An early warning system for variants

TV Jayan | Updated on September 05, 2021

Many avatars: Genome sequencing is helping formulate policies to slow the spread of Covid-19

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Genomic sequencing efforts in different parts of the country are aimed at halting the mutating Covid-19 virus in its track

Health workers in Palakkad district in Kerala, who have been on their toes since the first Covid-19 case broke out in the State on January 30 last year, had an additional task in May this year. They embarked on a more focused testing and vaccination campaign in and around the village that reported Kerala’s first AY.1 variant — a mutant derived from the Delta variant, which was responsible for the country’s devastating second Covid wave.

The health workers vaccinated all those eligible in the region and tested all who had come in contact with the infected person.

Health authorities could identify Kerala’s first AY.1 case — a month after the variant was first detected in Maharashtra’s Ratnagiri district — because of an active genomic sequencing programme that Kerala has undertaken since December last year.

“Recent reports show that nearly 5 per cent of early-August cases from Kerala were caused by AY.1,” said Dr Vinod Scaria, a scientist at the Institute of Genomics and Integrative Biology (CSIR-IGIB), a Council of Scientific and Industrial Research lab in New Delhi, who convinced Kerala to systematically undertake Covid-19 genome sequencing from the beginning.

Thanks to him, Kozhikode’s Government Medical College (Dr Scaria’s alma mater) launched what is believed to be the country’s first SARS-CoV2 genome sequencing exercise in June-July last year, by sequencing around 200 samples from different parts of the district. “The State government, which found merit in such a sequencing effort, extended it to all the districts in December last year. Every district has been collecting 25 samples each week and sending them monthly to CSIR-IGIB for genomic analysis,” said Dr Chandni Sajeevan, Professor of general medicine at GMC.

Besides these 100 to 150 samples, samples of breakthrough infections, reinfections, persistent infections and cases of unusual symptoms collected from ICUs are sent to the New Delhi lab for analysis, Dr Sajeevan said, adding that the entire exercise is coordinated by the district surveillance officers and Dr Scaria’s team at CSIR-IGIB.

“Systematic genome sequencing is essential to provide early warnings, enable evidence for policies as well as validate the efficacy of some policies, as seen in Kerala,” said Dr Scaria. The State decided to insist on double masks in April as well as a Statewide lockdown in May, along with augmenting beds and oxygen supply, based on inputs from the CSIR-IGIB scientists.

Maharashtra is another State that has been undertaking similar efforts since April-May this year. All 36 districts have been sending 100 samples a month to CSIR-IGIB. Based on insights from the CSIR-IGIB scientists, the Maharashtra government imposed a lockdown in three districts where the Delta-plus variant was detected early this year.

More states and projects are now setting up these early warning systems.

“Gujarat, too, has undertaken genomic sequencing, though not on the scale of Kerala and Maharashtra,” said Dr Scaria.

The Centre launched a nationwide consortium for sequencing SARS-CoV2 genome (INSACOG) after variants of concern identified in other countries were reported in India. Though targeted at international travellers, it was soon extended to others too. Today the consortium has 28 genomic labs.

Last month, scientists in Bengaluru, Delhi, Hyderabad and Pune — which saw a spike in cases — launched a three-year SARS-CoV2 genome sequencing project, funded by Rockefeller Foundation.

“This is more of a retrospective sequencing, which will help us understand the mutation history of the virus and, hopefully, help in faster identification of newly emerging variants,” said Rakesh Mishra, former director at Hyderabad-based CSIR lab, Centre for Cellular and Molecular Biology, who spearheads this project.

Published on September 05, 2021

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