Kerala to commission genome survey for SARS-CoV-2

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To better understand the genomic variation in the strains of SARS-CoV-2 in the State, the Kerala government has tied up with the CSIR-Institute of Genomics and Integrative Biology (IGIB) for a survey.

The study, commissioned on November 11, will collect 100 samples from 14 districts every month, for three months. The exercise is a follow-up of a pilot study that the same group of scientists did in Kozhikode, from which it emerged that outbreaks in the State were less due to international expatriates and more due to reduced monitoring of inter-State movement once the restrictions were eased.

‘NextGen’ sequencing

The genome sequencing uses an approach called ‘NextGen’ sequencing, in which 1000s of individual genomes can be simultaneously analysed, rare variations picked up and occasionally, SARS-CoV-2 missed by the gold standard RT-PCR test, detected.

“This could demonstrate the utility in identifying apparently unconnected outbreaks and evidence to design or validate policy interventions—like strict quarantine of foreign travellers,” Vinod Scaria of the CSIR-IGIB and among those closely involved in the project told The Hindu.

Kerala recorded the first cases of COVID-19 in India, and for several months managed to contain the transmission to limited pockets. However, with the easing of restrictions and Onam festivities, congregations multiplied and led to huge spikes in cases.

Kerala had about 87,000 active cases as of Wednesday but has confirmed only 884 deaths so far.

For the project, the State has budgeted ₹ 68 lakh, according to a note issued by the Health Department.

Used in U.K., Australia

The United Kingdom and Australia have employed genome sequencing to map the outbreaks.

The earlier pilot study had found that virus samples sequenced from Kerala belonged to the A2a clade, which is predominant in India, within which there were three clusters. The largest one had genomes from Odisha; the second cluster’s ancestry was traced to Maharashtra and the third from Karnataka.

The study also uncovered four novel genetic variants and 89 variants that were specific to Kerala and not reported from elsewhere in the country.

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Printable version | Jan 20, 2021 9:13:57 PM |

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