title: Evaluation of phenotypic markers in full genome sequences of avian influenza isolates from California.
abstract: We evaluated phenotypic markers in full-genome sequences of avian influenza isolates to identify avian strains with increased potential for transmission and pathogenicity in mammals. Of 149 markers examined, 67 were positive in the consensus sequences from 206 avian isolates. Analysis of deep sequencing data in a subset of 24 isolates revealed that 344 subpopulations occurred at marker positions. Markers in subpopulations were significantly more likely to be negative (258/344) than positive (86/344), but nearly all of the marker-positive subpopulations (78/86) were associated with marker-negative consensus sequences. Our analysis revealed significant variation in important markers among avian isolates, and showed that consensus sequences do not fully convey an isolate's potential for increased transmissibility and pathogenicity in mammals.
authors.affiliation: Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA.
authors.forename: Eva
authors.initials: E
authors.lastname: Mertens
authors.forename: Vivien G
authors.initials: VG
authors.lastname: Dugan
authors.forename: Timothy B
authors.initials: TB
authors.lastname: Stockwell
authors.forename: Leann L
authors.initials: LL
authors.lastname: Lindsay
authors.forename: Magdalena
authors.initials: M
authors.lastname: Plancarte
authors.forename: Walter M
authors.initials: WM
authors.lastname: Boyce
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001717:Birds; D002140:California; D005819:Genetic Markers; D014644:Genetic Variation; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics* / Q000302:isolation & purification; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics* / Q000302:isolation & purification; D005585:Influenza in Birds / Q000235:genetics* / Q000635:transmission; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA
chemical_list: D005819:Genetic Markers; D019267:Hemagglutinin Glycoproteins, Influenza Virus
keywords: Avian influenza virus; Database; Host adaptation; Influenza research; Phenotype markers; Surveillance