tetano
Editor, Senior Moderator
J Clin Microbiol. 2013 Dec 18. [Epub ahead of print]
PhyloFlu, a DNA microarray to determine the phylogenetic origin of influenza A gene segments and the genomic fingerprint of viral strains.
Paulin LF, Soto-Del R?o MD, S?nchez I, Hern?ndez J, Guti?rrez-R?os RM, L?pez-Mart?nez I, Wong-Chew RM, Parissi-Crivelli A, Isa P, L?pez S, Arias CF.
Author information
Abstract
Recent evidence suggests that most influenza A gene segments can contribute to the pathogenicity of the virus. In this regard the HA subtype of the circulating strains is closely surveyed, but the reassortment of internal gene segments as a potential source of an increased pathogenicity is usually not monitored. In this work, an oligonucleotide DNA microarray (PhyloFlu) designed to determine the phylogenetic origin of the eight segments of the influenza genome was constructed and validated. Clades were defined for each segment and also for the 16 HA and 9 NA subtypes. Viral genetic material was amplified by RT-PCR with primers specific to the conserved 5' - and 3' -ends of the influenza A virus genes, followed by PCR amplification with random primers and Cy3-labeling. The microarray unambiguously determined in 74% of the samples (28/38) the clades for all eight influenza genes. The microarray was validated with reference strains from different animal origin, as well as from human, swine and avian viruses from field or clinical samples. In most cases, the phylogenetic clade of each segment defined its animal host of origin. The genomic fingerprint deduced by the combined information of the individual clades allowed the determination of the time and place strains with the same genomic pattern were previously reported. PhyloFlu is useful to characterize and survey the genetic diversity and variation of animal viruses circulating in different environmental niches, as well as for a more detailed surveillance and follow-up of reassortant events that could potentially modify virus pathogenicity.
PMID:
24353006
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/24353006
PhyloFlu, a DNA microarray to determine the phylogenetic origin of influenza A gene segments and the genomic fingerprint of viral strains.
Paulin LF, Soto-Del R?o MD, S?nchez I, Hern?ndez J, Guti?rrez-R?os RM, L?pez-Mart?nez I, Wong-Chew RM, Parissi-Crivelli A, Isa P, L?pez S, Arias CF.
Author information
Abstract
Recent evidence suggests that most influenza A gene segments can contribute to the pathogenicity of the virus. In this regard the HA subtype of the circulating strains is closely surveyed, but the reassortment of internal gene segments as a potential source of an increased pathogenicity is usually not monitored. In this work, an oligonucleotide DNA microarray (PhyloFlu) designed to determine the phylogenetic origin of the eight segments of the influenza genome was constructed and validated. Clades were defined for each segment and also for the 16 HA and 9 NA subtypes. Viral genetic material was amplified by RT-PCR with primers specific to the conserved 5' - and 3' -ends of the influenza A virus genes, followed by PCR amplification with random primers and Cy3-labeling. The microarray unambiguously determined in 74% of the samples (28/38) the clades for all eight influenza genes. The microarray was validated with reference strains from different animal origin, as well as from human, swine and avian viruses from field or clinical samples. In most cases, the phylogenetic clade of each segment defined its animal host of origin. The genomic fingerprint deduced by the combined information of the individual clades allowed the determination of the time and place strains with the same genomic pattern were previously reported. PhyloFlu is useful to characterize and survey the genetic diversity and variation of animal viruses circulating in different environmental niches, as well as for a more detailed surveillance and follow-up of reassortant events that could potentially modify virus pathogenicity.
PMID:
24353006
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/24353006