Genomic Surveillance of SARS-CoV-2 in Bangalore, India 2021-2022

Author(s): Pulleri Kandi Harsha, Chitra Pattabiraman, Anson Kunjumon George, Madhusudhan J, Saumitra Mardikar, Mudasir Nazaa, Srivathsan Adimoolam, Divya Priya A, Jayee Pitale, Mahesh Nagarajan, Srikant Sridharan, Yasodha Sivasamy, Anand Janakiraman, Vamsi Veeramachaneni, Ramesh Hariharan, Vishal US Rao, Thrilok Chandra, Sudhakar K, Randeep Dev, Ashwath Narayan CN, Vasanthapuram Ravi, Vijay Chandru

A comprehensive SARS-CoV-2 genomic surveillance programme that integrates logistics, laboratory work, bioinformatics, analytics, and timely reporting was deployed through a public- private partnership in the city of Bengaluru, Karnataka in India. As a result, 13641 samples were sequenced and reported to the Karnataka state public health officials as time-sensitive, decision support from June 2021 to July 2022 and uploaded in global public databases in a timely manner. As part of the programme, an analytics platform for studying SARS-CoV-2 sequences and their epidemiological context was also developed. These continuous sequencing efforts enabled timely detection of the Omicron variant in India and its subsequent spread via multiple sub-lineages (BA.10, BA.12, BA.2.75 and BA.5) in Bengaluru. Our data also helped to determine which of the globally tracked Variants of Concern were observed in Bengaluru, thus ensuring targeted efforts on the ground reducing unwarranted fear. This effort highlights the importance of, and the urgent need for, increased genomic surveillance to support the health authorities in regions with limited sequencing and bioinformatics capacity. We describe the development and deployment of this end- to-end solution for genomic surveillance of SARS-CoV-2 in the city of Bengaluru.