Phylogenetic and diversity analyses of Garlic common latent virus based on the TGB and CP gene sequence

Garlic common latent virus (GarCLV, Carlavirus), in co-infection, often worsens the severity of other Allium viruses on garlic (Allium sativum Linnaeus). The nucleotide (nt) and amino acid (aa) sequences TGB CP genes were analysed to get first deep insight into genomic variations population structure GarCLV. Global recombinant-free isolates clustered three clades both nt-based phylogenetic trees CP. clade 3 shared low similarity percentages among themselves, as well 1 2 isolates. Most major aa changes observed its 5' 3' ends. Clade obtained lowest S, η, k, π values for CP, which indicated Both have undergone a negative selection, with being under stronger pressure than TGB. Neutrality tests estimated non-significant all except Tajima's D results Ks*, Kst*, Z*, Snn suggested that phylogroups divergent each high Fst comparisons showed large gene flow clades.