The novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is causing an unprecedented pandemic, threatening global health, lifestyle, and economy. Genomic surveillance continues to be a critical effort towards tracking and containing the virus. We here report the successful assembly of one single gapless, unambiguous contiguous sequence representing the complete viral genome from a nasopharyngeal swab of an infected healthcare worker in Cairo, Egypt. The genome has all typical features of SARS-CoV-2 genomes, with no protein-disrupting mutations; however, three mutations are worth highlighting and future tracking: a synonymous mutation causing a rare spike S-813-I variation) and two less frequent ones leading to an A41V variation in NSP3, encoded by ORF1a, and a Q677H variation in the spike protein. Both affected proteins, S and NSP3, are relevant to vaccine and drug development.