2.7 Phylogenetic, recombination and statistical analysis
Nucleotide and amino acid sequences downloaded from NCBI GenBank were
used for phylogenetic analysis and aligned employing the E-INS-I
algorithm in MAFFT version 7 (Katoh et al., 2013). IQ-TREE version 1.6.7
(Nguyen et al., 2015) was used to determine the best-fit nucleotide and
amino acid substitution models for each alignment using the ModelFinder
program and the Akaike information criterion (AIC) (Kalyaanamoorthy et
al., 2017). Phylogenetic trees were inferred using the maximum
likelihood method in IQ-TREE employing the SH-like approximate
likelihood ratio test (SH-aLRT) and ultrafast bootstrap with 1000
replicates to assess nodal support (Hoang et al., 2018). Branch support
of >70 SH-aLRT and >70% UFBoot is shown as a
grey circle on the branch node of all phylogenetic trees. Nucleotide
alignments using MAFFT version 7 were screened for recombination events
using RDP4 and possible recombination events were then confirmed using
Simplot. To compare the virus composition in FPV-cases and healthy
controls, a two-tailed Fisher’s Exact Test was used and a p-value of
<0.05 was considered significant.