Digital genotyping of avian influenza viruses of H7 subtype detected in central Europe in 2007-2011
Jazyk angličtina Země Nizozemsko Médium print-electronic
Typ dokumentu časopisecké články
PubMed
22342598
DOI
10.1016/j.virusres.2012.02.005
PII: S0168-1702(12)00053-6
Knihovny.cz E-zdroje
- MeSH
- fylogeneze MeSH
- genotyp MeSH
- molekulární epidemiologie metody MeSH
- molekulární sekvence - údaje MeSH
- molekulární typizace metody MeSH
- ptačí chřipka u ptáků epidemiologie virologie MeSH
- ptáci MeSH
- sekvenční analýza DNA MeSH
- shluková analýza MeSH
- virologie metody MeSH
- virus chřipky A klasifikace genetika izolace a purifikace MeSH
- výpočetní biologie metody MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Evropa epidemiologie MeSH
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 800 km and 15 months, 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.
Citace poskytuje Crossref.org
GENBANK
JN966902, JN966903, JN966904, JN966905, JN966906, JN966907, JN966908, JN966909
