SARS-CoV-2 is a betacoronavirus, the etiologic agent of the novel Coronavirus disease 2019 (COVID-19). In December 2019, an outbreak of COVID-19 began in Wuhan province of the Hubei district in China and rapidly spread across the globe. On March 11th, 2020, the World Health Organization officially designated COVID-19 as a pandemic. Across the continents and specifically in Africa, all index cases were travel related. Thus, it is crucial to compare COVID-19 genome sequences from the African continent with sequences from COVID-19 hotspots (including China, Brazil, Italy, United State of America and the United Kingdom). To identify if there are distinguishing mutations in the African SARS-CoV-2 genomes compared to genomes from other countries, including disease hotspots, we conducted in silico analyses and comparisons. Complete African SARS-CoV-2 genomes deposited in GISAID and NCBI databases as of June 2020 were downloaded and aligned with genomes from Wuhan, China and other SARS-CoV-2 hotspots. Using phylogenetic analysis and amino acid sequence alignments of the spike and replicase (NSP12) proteins, we searched for possible targets for vaccine coverage or potential therapeutic agents. Our results showed a similarity between the African SARS-CoV-2 genomes and genomes in countries including China, Brazil, France, the United Kingdom, Italy, France and the United States of America. This study shows for the first time, an in-depth analysis of the SARS-CoV-2 landscape across Africa and will potentially provide insights into specific mutations to relevant proteins in the SARS-CoV-2 genomes in African populations.