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

Abstract

We established rapid local viral sequencing to document the genomic diversity of severe acute respiratory syndrome coronavirus 2 entering Uganda. Virus lineages closely followed the travel origins of infected persons. Our sequence data provide an important baseline for tracking any further transmission of the virus throughout the country and region.

Keywords: 2019 novel coronavirus disease; COVID-19; SARS-CoV-2; Uganda; coronavirus disease; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

Figure 1

International flight routes of imported cases (colored lines) and the 4 main points of land entry into Uganda from Kenya, Tanzania, and South Sudan (colored dots).

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.