title: Intrahost evolutionary dynamics of canine influenza virus in naive and partially immune dogs.
abstract: The patterns and dynamics of evolution in acutely infecting viruses within individual hosts are largely unknown. To this end, we investigated the intrahost variation of canine influenza virus (CIV) during the course of experimental infections in naïve and partially immune dogs and in naturally infected dogs. Tracing sequence diversity in the gene encoding domain 1 of the hemagglutinin (HA1) protein over the time course of infection provided information on the patterns and processes of intrahost viral evolution and revealed some of the effects of partial host immunity. Viral populations sampled on any given day were generally characterized by mean pairwise genetic diversities between 0.1 and 0.2% and by mutational spectra that changed considerably on different days. Some observed mutations may have affected antigenicity or host range, including reversions of CIV host-associated mutations. Patterns of sequence diversity differed between naïve and vaccinated dogs, with some presumably antigenic mutations transiently reaching high frequency in the latter. CIV populations are therefore characterized by the rapid generation and clearance of genetic diversity. Potentially advantageous mutations arise readily during the course of single infections and may give rise to antigenic escape or host range variants.
authors.affiliation: Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Hungerford Hill Road, Ithaca, NY 14853, USA.
authors.forename: Karin
authors.initials: K
authors.lastname: Hoelzer
authors.forename: Pablo R
authors.initials: PR
authors.lastname: Murcia
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Baillie
authors.forename: James L N
authors.initials: JL
authors.lastname: Wood
authors.forename: Stephan M
authors.initials: SM
authors.lastname: Metzger
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Osterrieder
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Dubovi
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.forename: Colin R
authors.initials: CR
authors.lastname: Parrish
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D004283:Dog Diseases / Q000276:immunology / Q000821:virology*; D004285:Dogs; D019143:Evolution, Molecular; D006389:Hemagglutinins, Viral / Q000235:genetics; D009980:Influenza A virus / Q000145:classification* / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D020125:Mutation, Missense; D009976:Orthomyxoviridae Infections / Q000276:immunology / Q000662:veterinary* / Q000821:virology; D011110:Polymorphism, Genetic; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D006389:Hemagglutinins, Viral; D012367:RNA, Viral; C458881:hemagglutinin fusogenic peptide, influenza virus