DATA AVAILABILITY STATEMENT : Sequences generated in this study are deposited in the GISAID EpiFlu
database under the accession numbers EPI2131759-EPI2131784, EPI2121793-EPI2131801, EPI2131810-
EP12131826, EP12131838-EPI2131851 and EPI2131857-EPI2131864.
SUPPLEMENTARY MATERIAL : FIGURE S1 (a): Maximum likelihood phylogenetic tree of the PB2 genes (2153 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; Figure S1 (b): Maximum likelihood phylogenetic tree of the PB2 genes (839 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S2: Maximum likelihood phylogenetic tree of the PB1 genes (2271 bp alignment). Viral sequences from the present study are indicated with black dots; FIGURE S3: Maximum likelihood phylogenetic tree of the PA genes (1940 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S4: Maximum likelihood phylogenetic tree of the NP genes (1372 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S5: Maximum likelihood phylogenetic tree of the N2 subtype NA genes (902 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S6: Maximum likelihood phylogenetic tree of the M genes (979 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S7: Maximum likelihood phylogenetic tree of the NS genes (832 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; TABLE S1: Samples analysed in the study and summary of results; TABLE S2: tMRCA analysis.