Journal Article

Prediction of Directional Changes of Influenza A Virus Genome Sequences with Emphasis on Pandemic H1N1/09 as a Model Case

Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Masae Itoh and Toshimichi Ikemura

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 18, issue 2, pages 125-136
Published in print April 2011 | ISSN: 1340-2838
Published online March 2011 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsr005

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Influenza virus poses a significant threat to public health, as exemplified by the recent introduction of the new pandemic strain H1N1/09 into human populations. Pandemics have been initiated by the occurrence of novel changes in animal sources that eventually adapt to human. One important issue in studies of viral genomes, particularly those of influenza virus, is to predict possible changes in genomic sequence that will become hazardous. We previously established a clustering method termed ‘BLSOM’ (batch-learning self-organizing map) that does not depend on sequence alignment and can characterize and compare even 1 million genomic sequences in one run. Strategies for comparing a vast number of genomic sequences simultaneously become increasingly important in genome studies because of remarkable progresses in nucleotide sequencing. In this study, we have constructed BLSOMs based on the oligonucleotide and codon composition of all influenza A viral strains available. Without prior information with regard to their hosts, sequences derived from strains isolated from avian or human sources were successfully clustered according to the hosts. Notably, the pandemic H1N1/09 strains have oligonucleotide and codon compositions that are clearly different from those of human seasonal influenza A strains. This enables us to infer future directional changes in the influenza A viral genome.

Keywords: influenza virus; pandemic; self-organizing map; oligonucleotide composition; codon usage

Journal Article.  6906 words.  Illustrated.

Subjects: Genetics and Genomics

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