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Highlights Whilst African countries were relatively spared initially when COVID-19 was first reported from China, the frequent travel links between China, Europe and Africa, meant importation of SARS-CoV-2 into Africa was inescapable. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 hours of the individual entering the country by air travel from a trip to France. Phylogenomic analysis showed that the detected SARS-CoV-2 belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that lineage B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance activities to monitor the origin and evolution of SARS-CoV-2 lineages across Africa.