NCM 2021: Genomic surveillance for future pandemic preparedness

Rajesh stated that genomic surveillance of SARS-CoV-2 in India required both high-throughput and high-priority sequencing. These criteria were met by nanopore sequencing, which proved even more critical in resource-limited settings. Nanopore sequencing provided a balance between scale, speed, and sensitivity — whilst offering the unique ability to bring the ‘lab to the samples’. Rajesh explained the protocol for sample to sequencing which has been optimised for not only SARS-CoV-2, but also dengue and chikungunya viruses. Rajesh described how their protocol successfully uncovered a new India-specific clade of SARS-CoV-2, for which the linage could be traced back to East Asia. Further down the line of the pandemic, nanopore sequencing ‘came to the rescue’, and revealed the genomic architecture of SARS-CoV-2 causing re-infections, vaccination breakthrough infections, and other variants of concern. Rajesh recognised the importance of translating the strengths of genomic epidemiology exhibited during the SARS-CoV-2 outbreak for other pathogens of concern, and posed the question, are we prepared for future pandemics? Rajesh is taking this forward for TB, DENV, chikungunya and HPV. Rajesh and his team are developing nanopore-based mobile sequencing sites for proactive genomics surveillance of pathogens.