tetano
Editor, Senior Moderator
Comp Immunol Microbiol Infect Dis. 2013 Jul 25. pii: S0147-9571(13)00053-2. doi: 10.1016/j.cimid.2013.06.003. [Epub ahead of print]
Evaluation of phenotypic markers in full genome sequences of avian influenza isolates from California.
Mertens E, Dugan VG, Stockwell TB, Lindsay LL, Plancarte M, Boyce WM.
Source
Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA.
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.
Copyright ? 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.
KEYWORDS:
Avian influenza virus, Database, Host adaptation, Influenza research, Phenotype markers, Surveillance
PMID:
23891310
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/23891310
Evaluation of phenotypic markers in full genome sequences of avian influenza isolates from California.
Mertens E, Dugan VG, Stockwell TB, Lindsay LL, Plancarte M, Boyce WM.
Source
Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA.
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.
Copyright ? 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.
KEYWORDS:
Avian influenza virus, Database, Host adaptation, Influenza research, Phenotype markers, Surveillance
PMID:
23891310
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/23891310