Feline coronavirus isolates from a part of Brazil: insights into molecular epidemiology and phylogeny inferred from the 7b gene

MYRRHA, Luciana Wanderley; SILVA, Fernanda Miquelitto Figueira; VIDIGAL, Pedro Marcus Pereira; RESENDE, Maurício; BRESSAN, Gustavo Costa; FIETTO, Juliana Lopes Rangel; SANTOS, Marcus Rebouças; SILVA, Laura Morais Nascimento; ASSAO, Viviane Sisdelli; SILVA-JÚNIOR, Abelardo; de ALMEIDA, Márcia Rogéria

The BI phylogenetic trees were calculated using the Bayesian Markov Chain Monte Carlo (MCMC) method, in two runs with 50,000,000 generations and a sample frequency of 1.000. At the end of each run, the average standard deviation of the split frequencies was 0.015022. The convergence of the parameters was analyzed in TRACER v1.5.0, and the chains reached a stationary distribution after 500,000 generations. Then, a total of 1% of the trees generated was burned to produce the consensus trees. The TIM3ef+I+G substitution model was selected in the GARLI settings (ratematrix=(0 1 2 0 3 2); statefrequencies=estimate; ratehetmodel=gamma; numratecats=4; invariantsites=estimate), and the statistical support of the ML phylogenetic trees was calculated by 1,000 bootstrap replicates. The 50% majority rule consensus trees of all bootstrap replicates were summarized using the SumTrees of DendroPy 3.8.0 [30] .