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

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• 作者：Eva Mertens ; Vivien G. Dugan ; Timothy B. Stockwell ; LeAnn L. Lindsay ; Magdalena Plancarte ; Walter M. Boyce
• 关键词：Avian influenza virus ; Surveillance ; Host adaptation ; Phenotype markers ; Influenza research ; Database
• 刊名：Comparative Immunology, Microbiology and Infectious Diseases
• 出版年：2013
• 出版时间：September, 2013
• 年：2013
• 卷：36
• 期：5
• 页码：521-536
• 全文大小：6555 K

文摘

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.