title: A quantitative genotype algorithm reflecting H5N1 Avian influenza niches.
abstract: BACKGROUND
  Computational genotyping analyses are critical for characterizing molecular evolutionary footprints, thus providing important information for designing the strategies of influenza prevention and control. Most of the current methods that are available are based on multiple sequence alignment and phylogenetic tree construction, which are time consuming and limited by the number of taxa. Arbitrarily defining genotypes further complicates the interpretation of genotyping results.
  
  
  METHODS
  In this study, we describe a quantitative influenza genotyping algorithm based on the theory of quasispecies. First, the complete composition vector (CCV) was utilized to calculate the pairwise evolutionary distance between genotypes. Next, Hierarchical Bayesian Modeling using the Gibbs Sampling algorithm was applied to identify the segment genotype threshold, which is used to identify influenza segment genotype through a modularity calculation. The viral genotype was defined by combining eight segment genotypes based on the genetic reassortment feature of influenza A viruses.
  
  
  RESULTS
  We applied this method for H5N1 avian influenza viruses and identified 107 niches among 283 viruses with a complete genome set. The diversity of viral genotypes, and their correlation with geographic locations suggests that these viruses form local niches after being introduced to a new ecological environment through poultry trade or bird migration. This novel method allows us to define genotypes in a robust, quantitative as well as hierarchical manner.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Microbiology, Miami University, Oxford, OH 45056, USA. wanhenry@yahoo.com
authors.forename: Xiu-Feng
authors.initials: XF
authors.lastname: Wan
authors.forename: Guorong
authors.initials: G
authors.lastname: Chen
authors.forename: Feng
authors.initials: F
authors.lastname: Luo
authors.forename: Michael
authors.initials: M
authors.lastname: Emch
authors.forename: Ruben
authors.initials: R
authors.lastname: Donis
mesh_terms: D000818:Animals; D005075:Biological Evolution; D001717:Birds; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D005838:Genotype; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics*; D005585:Influenza in Birds / Q000821:virology*; D016865:Reassortant Viruses / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*