From Endemic to Pandemic: The promise & utility of real-time phylogenetics
The current COVID-19 pandemic has brought phylogenetics to the fore, highlighting how real-time sequencing can enable invaluable insights into how a pathogen spreads and changes over time.
When a new variant first catches the attention of scientists and governments, one of the most critical questions is whether it has a significant impact on transmission, immune evasion, and/or clinical outcome. However, this can be difficult to determine. SARS-CoV-2 variant 20E (EU1) spread from Spain and dominated Europe in the autumn of 2020, and was initially feared to be more-transmissible. But by integrating phylogenetics, mobile phone roaming data, and modelling, we showed that travel and behaviour were the most important factors in EU1’s success.
Many variants of concern identified since then do show concerning increases in transmissibility and immune evasion. To help track and monitor existing and emerging variants, I developed CoVariants.org, an interactive platform that combines variant frequency dynamics with focal phylogenies and curated information.
As immunity through previous infection and vaccination is key in ending the pandemic, a better understanding of how SARS-CoV-2 evolution and long-term immunity is critical, particularly as the virus moves from pandemic to endemic. My previous work on pathogens like Enterovirus D68, which almost everyone is exposed to by adulthood, highlights that even pathogens that do not cause serious illness can offer insights into reinfection, the epidemiology of antigenically evolving pathogens and the importance of effects like ‘original antigenic sin’.
We are surrounded by tens to hundreds of pathogens that have adapted to living alongside human immunity – continuously circulating but not commonly causing serious disease. By harnessing the tools and insights gained in the pandemic and turning the lens of sequencing to these pathogens, we can truly enhance our understanding of virus evolution.