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COVID-19: Genome sequencing efforts at IISER Pune

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Variants of the SARS-CoV-2 virus pose a major challenge as some of these may have altered virulence, transmissibility, the potential to cause re-infections, and even breakthrough infections in the fully vaccinated. It is essential in this scenario to identify virus variants rapidly, at scale, along with associated epidemiological and clinical data. 

The COVID-19 genome sequencing work at IISER Pune is being carried out through two channels of collaboration: as a member of INSACOG and as a member of a consortium led by CSIR-CCMB.

IISER Pune is a member of the Indian SARS-CoV-2 Consortium on Genomics (INSACOG), a consortium of National Laboratories established by the Ministry of Health and Family Welfare and the Department of Biotechnology. INSACOG aims to carry out genomic surveillance of circulating SARS-CoV-2 variants. 

IISER Pune is also part of a consortium led by CSIR-CCMB, Hyderabad for SARS CoV-2 genome sequencing and environmental surveillance across four major Indian cities (Hyderabad, Bengaluru, Pune and Delhi). IISER Pune, the Pune Knowledge Cluster and NCL Pune represent Pune city in the consortium. The bulk of the clinical samples and all the environmental surveillance samples from Pune city are sequenced at IISER Pune. 

The SARS-CoV-2 genome sequencing effort at IISER Pune is currently supported by the Rockefeller Foundation, the Villoo Poonawalla Foundation (VPF) and the Jankidevi Bajaj Gram Vikas Sanstha (JBGVS). 

This work is carried out at on IISER Pune campus in an independent COVID-19 Genome Sequencing initiative at the National Facility for Gene Function in Health and Disease (NFGFHD) building. Here, dedicated and well-equipped facilities for RNA handling, cDNA and library preparation, and next-generation sequencing enable the sequencing effort and data is uploaded to Government-approved online portals. The facility is run by a dedicated team of 8 members. 

Faculty members in the Biology department Dr. Krishanpal Karmodiya and Dr. Aurnab Ghose and faculty member in the Earth and Climate Science department Dr. Joy Merwin Monteiro are coordinating this initiative.  

Currently, IISER Pune receives isolated RNA samples from Government laboratories and hospitals and processes these maintaining appropriate biosafety precautions. The facility has the capacity of processing 386 samples in four days. The initiative has sequenced more than 10,000 SARS-CoV-2 genomes, as of February 13, 2022. The sequences have been submitted to public databases like GISAID and the India-centric INSACOG-IGIB portal.