Virus Characterization

Virus Evolution

Evolution

Where are new zoonotic viruses most likely to evolve?

Forecasting the risk of spillover is a multidimensional problem that goes beyond cataloging individual viruses and their associated hazards. Viral traits can be highly dynamic and change in response to a multitude of ecological and evolutionary pressures. Evolutionary mechanisms like recombination, which is common in coronaviruses, can quickly shuffle genes and create novel viruses with unpredictable zoonotic potential. Efforts to forecast zoonotic spillover must therefore consider the threat posed by viruses currently circulating in wildlife, but also the threat posed by viruses that have yet to evolve.

In the Anthony Lab, we study virus evolution to understand how viruses acquire, or lose, zoonotic potential. We study the drivers and limitations of evolutionary mechanisms, like recombination, so we can forecast host and geographic hotspots where novel viruses are most likely to evolve.
 

Recombination
Coronavirus Recombination


Recombination is the process by which two viruses exchange part of their genomes to create a daughter strain with a new and distinct set of traits.


A major research focus in our lab is coronavirus recombination. This evolutionary mechanism is an important driver of genetic diversity in coronaviruses and there is growing evidence that it also promotes host-switching (spillover). The goal of our current research, funded by NIH, is to examine laboratory and natural recombination events to better understand the genetic and ecological drivers of recombination.

Read more about coronavirus recombination in our recent review, published in Cell Host and Microbe:
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Watch the Evolution of Coronavirus:

 

Our Contributions

Our research focuses on uncovering the complexity of recombination in coronaviruses and its role in viral emergence. In our recent PLoS Pathogenspaper, we show how timing and co-infection shape recombination frequency in coronaviruses, offering new insights into when and how viral variants arise.

In an earlier Cell Host & Microbe study, we highlight that recombination doesn’t happen in isolation! We dissected the multi-step pathway of recombination, showing how each step—co-infection, template switching, and beyond—contributes to recombinant success.

Prior to this, our Virus Evolution paper explored how recombination alters receptor usage patterns in Sarbecoviruses, contributing to shifts in host specificity and zoonotic potential.

And our earliest foundational work in mBio highlighted how spike gene recombination played a critical role in the evolutionary history of MERS-like coronaviruses in bats, further underscoring the importance of recombination in cross-species transmission.

Together, these studies emphasize that recombination is not a singular event but a complex evolutionary pathway that must be understood to anticipate viral emergence and zoonotic risk.