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Volume 28, Number 5—May 2022
Dispatch

Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021

Nicholas BbosaComments to Author , Deogratius Ssemwanga, Hamidah Namagembe, Ronald Kiiza, Jocelyn Kiconco, John Kayiwa, Tom Lutalo, Julius Lutwama, Alfred Ssekagiri, Isaac Ssewanyana, Susan Nabadda, Henry Kyobe-Bbosa, Jennifer Giandhari, Sureshnee Pillay, Upasana Ramphal, Yajna Ramphal, Yeshnee Naidoo, Derek Tshiabuila, Houriiyah Tegally, Emmanuel J. San, Eduan Wilkinson, Tulio de Oliveira, and Pontiano Kaleebu
Author affiliations: Medical Research Council/Uganda Virus Research Institute, Entebbe, Uganda (N. Bbosa, D. Ssemwanga, H. Namagembe, J. Kiconco, J. Kayiwa, T. Lutalo, J. Lutwama, A. Ssekagiri, P. Kaleebu); London School of Hygiene and Tropical Medicine Uganda Virus Research Unit, Entebbe (D. Ssemwanga, R. Kiiza, J. Kiconco, J. Kayiwa, T. Lutalo, J. Lutwama, A. Ssekagirl, P. Kaleebu); Ministry of Health, Kampala, Uganda (I. Ssewanyana, S. Nabadda, H. Kyobe-Bbosa); University of KwaZulu-Natal, Durban, South Africa (J. Giandhari, S. Pillay, U. Ramphal, Y. Ramphal, Y. Naidoo, D. Tshiabuila, H. Tegally, E.J. San, E. Wilkinson, T. de Oliveira); Stellenbosch University, Stellenbosch, South Africa (E. Wilkinson, T. de Oliveira)

Main Article

Figure 2

Rapid replacement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants by Delta and subsequent arrival of Omicron, Uganda, 2021. A) Coronavirus disease pandemic waves. Confirmed cases of daily coronavirus disease and trends of the SARS-CoV-2 pandemic over time. Three waves of the pandemic dominated by the A.23.1 in the first wave (December 2020‒January 2021), Delta in the second wave (May‒July 2021), and the Delta and Omicron variants in the third wave (Omicron emerged in late November 2021 and the wave began in December 2021). B, C) SARS-CoV-2 variants over time (950 genomes deposited in the GISAID database [https://www.gisaid.org] by January 10, 2022). D) SARS-CoV-2 variants during the third wave among travelers and community samples. E) Violin plots showing the distribution of whole-genome nucleotide mutations in each of the SARS-CoV-2 lineages by using the wild-type Wuhan-Hu-1/2019 isolate (GenBank accession no. MN908947) as the reference. Black dots indicate median number of nucleotide mutations. Error bars indicate interquartile ranges.

Figure 2. Rapid replacement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants by Delta and subsequent arrival of Omicron, Uganda, 2021. A) Coronavirus disease pandemic waves. Confirmed cases of daily coronavirus disease and trends of the SARS-CoV-2 pandemic over time. Three waves of the pandemic dominated by the A.23.1 in the first wave (December 2020‒January 2021), Delta in the second wave (May‒July 2021), and the Delta and Omicron variants in the third wave (Omicron emerged in late November 2021 and the wave began in December 2021). B, C) SARS-CoV-2 variants over time (950 genomes deposited in the GISAID database [https://www.gisaid.org] by January 10, 2022). D) SARS-CoV-2 variants during the third wave among travelers and community samples. E) Violin plots showing the distribution of whole-genome nucleotide mutations in each of the SARS-CoV-2 lineages by using the wild-type Wuhan-Hu-1/2019 isolate (GenBank accession no. MN908947) as the reference. Black dots indicate median number of nucleotide mutations. Error bars indicate interquartile ranges.

Main Article

Page created: February 28, 2022
Page updated: April 19, 2022
Page reviewed: April 19, 2022
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