Computational protocol: Reassortment compatibility between PB1, PB2, and HA genes of the two influenza B virus lineages in mammalian cells

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Protocol publication

[…] Complete genome sets of 431 IBVs circulating between 1986 and 2012 years were downloaded from the database of the National Center for Biotechnology Information. The eight genetic segment sets of the viruses were aligned using the MAFFT program. Phylogenetic relationships were then reconstructed using a time-framed Bayesian evolution analysis approach via a Markov Chain Monte Carlo (MCMC) inference method, implemented in the BEAST package (v1.8.2). To reconstruct the evolutionary relationships of each genetic sequence set, we adopted flexible and consistent models for all segments, including a GTR+I+Γ substitution model, a lognormal relaxed molecular clock, and a Bayesian skygrid tree models as a tree prior. MCMC analyses were run for 50 million iterations, sampling every 50 thousand iterations after a 10% burn-in. Two independent runs were ensured for their convergence in Tracer (v1.6) (http://tree.bio.ed.ac.uk/software/tracer/). Maximum clade credibility (MCC) trees were obtained from the MCMC tree samples using TreeAnnotator v1.8.2 and were visualized using Fig Tree (v1.4.2) (http://tree.bio.ed.ac.uk/software/figtree/). [...] Reassortment events were analyzed using the graph incompatibility-based reassortment finder (GiRaF) program. Aligned nucleotide sequence sets of the eight genetic segments were used for the phylogenetic relationship reconstruction in MrBayes (GTR+I+Γ, 1,000,000 iterations, 10% burn-in and sampling every 10,000 iterations). The trees were then used for the phylogenetic uncertainty modeling using the GiRaF program. It was repeated 10 times, and the results were summarized using the catalog reassortment events exhibiting more than 0.6 detection frequency. […]

Pipeline specifications

Software tools MAFFT, BEAST, FigTree, GiRaF, MrBayes
Application Phylogenetics
Organisms Homo sapiens, Human poliovirus 1 Mahoney, Viruses
Diseases Hepatitis B, Genetic Diseases, Inborn