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

Abstract

As the coronavirus pandemic continues, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence data are required to inform vaccine efforts. We provide SARS-CoV-2 sequence data from South Sudan and document the dominance of SARS-CoV-2 lineage B.1.525 (Eta variant) during the country's second wave of infection.

Keywords: COVID-19; SARS-CoV-2; South Sudan; coronavirus disease; respiratory infections; severe acute respiratory syndrome coronavirus 2; variants; viruses; zoonoses.

Figure 1

Locations of severe acute respiratory syndrome coronavirus 2 infection case-patients from whom genomes were isolated, South Sudan. Red circles indicate viruses of lineage B.1.525; dark gray circles indicate lineage A.23.1. Circle size is proportional to number of genomes. Blue text shows the number of A.23.1 and B.1.525 genomes reported from neighboring countries. CAR, Central African Republic; DRC, Democratic Republic of the Congo.

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.