SARS-CoV-2 Omicron BA.5 Infections in Vaccinated Persons, Rural Uganda

Abstract

We describe a cluster of COVID-19 breakthrough infections after vaccination in Kyamulibwa, Kalungu District, Uganda. All but 1 infection were from SARS-CoV-2 Omicron strain BA.5.2.1. We identified 6 distinct genotypes by genome sequencing. Infections were mild, suggesting vaccination is not protective against infection but may limit disease severity.

Keywords: COVID-19; Omicron; SARS-CoV-2; Uganda; coronavirus disease; infections; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

Figure

Nucleotide changes between SARS-CoV-2 genomes from a cluster of COVID-19–positive persons in Kyamulibwa, Kalungu District, rural Uganda. The lower portion of the chart shows nucleotide differences from the case 1 genome, plotted as white bars. The absence of bars in the BA.5.2.1 genomes from cases 1, 2, 7, and 10 indicates identical sequences. Case 5 was determined to be lineage BA.2.31, and cases 4, 6, 11, and 12 genomes demonstrated virus variants of lineage BA.5.2.1 distinct from the genomes from cases 1, 2, 7, and 10. A schematic of the SARS-CoV-2 genome is shown in the top portion of the chart, with protein coding regions marked.