Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease (COVID-19), has been spreading globally since it was first reported in Wuhan, China, on December 30, 2019, infecting >10 million persons and causing massive disruption of daily lives and substantial economic consequences. Given the expanding pandemic and the absence of effective vaccines and antiviral drugs, the best strategy to control the spread of SARS-CoV-2 might be testing, contact tracing, and quarantining. Early implementation of diagnostic testing enables contact tracing and quarantining to reduce transmission in the community and can protect limited healthcare resources.

The importation of SARS-CoV-2 into Africa was inevitable given the volume of air travel and movement of tourists, traders, and workers between countries. We document COVID-19 outbreak preparedness and response in Uganda, a landlocked country in East Africa with entry by international flight or overland from bordering countries. The experience in Uganda provides a unique opportunity to follow virus transmission when early strong interventions are applied. We describe the importation of COVID-19 into Uganda and SARS-CoV-2 genomic data acquired from local sequencing efforts.

We established rapid local viral sequencing to document the genomic diversity of severe acute respiratory syndrome coronavirus 2 entering Uganda. Virus lineages closely followed the travel origins of infected persons. Our sequence data provide an important baseline for tracking any further transmission of the virus throughout the country and region.