First COVID-19 case in Zambia - Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries

Abstract

Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. While 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 h 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 that 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 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.

Keywords: COVID-19; Diagnosis; Phylogenetic analyses; SARS-CoV-2; Zambia.

Figure 1

Chest X-ray (CXR) of the first case of COVID-19 in Zambia. The CXR was taken on day 4 after the onset of illness. White arrow shows nodular infiltrates suspected to be micro-abscesses. Black arrows show bilateral infiltrates affecting lower zones mostly peripheral and the centre.

Figure 2

A maximum likelihood tree showing phylogenetic relationships of the complete genome of SARS-CoV-2 detected in a patient in Zambia and other 73 SARS-CoV-2 genomes retrieved from the GISAID database. Of the 73 genomes, 59 were a selection representing African countries that had deposited whole genomes in the GISAID database. The genome generated in this study is shown in red. Viral lineages are shown as shaded areas. The scale shows nucleotide substitutions per site (see attached file for clearer image).