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Volume 26, Number 10—October 2020
Dispatch

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

Daniel Lule Bugembe1, John Kayiwa1, My V.T. Phan1, Phiona Tushabe, Stephen Balinandi, Beatrice Dhaala, Jonas Lexow, Henry Mwebesa, Jane Aceng, Henry Kyobe, Deogratius Ssemwanga, Julius Lutwama, Pontiano Kaleebu, and Matthew CottenComments to Author 
Author affiliations: UK Medical Research Council–Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda (D. Lule Bugembe, B. Dhaala, J. Lexow, D. Ssemwanga, P. Kaleebu, M. Cotten); Uganda Virus Research Institute, Entebbe (J. Kiyawa, P. Tushabe, S. Balinandi, D. Ssemwanga, J. Lutwama, P. Kaleebu); Erasmus Medical Center, Rotterdam, the Netherlands (M.V.T. Phan); Uganda Ministry of Health, Kampala, Uganda (H. Mwebesa, J. Aceng, H. Kyobe); UK Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK (M. Cotten)

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Figure 2

Maximum-likelihood phylogenetic tree of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes in Uganda. The full SARS-CoV-2 genomes used for phylogenetic lineage nomenclature (A. Rambaut et al., unpub. data, https://doi.org/10.1101/2020.04.17.046086) as defined on May 19, 2020, were retrieved from GISAID (http://www.gisaid.org) (8). Identical sequences were removed, and a total of 395 global representative sequences from each phylogenetic lineage type were selected for further ph

Figure 2. Maximum-likelihood phylogenetic tree of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes in Uganda. The full SARS-CoV-2 genomes used for phylogenetic lineage nomenclature (A. Rambaut et al., unpub. data, https://doi.org/10.1101/2020.04.17.046086) as defined on May 19, 2020, were retrieved from GISAID (http://www.gisaid.org) (8). Identical sequences were removed, and a total of 395 global representative sequences from each phylogenetic lineage type were selected for further phylogenetic analyses. The reported Uganda sequences, combined with the global SARS-CoV-2 sequences, were aligned by using MAFFT (9) and untranslated regions at 5′ and 3′ were trimmed. Maximum-likelihood phylogenetic tree was constructed in RAxML (10), under the general time-reversible plus gamma distribution model as best-fitted substitution model determined by IQ-TREE (11) and run for 100 pseudo-replicates. The resulting tree was visualized in Figtree (12) and rooted at the point of splitting lineage A and B. Scale bar indicates 6 × 10–5 nucleotide substitutions per site. The branch length is drawn to the scale of nucleotide substitutions per site. The Uganda genomes are indicated in red. The 2 major lineages of SARS-CoV-2 (A and B) are indicated to the left of the tree; the main groups of the Uganda genomes (A, B1.1.1, B4) are indicated by colored boxes to the right of the tree.

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1These first authors contributed equally to this article.

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