Drop-based microfluidics is a method in which controlled numbers of individual infected host cells can be cultured and assayed within microscale drops. 
The host cell and virus are compartmentalized within picoliter-sized drops, allowing for high-throughput analysis of all the virions produced by each individual cell using next generation sequencing. 
Drop-based microfluidics provides an ideal platform for the study of fast evolving RNA viruses in the laboratory, as thousands to millions of single cells can be assayed per experiment. 

 Characterizing evolutionary processes of mutation and selection that contribute to virulence and transmission of viral pathogens. Avian IAV is an extraordinarily adaptable virus, capable of infecting a wide variety of animal species, including poultry, humans, pigs, and others. Zoonotic spillover into humans with avian IAV subtypes, such as H5N1, has led to illnesses with mortality rates as high as 60%. These spillover events remain rare due to host restrictions that limit efficient viral replication and human to human transmission. However, new pandemic IAV strains can arise when viral evolution results in host adaptation that facilitate human to human spread.  This research project focuses on using drop-based microfluidics to evaluate novel evolutionary landscapes and adaptive trajectories of avian IAV viral populations at the single cell level, allowing for better modeling of virus evolution and adaptation. We are working on characterizing both extracellular and intracellular viral diversity with next generation sequencing techniques following infection of human primary nasal and bronchial epithelial cells. Studies are focused on avian IAV strains that maintain pandemic potential within the natural environment, including the strains currently infecting dairy cattle. 

Interrogating IAV infections in primary duck and chicken gut and lung cell organoid models. Migratory aquatic birds serve as the natural reservoirs of IAV, and their co-evolution has led to the emergence of novel influenza strains that can cause high levels of morbidity and mortality in other hosts. The emergence of new strains of IAV poses a significant threat to public health including the currently circulating highly pathogenic avian IAV H5N1 strain (clade 2.3.4.4b) which has resulted in multiple spillover infections in terrestrial and marine mammals. However, despite the pivotal role played by birds as the natural reservoir of IAV, and as incidental hosts that can facilitate mammalian infection, there is an absence of reliable cell culture models for studying IAV in domesticated and aquatic birds. This research project is focused on establishing a set of novel primary and organoid cell models from duck and chicken respiratory and intestinal tissue to study differential pathogenesis of avian IAV infections. This work is a collaboration with Drs. Emily Bruce and Bruno Martorelli di Genova at the University of Vermont (UVM) and will allow us to address fundamental mechanistic questions about avian IAV infection in natural and incidental avian hosts.