@article {Martin752329, author = {Brigitte E. Martin and Jeremy D. Harris and Jiayi Sun and Katia Koelle and Christopher B. Brooke}, title = {Cellular co-infection increases the speed and efficiency of influenza A virus production and shapes the interferon response to infection}, elocation-id = {752329}, year = {2019}, doi = {10.1101/752329}, publisher = {Cold Spring Harbor Laboratory}, abstract = {During viral infection, the numbers of virions infecting individual cells can vary significantly over time and space. The functional consequences of this variation in cellular multiplicity of infection (MOI) remain poorly understood. Here, we rigorously quantify the phenotypic consequences of cellular MOI during influenza A virus (IAV) infection over a single round of replication in terms of cell death rates, viral output kinetics, interferon production, and superinfection potential. By statistically fitting mathematical models to our data, we precisely define the specific functional forms that govern the modulation of these phenotypes by MOI at the single cell level. We find that cellular co-infection increases the rate and efficiency of virus production, suggesting a potential role for co-infection in influencing viral fitness. We also find that infected cell death rates and type I interferon expression are independent of viral input while type III interferon induction is highly dependent on cellular MOI, identifying a role for cellular co-infection in shaping the host immune response to IAV infection. Finally, we show that increasing viral input is associated with more potent superinfection exclusion, thus limiting the total number of virions capable of infecting a cell. Overall, this study suggests that the extent of cellular co-infection by influenza viruses may be a critical determinant of both viral fitness and infection outcome.AUTHOR SUMMARY During influenza A virus (IAV) infection the number of virions to enter individual cells can be highly variable. Cellular co-infection appears to be common and plays an essential role in facilitating reassortment for IAV, yet little is known about how cellular co-infection influences infection outcomes at the cellular level. Here, we combine quantitative in vitro infection experiments with statistical model fitting to precisely define the phenotypic consequences of cellular co-infection. We reveal that cellular co-infection both accelerates and increases the efficiency of IAV production, identifying it as a potential determinant of viral fitness. We also show that induction of type III, but not type I, interferon is highly dependent upon the number of virions that infect a given cell, implicating cellular co-infection as an unappreciated determinant of the host innate immune response to infection. Altogether, our findings show that cellular co-infection plays a crucial role in determining infection outcome. The integration of experimental and statistical modeling approaches detailed here represents a significant advance in the quantitative study of influenza virus infection and should aid ongoing efforts focused on the construction of mathematical models of IAV infection.}, URL = {https://www.biorxiv.org/content/early/2019/08/30/752329}, eprint = {https://www.biorxiv.org/content/early/2019/08/30/752329.full.pdf}, journal = {bioRxiv} }