2.4. Full-length genome sequence

The full-length genome sequences of twenty isolates from the West African data set were retrieved from NCBI (1 November 2020). In addition, seventeen isolates, including five isolates from the Republic of the Niger, were fully sequenced (Table S2). The thirty-seven full sequences were aligned using CLUSTAL X with default parameters (Thompson, Higgins, and Gibson 1994). The pairwise homoplasy (PHI) test was applied to detect the evidence of recombination events in a set of aligned sequences (Bruen, Philippe, and Bryant 2006). This test measures the significance of the phylogenetic discrepancy across sites in an alignment and yields a P-value. The PHI test is implemented in SplitsTree 4 software (Bryant and Moulton 2004). The full-length sequence alignment was also screened for recombination signals using RDP version 5.5 software (Martin et al., 2020). The default settings were used for each of the seven recombination detection algorithms that RDP incorporates, with a Bonferroni corrected P-value cut-off of 0.001. Only recombination events detected by more than three of the seven methods implemented in RDP were considered. The neighborNet phylogenetic network of the 37 fully sequenced isolates under a HKY85 distance model was inferred (Bryant and Moulton 2004). The neighborNet phylogenetic network illustrates the genetic relationships between sequences taking into account, in the internal box-like structures, the conflicting phylogenetic signals that are possibly due to recombination events.