title: Experimental evolution of an RNA virus in wild birds: evidence for host-dependent impacts on population structure and competitive fitness.
abstract: Within hosts, RNA viruses form populations that are genetically and phenotypically complex. Heterogeneity in RNA virus genomes arises due to error-prone replication and is reduced by stochastic and selective mechanisms that are incompletely understood. Defining how natural selection shapes RNA virus populations is critical because it can inform treatment paradigms and enhance control efforts. We allowed West Nile virus (WNV) to replicate in wild-caught American crows, house sparrows and American robins to assess how natural selection shapes RNA virus populations in ecologically relevant hosts that differ in susceptibility to virus-induced mortality. After five sequential passages in each bird species, we examined the phenotype and population diversity of WNV through fitness competition assays and next generation sequencing. We demonstrate that fitness gains occur in a species-specific manner, with the greatest replicative fitness gains in robin-passaged WNV and the least in WNV passaged in crows. Sequencing data revealed that intrahost WNV populations were strongly influenced by purifying selection and the overall complexity of the viral populations was similar among passaged hosts. However, the selective pressures that control WNV populations seem to be bird species-dependent. Specifically, crow-passaged WNV populations contained the most unique mutations (~1.7× more than sparrows, ~3.4× more than robins) and defective genomes (~1.4× greater than sparrows, ~2.7× greater than robins), but the lowest average mutation frequency (about equal to sparrows, ~2.6× lower than robins). Therefore, our data suggest that WNV replication in the most disease-susceptible bird species is positively associated with virus mutational tolerance, likely via complementation, and negatively associated with the strength of selection. These differences in genetic composition most likely have distinct phenotypic consequences for the virus populations. Taken together, these results reveal important insights into how different hosts may contribute to the emergence of RNA viruses.
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Grubaugh
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Darci R
authors.initials: DR
authors.lastname: Smith
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Doug E
authors.initials: DE
authors.lastname: Brackney
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Angela M
authors.initials: AM
authors.lastname: Bosco-Lauth
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Fauver
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Corey L
authors.initials: CL
authors.lastname: Campbell
authors.affiliation: United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Lakewood, Colorado, United States of America.
authors.forename: Todd A
authors.initials: TA
authors.lastname: Felix
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America; Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America.
authors.forename: Hannah
authors.initials: H
authors.lastname: Romo
authors.affiliation: Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America.
authors.forename: Nisha K
authors.initials: NK
authors.lastname: Duggal
authors.affiliation: Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Dietrich
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Tyler
authors.initials: T
authors.lastname: Eike
authors.affiliation: Section for Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Beane
authors.affiliation: Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Bowen
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: William C
authors.initials: WC
authors.lastname: Black
authors.affiliation: Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America.
authors.forename: Aaron C
authors.initials: AC
authors.lastname: Brault
authors.affiliation: Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Ebel
mesh_terms: D000818:Animals; D000835:Animals, Wild / Q000235:genetics; D005075:Biological Evolution; D001715:Bird Diseases / Q000821:virology*; D001717:Birds; D056084:Genetic Fitness; D009154:Mutation / Q000235:genetics; D013045:Species Specificity; D014779:Virus Replication; D014901:West Nile Fever / Q000821:virology*; D014902:West Nile virus / Q000235:genetics*