SARS-CoV-2 evolution within and between hosts

The global population of SARS-CoV-2 is structured into discrete infections within hosts. How does this affect the evolution of the pandemic? First, I will show how one can use the evolution between pairs of hosts to infer how many virus particles contribute to a new infection. Second, I will discuss how the observed timing and dynamics of the Variants of Concern suggest that rare chronic infections are the key drivers of global infection. Finally, I will briefly touch on a case study of rapid evolution and diversification within a chronic infection.