. The funds, provided by Rockefeller Foundation, will be used mainly for consumables and human resources, with building and infrastructure support coming from the existing labs,” said Mishra.

A number of research institutions in these four cities are participating in this SARS-CoV2 genomic sequencing effort. “What is unique in this project is that we will sequence only those samples for which there is a reasonable amount of metadata such as age, date of infection, symptoms available, so that we can link the phenomenon that was observed to mutation or emergence of variant if there is any,” said Mishra.

The scientists said the project will be complimentary to what the Indian SARS-CoV-2 Consortium on Genomics (INSACOG) is doing. Even though its primary objective is retrospective sampling, they will also be sequencing fresh samples, particularly those picked up from vaccine breakthrough cases and reinfections.

“Since we are also part of INSACOG, this project will help increase the scale, which, in turn, will help get more granular data for better understanding of the pandemic and also for taking steps for prevention and control of future waves,” said Mishra.

Shashidhara, who is also associated with Ashoka University in Sonipat, said INSACOG has already scaled up its sequencing efforts.

“But it is not enough, considering the scale. The new variant can emerge anywhere. The attempt is to map four-five megacities to understand how variants are evolving and spreading. These are the places where a large number of cases reported. They are also the places that had reported cases throughout the year,” he said. He said there is a possibility of extending the study to Chennai and Mumbai.

Gets approval

According to Mayor, who is coordinating the efforts of the Bengaluru cluster, they have already been able to secure approvals from the Karnataka government for collection of samples.

They plan to collect around 10,000 samples from cases reported in the last few months for genomic analysis.

“The objective is somewhat more rarefied than very broad kind of efforts. It is more about looking at what is the nature of variations that happened in the viral genome,” said Mayor, adding that this could help them understand how and when variants emerge.