Study: Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2
The coronavirus responsible for the COVID-19 pandemic, SARS-CoV-2, has shown a remarkable ability to evolve novel, increasingly transmissible variants. Identifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic.
Using rich viral genomic data sets, the study shows that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly abrupt collapses of diversity. This is in contrast to the pattern previously identified for influenza, which does not show similarly sudden increases in diversity.
The study introduces a mechanistic model of saltational evolution with epistasis and demonstrate that these features parsimoniously account for the observed temporal dynamics of inter-genomic diversity. The results provide support for recent proposals that saltational evolution may be a signature feature of SARS-CoV-2, allowing the pathogen to more readily evolve highly transmissible variants. These findings lend theoretical support to a heightened awareness of biological contexts where increased diversification may occur. They also underline the power of pathogen genomics and other surveillance streams in clarifying the phylodynamics of emerging and endemic infections. In public health terms, the results further underline the importance of equitable distribution of up-to-date vaccines.