Fig 3. Maximum likelihood tree displaying phylogeny for influenza A(H3N2) HA1 sequences (18) derived from household transmission study index cases and household contacts.

Sequences from 6 lineages are derived from 8 households. Study sequences aligned with 4 geographic control influenza HA sequences derived from South Africa between 2012 and 2014 as well as 2013 Southern Hemisphere H3N2 vaccine strain reference sequence, A/Victoria/361/2011. Corresponding household strains are marked with the same colour symbols at terminal nodes. Arrows highlight serial samples displaying sequence drift. Sequence nomenclature: Household ID_Study participant ID_Time point post-enrollment_Sample ID_(location ID). Pietermaritzburg (PMB); Klerksdorp (KDP). The scale bar represents genetic distance between sequences (nucleotide substitutions per site).