Fig. 3

Epidemiological validation of the co-infections. Each bar corresponds to the mean pairwise SNP distance and standard deviation between any two circulating strains in our population in each 2-month period during the pandemic. Each black dot or open circle corresponds to a co-infected case and is plotted by taking into account the number of SNPs between co-infecting strains. Co-infections involving strains from the same or different lineage/sublineages are shown as black dots or open circles, respectively. The majority and minority lineages involved in each co-infection are shown top and bottom, respectively (except for the first 2-month period where they are shown as left and right). The colour of the bar indicates the majority lineage in each period (see legend)