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Volume 27, Number 12—December 2021
Dispatch

SARS-CoV-2 Variants, South Sudan, January–March 2021

Daniel Lule Bugembe, My V.T. Phan, Abe G. Abias, James Ayei, Lul Lojok Deng, Richard Lino Loro Lako, John Rumunu, Pontiano Kaleebu, Joseph Francis Wamala, Juma John HM, Dennis Kenyi Lodiongo, Sudhir Bunga, and Matthew CottenComments to Author 
Author affiliations: Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda (D.L. Bugembe, M.V.T. Phan, P. Kaleebu, M. Cotten); National Public Health Laboratory—Ministry of Health, Juba, South Sudan (A.G. Abias, J. Ayei, L.L. Deng, R.L.L. Lako, J. Rumunu); World Health Organization, Juba (J.F. Wamala, J.J. HM); US Centers for Disease Control and Prevention, Juba, South Sudan (D.K. Lodiongo, S. Bunga); 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 viruses from South Sudan (red dots) and reference sequences. A) Lineage A.23.1. All sequences from South Sudan were combined with a subset of all available global A.23.1 genomes, algorithmically thinned. All available global A.23.1 genomes were retrieved from GISAID (https://www.gisaid.org) and aligned, and for the first genome, all genomes closer than 5 hamming distance were removed. This process was continued until the entire set was thinned. This global, thinned A.23.1 set was combined with all South Sudan A.23.1 genomes and used to infer the A.23.1 maximum-likelihood tree. The tree was rooted with the A.23 strain (UG109/PR_Amuru|A.23|2020–08–14). B) Lineage B.1.525. The B.1.525 genome sequences were prepared in the same manner as those for A.23.1 except the hamming distance of 20. Maximum-likelihood phylogenetic trees were constructed in RaxML-NG (8) under the general time reversible plus gamma 4 plus invariate sites model as the best-fit model of substitution according to the Akaike information criterion determined by modeltestNG (9) and run for 100 pseudoreplicates and visualized using FigTree version 1.4.4 (http://tree.bio.ed.ac.uk/software/figtree). For B.1.525, the tree was midpoint rooted for clarity. Scale bar indicates nucleotide substitutions per site.

Figure 2. Maximum-likelihood phylogenetic tree of severe acute respiratory syndrome coronavirus 2 viruses from South Sudan (red dots) and reference sequences. A) Lineage A.23.1. All sequences from South Sudan were combined with a subset of all available global A.23.1 genomes, algorithmically thinned. All available global A.23.1 genomes were retrieved from GISAID (https://www.gisaid.org) and aligned, and for the first genome, all genomes closer than 5 hamming distance were removed. This process was continued until the entire set was thinned. This global, thinned A.23.1 set was combined with all South Sudan A.23.1 genomes and used to infer the A.23.1 maximum-likelihood tree. The tree was rooted with the A.23 strain (UG109/PR_Amuru|A.23|2020–08–14). B) Lineage B.1.525. The B.1.525 genome sequences were prepared in the same manner as those for A.23.1 except the hamming distance of 20. Maximum-likelihood phylogenetic trees were constructed in RaxML-NG (8) under the general time reversible plus gamma 4 plus invariate sites model as the best-fit model of substitution according to the Akaike information criterion determined by modeltestNG (9) and run for 100 pseudoreplicates and visualized using FigTree version 1.4.4 (http://tree.bio.ed.ac.uk/software/figtree). For B.1.525, the tree was midpoint rooted for clarity. Scale bar indicates nucleotide substitutions per site.

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References
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