Genomic surveillance in Uganda showed rapid replacement of severe acute respiratory syndrome coronavirus 2 over time by variants, dominated by Delta. However, detection of the more transmissible Omicron variant among travelers and increasing community transmission highlight the need for near-real-time genomic surveillance and adherence to infection control measures to prevent future pandemic waves.
Keywords: COVID-19; Delta; Omicron; SARS-CoV-2; Uganda; coronavirus disease; coronaviruses; genomic surveillance; rapid replacement; respiratory infections; severe acute respiratory coronavirus 2; variants; viruses; whole-genome deep sequencing; zoonoses.