Digital genotyping of avian influenza viruses of H7 subtype detected in central Europe in 2007–2011

• Published in: Virus research Vol. 165; no. 2; pp. 126 - 133
• Main Authors: Nagy, Alexander, Černíková, Lenka, Křivda, Vlastimil, Horníčková, Jitka
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2012
• Subjects: Animals; Birds; Cluster Analysis; Computational Biology - methods; Digital genotyping; Europe - epidemiology; Genotype; Genotyping; H7N7; H7N9; Influenza; Influenza A virus - classification; Influenza A virus - genetics; Influenza A virus - isolation & purification; Influenza in Birds - epidemiology; Influenza in Birds - virology; LPAI; Molecular Epidemiology - methods; Molecular Sequence Data; Molecular Typing - methods; Phylogeny; Sequence Analysis, DNA; Virology - methods; Europe; H7N7; H7N9; Genotyping; Influenza; Digital genotyping; LPAI
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2012.02.005

► We developed a digital genotyping of avian influenza viruses. ► We characterized the central European H7 influenza A viruses from 2007 to 2011. ► We characterized the genetic relationships between various influenza virus subtypes. ► The digital genotyping provides a novel and powerful genotyping approach. The objective of our study was to provide a genotype analysis of H7N7 and H7N9 influenza A viruses (IAV) and infer their relationships to co-circulating non-H7 IAV genomes. The H7N7 strains were collected in central Europe (Hungary-1, Czech Republic-1, Slovenia-1 and Poland-4) and the H7N9 in the Czech Republic and Spain between 2007 and 2011. Hand in hand with this effort, a novel IAV genotype visualization approach called digital genotyping was developed. This approach relies on phylogenetic data summarization and transformation into a pixel array called a segment identity matrix. The digital genotyping revealed a complicated genetic interplay between the H7 and co-circulating non-H7 IAV genotypes. At the H7 IAV level the most obvious relationships were observed between one Polish H7N7/446/09 and Czech H7N7/11 viruses which, despite the special and temporal distance of 800km and 15months, retained at least 6/8 genome segments. Close relationships were also observed between the Czech H7N9, Polish and Slovenian H7N7 on one hand and Hungarian and Slovenian H7N7 isolates on the other. In addition the former genomes exhibited close interplays with the Czech H6N2/09 and H11N9/10-like viruses. The Czech and Spanish H7N9 genomes were completely different and 6/8 of the Czech H7N9-like segments were traced to either the Czech H3N8/07, H11N9/09 and Polish H7N7/09-like viruses. The results of digital genotyping correlated with the previous observations obtained on the Polish H7N7 isolates. As was demonstrated, the digital genotyping provides a well-arranged and easily interpretable output and may serve as an alternative genotyping tool useful for handling and analysing even a large panel of IAV genomes.