First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries
Edgar Simulundu, Francis Mupeta, Pascalina Chanda‐Kapata, Ngonda Saasa, Katendi Changula, Walter Muleya, Simbarashe Chitanga, Miniva Mwanza, Paul Simusika, Herman M. Chambaro, Benjamin Mubemba, Masahiro Kajihara, Duncan Chanda, Lloyd Mulenga, Sombo Fwoloshi, Aaron Shibemba, Fred Kapaya, Paul Msanzya Zulu, Kunda Musonda, Mwaka Monze, Nyambe Sinyange, Mazyanga L. Mazaba, Muzala Kapina, Peter J. Chipimo, Raymond Hamoonga, Davie Simwaba, William Ngosa, Albertina N. Morales, Nkomba Kayeyi, John Tembo, Matthew Bates, Yasuko Orba, Hirofumi Sawa, Ayato Takada, King S. Nalubamba, Kennedy Malama, Victor Mukonka, Alimuddin Zumla, Nathan Kapata
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.