Evaluation of phenotypic markers in full genome sequences of avian influenza isolates from California

Eva Mertens, Vivien G. Dugan, Timothy B. Stockwell, LeAnn L. Lindsay, Magdalena Plancarte, Walter M Boyce

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)521-536
Number of pages16
JournalComparative Immunology, Microbiology and Infectious Diseases
Issue number5
StatePublished - Sep 2013


  • Avian influenza virus
  • Database
  • Host adaptation
  • Influenza research
  • Phenotype markers
  • Surveillance

ASJC Scopus subject areas

  • Immunology
  • Microbiology
  • Infectious Diseases
  • Immunology and Allergy
  • veterinary(all)


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