Computational protocol: Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

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Protocol publication

[…] Reassortment events confuse the codon usage pattern, and phylogenetic tree topology; therefore, reassortant strains were removed based on previous studies and evidenced from the phylogenetic trees. Alignments were performed using Muscle. Timescaled phylogenetic trees were reconstructed using BEAST (version 1.8.0). We used Bayesian Markov Chain Monte Carlo (MCMC) method to infer phylogenetic trees. The optimal nucleotide substitution model was estimated using MEGA 7.0. The HKY85 plus gamma distribution substitution model was used in BEAST. Additionally, Bayesian skyline coalescent prior was assumed with a relaxed lognormal clock. The MCMC chains were run twice independently for 108 generations and sampled every 10‚ÄČ000 steps. Runs were further combined using LogCombiner software. Using the TreeAnnotator program in the BEAST package, a target tree was summarized by selecting the tree with the largest posterior probability with a 10% burn-in. Additionally, 597 complete H3N2 HA and NA sequences, including 43 CIV sequences, 259 complete avian influenza virus sequences, and 295 complete human influenza virus sequences, were used to reconstruct the maximum likelihood phylogenetic tree using RAxML. [...] dN/dS values of all reported avian influenza viral strains and the selected CIV and human influenza virus strains were estimated using DATAMONKEY (http://www.datamonkey.org/). Alignments were performed using Muscle after removing termination codons. [...] The frequencies of 16 dinucleotides per strain were calculated using DAMBE software. The ratio was calculated as follows:Pxy=rxyryrxwhere rx and ry represent the frequency of nucleotides X and Y, respectively, while rxy represents the observed dinucleotide XY value, and ryrx represents the expected value of the dinucleotide XY. It is normally considered that the XY dinucleotide is overrepresented when Pxy is >1.23 and underrepresented when it is <0.78. […]

Pipeline specifications

Software tools Datamonkey, DAMBE
Applications Phylogenetics, Population genetic analysis
Organisms Canis lupus familiaris, Invertebrate iridescent virus 6, Viruses, Homo sapiens, Felis catus
Diseases Influenza, Human