Genomic analysis of an atypical Mexican low-pathogenic H5N2 avian influenza virus

Abstract

We analysed the genome of a low-pathogenic avian H5N2 influenza virus isolated from the faeces of experimentally infected Pekin ducks and Leghorn-type chickens to determine its origin and molecular characteristics. The complete genomic sequence was determined using a Sanger-based genome sequencing method and was subsequently characterized by phylogenetic analysis and genetic comparison. The results of this study showed that 8 genomic segments corresponded to an avian influenza virus that were related with strains isolated in Mexico. Investigation of the haemagglutinin gene revealed the presence of few basic amino acids at the cleavage site and lack of a potential N-glycosylation site at position 11. The gene encoding the PB1 protein lacked PB1-F2 and the basic polymerase gene codes for PA-X. In addition, the basic polymerase gene contained the consensus ribosomal frameshifting motif TCC TTT CGT C, which is required for the expression of the PA-X. Molecular characteristics showed that the virus has features of a low-pathogenic H5 influenza virus with the exception of a potential N-glycosylation site at position 11. The genome information for this particular virus will provide a molecular map for further in vivo studies to identify why some influenza viruses can persist in chickens for long periods of time. Such information will be useful in countries such as Mexico, where the virus has been a poultry health problem since 1994 and has the potential to evolve high pathogenicity.