ABSTRACT
Introduction/ Background: In this cross-sectional study, we conducted genomic surveillance of SARS-CoV-2 with the aim of identifying emerging variants and tracking the genomic evolution of the virus. Furthermore, we analyzed the trends of SARS-CoV-2 lineages over time in Uganda. Methods: We performed SARS-CoV-2 whole-genome deep sequencing on samples collected between June- August 2021 from 107 patients (RT-PCR Ct values < 26) from 10 Districts in central (Kampala, Wakiso, Mpigi, Kalungu, Kalangala, Kassanda and Mityana) and northern (Dokolo, Amudat, Moroto) Uganda. Sequencing was done using the Illumina Miseq and Oxford Nanopore MinION next generation sequencing platforms. Deep sequence reads were assembled using Genome Detective and Nanopolish/Medaka (ARTIC). Quality control of the sequences was done using Nextclade and Geneious followed by lineage analysis using PANGOLIN (Phylogenetic Assignment of Named Global Outbreak LINeages). Results: 102 (95.3%) of 107 genomes were of the Delta variant (B.1.617.2). Delta AY sub-lineages detected at low prevalence included AY.1, AY.4, AY.16, AY.33 and AY.39. One AY.1 (delta plus) and 2 AY.16 sub-lineages were identified. Additionally, 1 Kappa B.1.617.1 variant was detected. Other minority lineages included A, B and Eta (B.1.525). By 20th September 2021, 712 SARSCoV- 2 sequences from Uganda had been deposited in GISAID (https://www.gisaid.org) and between December 2020 to January 2021, the A.23.1 variant dominated. The first Delta variant (B.1.617.1) sample was collected in March 2021 and by June 2021, Delta accounted for >90% of all detected variants. Impact: This study provides valuable information on the circulating variants and lineages in Uganda and contributes towards the national SARS-CoV-2 genomic surveillance. However, a major limitation of the study is the suboptimal sampling as a result of funding challenges. Conclusion: In Uganda, Delta has largely replaced other variants and is the dominant circulating SARS-CoV-2 variant. Study findings suggest that continued SARS-CoV-2 genomic surveillance from recently collected samples is critical to keep track of the circulating and emerging variants.