ORFs were located using the ORF Finder tool at NCBI (http:// www.ncbi.nlm.nih.gov/projects/gorf/). Annotation of the predicted proteins was performed by BLAST sequence similarity search against annotations in the NCBI RefSeq database. Multiple sequence alignments were constructed using MUSCLE version 3.8.31 [53] , and phylogenetic informative regions were extracted using BMGE [54] . Maximum-likelihood phylogenetic trees were constructed using PhyML version 3 [55] , under the best-fit protein evolution model as selected by ProtTest 3 [56] . Branch support values were estimated by calculation of SH-like aLRT values [57] . Recombination detection was performed by analysing the translated sequences of ORF1 and ORF2 separately using the Recombination Analysis Tool [58] .