key: cord-0932386-esotlorl authors: Bbosa, Nicholas; Ssemwanga, Deogratius; Namagembe, Hamidah; Kiiza, Ronald; Kiconco, Jocelyn; Kayiwa, John; Lutalo, Tom; Lutwama, Julius; Ssekagiri, Alfred; Ssewanyana, Isaac; Nabadda, Susan; Kyobe-Bbosa, Henry; Giandhari, Jennifer; Pillay, Sureshnee; Ramphal, Upasana; Ramphal, Yajna; Naidoo, Yeshnee; Tshiabuila, Derek; Tegally, Houriiyah; San, Emmanuel J.; Wilkinson, Eduan; de Oliveira, Tulio; Kaleebu, Pontiano title: Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021 date: 2022-05-03 journal: Emerg Infect Dis DOI: 10.3201/eid2805.220121 sha: a65e070e0174665607b5a0d0431bf319bdef8119 doc_id: 932386 cord_uid: esotlorl 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. (https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html) (for the Nanopore-generated sequence reads) to obtain high-quality SARS-CoV-2 genomes with >80% coverage. We performed quality control of all sequences to check for adequate coverage, indels, and frameshifts. We performed mutation calling by using Nextclade (https://clades.nextstrain. org), followed by SARS-CoV-2 lineage analysis with Pangolin (https://github.com/cov-lineages/pangolin). To analyze trends of SARS-CoV-2 lineages over time, we downloaded all sequences from Uganda in GISAID (https://www.gisaid.org) (950 sequences as of January 10, 2022). Results showed that most (195, 73 Figure 1 ). Uganda is in the third wave of the COVID-19 pandemic ( Figure 2 We performed a subanalysis of SARS-CoV-2 variants during the third wave ( Figure 2, panel D) . We also detected other Delta sublineages, such as AY.1 or B.1.617.2.1 (also known as Delta Plus and associated with a relatively higher transmissibility) (6), at a low prevalence. The AY.1 Delta sublineage has been associated with more antibody escaping properties because of the K417N mutation, which was identified in the Beta variant (7). We also provide the relative number of mutations for SARS-CoV-2 variants (Figure 2, panel E) . We deposited all sequences generated during this study in the GISAID public database (accession nos. EPI ISL 4548461-543, EPI_ISL_6262724-47, EPI_ISL_8307285-411, EPI_ISL_8523904-5, EPI_ISL_6506618, EPI_ ISL_6506627, EPI_ISL_6506639, EPI_ISL_6506648, EPI_ISL_6506655, EPI_ISL_6506666, EPI_ISL_6506674, EPI_ISL_6506689, EPI_ISL_6506697, EPI_ISL_6506706, EPI_ISL_6506713, EPI_ISL_6506721, EPI_ISL_6506726, EPI_ISL_6506738, EPI_ISL_6506747, EPI_ISL_6506751, EPI_ISL_6506760, EPI_ISL_6506767, EPI_ISL_6506773, EPI_ISL_6506784, EPI_ISL_6506791, EPI_ISL_6506802, EPI_ISL_6506812, EPI_ISL_6506824, EPI_ISL_6506829, EPI_ISL_6506835, EPI_ISL_6506841, EPI_ISL_6506844 , EPI_ISL_6506851, and EPI_ISL_6506857). Uganda showed a rapid replacement of variants since the beginning of the COVID-19 pandemic. Genomic sequencing involving 266 samples collected during June-December 2021 showed that the Delta variant was the dominant virus. However, the Omicron variant emerged in late November 2021 from travelers arriving through Entebbe International Airport (39.29% from South Africa, 28.57% from Nigeria, 14.29% from Kenya, 7.14% from the Democratic Republic of the Congo, 3.57% from Ethiopia, 3.57% Rwanda, and 3.57% from the United States), and Omicron community transmissions are increasing (based on PCR genotyping). Therefore, we anticipate that Delta is gradually being replaced by Omicron, which is consistent with the observed SARS-CoV-2 variants trajectory over time. Furthermore, results from a mutation-specific SARS-CoV-2 PCR screening (8, 9) suggest that Omicron, initially becoming dominant among travelers, will likely later predominate in the community. The Omicron variant has been associated with increased transmissibility and has quickly become a global concern (10). Speeding up genomic sequencing from prospective samples collected at points of entry and from the community will enable faster response to outbreaks as they emerge. A major limitation of this study was suboptimal sampling. Previously, convenience sampling that targeted points of entry and outbreak hotspots was more common. Sampling prioritized mostly moderate-tohigh community transmission sites and focused less on sampling low viral transmission communities. However, plans are under way to adopt effective sampling guidelines to ensure geographically representative sampling (11, 12) . In summary, the SARS-CoV-2 Delta variant rapidly replaced earlier virus variants after it was introduced into Uganda. The Omicron variant has followed the same trajectory. Our results highlight the need for surveillance and infection control measures to prevent future pandemic waves. 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The Ministry Interim operational guidance on SARS-CoV-2 genomic surveillance in Africa: an updated guide We thank the Uganda Ministry of Health and its COVID-19 Scientific Advisory Committee, the National COVID-19 Task Force, and the staff of the Emerging and Remerging Infections Department of the Uganda Virus Research Institute for their providing contributions; the team at the KwaZulu-Natal Research Innovation and Sequencing Platform for providing laboratory training and support; the staff at the Uganda Virus Research Institute for collecting field samples; and the persons who collected samples at borders or points of entry into Uganda.