Fig. 1

Flow chart of individuals included in the study, a rural and an urban site, South Africa, 2020-2021. PCR - polymerase chain reaction. * Sequencing and PCR - variant confirmed on whole genome sequencing and variant typing PCR, Sequencing - variant confirmed on sequencing only, PCR, variant confirmed on variant typing PCR only, from cluster - inferred from household cluster, from wave - inferred from wave timing