(176a) Propagating and Inflating Viral Progenies Using Drop-Based Microfluidics and Biophysics-Based Forward Evolutionary Models

Authors: 
Rotem, A., Harvard University
Chang, C., Harvard University
Zhang, H., Harvard University
Cheron, N., Harvard University
Weitz, D. A., Harvard University



The study of how viruses propagate is important for curing disease and preventing viral outbreaks, yet is challenging due to inability to access enough variants in the population, including ones that do not survive genetic drift and selection.  In nature, viruses can compete with one another, and the most evolutionary fit virus usually takes over a population.  Yet there exist variants in the population that can escape subjected evolutionary pressures and eventually dominate the population.  Successful studies of viral epidemics in vitro hinges on the ability to access these variants, in order to obtain a comprehensive understanding of fitness in an evolving population and to allow the exploration of multiple virus trajectories, as well as prediction of their direction. Unfortunately, measurements of fitness trajectories can currently be observed in the laboratory only when the mutations have a large effect on fitness in the population.  Accessing the richness of the background genomic diversity has only been performed upon a small number of species, since these experiments have been both labor intensive and time-consuming due to their large population sizes.  Thus, there remains a need for a simple experimental method that allows greater access to the genetic diversity in a large population, in order to allow exploration of fitness space. 

Here, we present the use of droplet-based microfluidics as a simple method to segregate and propagate a viral population as individual viral lineages, effectively eliminating competition between viral strains and minimizing natural selection.  We show that the population obtained from isolating viruses in drops is more diverse than that from bulk culture, thus allowing access to mutations and variants that would not otherwise occur be seen from natural selection events, allowing the potential to control mutation rates and accelerate evolution in vitro or in silico.  This general method of permitting smaller population sizes to propagate, similar in vein to mutation accumulation experiments, can be widely applied to other genetic systems to revolutionize our understanding of evolution and the distribution of fitness.