This paper presents a two-way factor design incorporating both spatial and temporal variation in the prediction of COVID 19 in Africa. In line with this, the impact of COVID-19on the GDP in Africa is well scrutinized. In contrast to the existing works [1–3], this work also extends the two-factor design into the one-way factor design through incorporating covariates into spatial effects. The data rely on the spatial and temporal obtained from WHO datasets [4, 5]. The one-factor design with more covariates is taken into consideration to identify the major potential predictor variables responsible for the deaths and confirmed cases due to COVID 19 in Africa. The MANCOVA considered population density, temperature, humidity; perception, and wind are all considered as co-variates. Simulations show that the two-way analysis of variance has shown that there is a statistically significant difference between the spatial (Fcal= 8.2704, Pvalue= 3.099∗10−6)and temporal (Fcal= 48.7964, Pvalue= 9.147∗10−16) effects. South Africa and Nigeria are highly influencing due to the pandemic where their GDP also relatively mostly declined. A significant economic change is observed before the pandemic and after the outbreak of the pandemic(tcal= 2.9548, Pvalue= 0.01805). COVID 19 negatively influenced the economy of1 most of the African countries. The population density, temperature, and wind are found to be statistically significantly associated with COVID 19 cases and deaths.