COVID-19 Genetic Epidemiology Kerala is a unique partnership between the Department of Health & Family Welfare, Government of Kerala, National health Mission Kerala, Govt, CSIR Institute of Genomics & Integrative Biology (CSIR-IGIB) and various clinical and public health centers in Kerala aimed at providing insights into the genetic epidemiology of COVID-19 in Kerala


Kerala is home to over 35 million people, and being a tropical population extensively connected with the global populations through over 1.6 million expatriates, trade and travel and being a global tourist destination, is in a unique position predisposed to local and global epidemics. Kerala has been one of the first states in India to report a case of COVID-19 in January 2020, very early in the epidemic. The state’s efforts to contain the epidemic has been widely recognised globally.

One of the initial studies of SARS-CoV-2 in the state (Radhakrishnan et al, 2020) suggested that the majority of cases were from inter-state rather than international introductions. This provided validation to the state policy of stringent quarantine for individuals travelling from abroad. Apart from providing a unique view of the genetic epidemiology of SARS-CoV-2 in the state, the study also suggested a virus with D614G variant formed the predominant type, associated with increased infectivity. The state of Kerala was also one of the leading states to use genetic epidemiology to drive and implement public outreach and policy towards containing the spread of the epidemic within the state.

To take these observations forward and also to understand the landscape of genetic epidemiology of SARS-CoV-2 across the state, it was proposed that a continuous approach of surveillance spanning all districts would potentially generate evidence, design policies as well as to validate the implementation strategies.

Why are we doing this

The initiative aims to combine genomic and epidemiological information to guide public health interventions and policies. The initiative would also enable the understanding of transmission patterns, outbreaks apart from enabling evidence based policies for testing, intervention. It is also expected that the initiative would also serve as a framework for evaluating policies.


The Initiative is supported by grants from the National Health Mission Kerala, Department of Health & Family Welfare, Government of Kerala and the Council of Scientific and Industrial Research (CSIR) India.