Danny Lyons Defends

Danny defended his PhD thesis on his birthday! He presented his work on viral mutational fitness effects as well as a theoretical project on epistasis that he developed with George Zhang in EEB. The image shows Danny’s now classic example of apple + chocolate pie epistasis. As an MD/PhD student, Danny will go back to medical school clerkships soon.

Within-host diversity of influenza B

Influenza B viruses (IBV) evolve more slowly than influenza A viruses (IAV), but the reasons for this difference are not fully understood. Andrew’s new paper demonstrates that IBV accumulates less genetic diversity during natural infection compared to IAV. Data from household transmission pairs suggests that like IAV, IBV also experiences a narrow transmission bottleneck. These findings are consistent with IBV’s lower mutation rate and slower global rate of evolution.

JT McCrone wins MacNeal Award

JT McCrone was this year’s recipient of the Department of Microbiology and Immunology MacNeal Outstanding Dissertation Award. JT came back to campus to give a seminar on Ebola virus phylogenetics, one of the projects he’s working on as a postdoc in Andrew Rambaut’s lab.

A speed fidelity trade-off

RNA viruses have extremely high mutation rates and most mutations are bad. In our latest paper, we asked “why hasn’t the virus evolved to have a lower mutation rate?” We used experimental evolution and a murine infection model to show that RNA virus mutation rates may actually be too high and are not necessarily adaptive. Rather, our data indicate that viral mutation rates are driven higher as a result of selection for viruses with faster replication kinetics. We suggest that viruses have high mutation rates, not because they facilitate adaptation, but because it is hard to be both fast and accurate.

Review on mutation rates

Kayla’s review on viral mutation rates is now published in the Journal of Virology. Our goal was to review the population genetics of mutation rates. We cover methods for mutation rate estimation, the forces that drive the evolution of mutation rates, and how the optimal mutation rate can be context-dependent. The article includes a link to a shiny app in our GitHub repo with updated information on mutation rates and evolutionary rates for your favorite viruses.

Influenza evolution within and between human hosts

Our study of influenza virus evolution in naturally infected people is out in eLife. In collaboration with Arnold Monto and Emily Martin (UM SPH), we sequenced virus populations from 200 infected individuals in the HIVE cohort. We found that positive selection is inefficient at the level of the individual host and that stochastic processes dominate the host-level evolution of influenza viruses. Here’s a profile of the work.

JT McCrone Defends

JT successfully defended his thesis on the within and between host evolution of influenza virus. He will stick around for a couple of months to wrap up some ongoing projects, then head to Edinburgh for a postdoctoral fellowship with Andrew Rambaut.

Burroughs Wellcome Grant

Adam receives a 5 year grant from the Investigators in the Pathogenesis of Infectious Disease Program. This generous and flexible support will allow us to explore new projects related to viral transmission and the evolution of virulence. Press Release