First COVID 19 case in Zambia Comparative phylogenomic analyses of SARS CoV 2 detected in African countries
Since its first discovery in December 2019 in Wuhan, China, COVID 19, caused by the novel coronavirus SARS CoV 2, has spread rapidly worldwide. Whilst African countries were relatively spared initially, the initial low incidence of COVID 19 cases was not sustained for long due to continuing travel links between China, Europe and Africa. 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. Contact tracing showed that SARS CoV 2 infection was contained within the patient's household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient's SARS CoV 2 strain showed it 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 and case detection activities in order to monitor the origin and evolution of SARS CoV 2 lineages across Africa.
International Journal of Infectious Diseases