Second wave of COVID-19 in India could be predicted with genomic surveillance of SARS-CoV-2 variants coupled with epidemiological data: A tool for future

Abstract India has witnessed a devastating second wave of COVID-19, which peaked during the last week of April and the second week of May, 2021. We aimed to understand whether the arrival of second wave was predictable and whether it was driven by the existing SARS-CoV-2 strains or any of the emerging variants. We analyzed the monthly distribution of the genomic sequence data for SARS-CoV-2from India and correlated that with the epidemiological data for new cases and deaths, for the corresponding period of the second wave. Our analysis shows that the first indications of arrival of the second wave were observable by January, 2021, and by March, 2021 it was clearly predictable. B.1.617 lineage variants drove the wave, particularly B.1.617.2 (a.k.a. delta variant). We propose that genomic surveillance of the SARS-CoV-2 variants augmented with epidemiological data can be a promising tool for predicting future COVID-19 waves.