Fig. 3

Unrooted phylogram of WGS from T13 V. cholerae isolates from Zambia, Tanzania and Uganda. The branch lines are proportional to the number of nucleotide differences between the sequences. CC2 and CC3 refer to the clonal complex defined by MLVA. The box indicates isolate Mz1 from Tanzania collected in 2016 that is an example of an isolate with many unique SNVs as seen by the long branch length. The seven isolates collected in Lusaka in 2016 are on a distinct branch from the six isolates collected 2017/2018 in Lusaka. The 2017/2018 isolates from Lusaka are less than 4 SNV differences from thirteen isolates from Tanzania collected in 2015, 2016 and 2017. The Chiengi isolate is 4 unique SNVs from the 2017/2018 isolates from Lusaka