Integrating genomic, serological and epidemiological information to understand the emergence, spread and establishment of novel SARS-CoV-2 variants

Emergence of SARS-CoV-2 variants has underscored the importance of genomic surveillance in enabling timely identification of new viral threats, and the role of transmission modelling in characterising the public-health risk they pose. These analyses have largely been considered independently of each other during the pandemic however, despite evidence that genomic and epidemiological data can provide complementary insights into virus dynamics. I will develop a Bayesian transmission-modelling framework reconciling both data-sources and use this framework to systematically compare the epidemiological properties (e.g. transmissibility, disease-severity and immune-evasion potential) of key variants (including but not limited to Alpha, Beta, Gamma and Delta), across settings including Brazil, Colombia, India, Panama, South Africa and the UK. I will explore how the dynamics of variant establishment and spread are shaped by intrinsic variant properties and their modification by epidemiological context (e.g. control measures or levels of population-immunity), and examine whether there is evidence for different contexts influencing the establishment of variants with particular properties. This work will improve our understanding of the types of SARS-CoV-2 variants likely to establish and spread in the future; inform decisions aimed at mitigating their potential public-health impact; and provide insight into the ways epidemiological pressures influence viral evolution.