Computational protocol: Evidence for the Circulation and Inter-Hemispheric Movement of the H14 Subtype Influenza A Virus

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Protocol publication

[…] Only the open reading frames of each segment were used for sequence comparison and phylogenetic analyses. Gene sequences were aligned using Geneious Pro (5.6.6) (Biomatters Ltd. Auckland, New Zealand) and Bioedit Sequence Alignment Editor (v. 5.0.6) (Ibis Biosciences Carlsbad, CA). Genetic sequences for segments available for the four H14 viruses isolated from birds in 1982 were obtained from the online public databases (). In addition, the Basic Local Alignment Search Tool (BLAST) from the National Center for Biotechnology Information was used to assess the relationship of each gene segment from the 2010 H14 isolates with those sequences available on public databases.To compare the level of genetic divergence within other HA subtypes over a similar time period as the H14 comparison, we obtained sequences of other HA subtypes by querying the Influenza Research Database , and restricting results by time period (Past: ≤1989; Present ≥2009) (). The availability of sequences for both the past and present classifications determined the range of years selected for each HA subtype. Narrower time periods were chosen from subtypes that were overrepresented in the database. MEGA5 was used to compare genomic sequences of the isolates from 2010 to other isolates obtained from GenBank. Maximum Likelihood (ML) phylogenetic trees were constructed using RAxML . We used a GAMMAGTR nucleotide model for nucleotide sequence trees and a BLOSUM62 amino acid model for protein trees. The highest likelihood tree for each segment was then run with 250 standard bootstrap replicates and the consensus trees with bootstrap support values and midpoint rooting are presented in the figures. […]

Pipeline specifications

Software tools Geneious, BioEdit, BLASTN, MEGA, RAxML
Databases IRD
Application Phylogenetics
Organisms Influenza A virus
Diseases Varicose Ulcer, HIV Infections