Molecular characterization of the 2022 Sudan virus disease outbreak in Uganda

Abstract

Ebola disease (EBOD) is a public health threat with a high case fatality rate. Most EBOD outbreaks have occurred in remote locations, but the 2013-2016 Western Africa outbreak demonstrated how devastating EBOD can be when it reaches an urban population. Here, the 2022 Sudan virus disease (SVD) outbreak in Mubende District, Uganda, is summarized, and the genetic relatedness of the new variant is evaluated. The Mubende variant exhibited 96% amino acid similarity with historic SUDV sequences from the 1970s and a high degree of conservation throughout the outbreak, which was important for ongoing diagnostics and highly promising for future therapy development. Genetic differences between viruses identified during the Mubende SVD outbreak were linked with epidemiological data to better interpret viral spread and contact tracing chains. This methodology should be used to better integrate discrete epidemiological and sequence data for future viral outbreaks.

Keywords: Ebola virus; Sudan virus; Uganda; viral hemorrhagic fever.

Fig 1

Epidemiological curve and the ratio of sequenced to total samples over time. (A) Epidemiological curve including probable and confirmed cases. (B) The ratio of sequenced to total samples over time.

Fig 2

Orthoebolavirus sudanense species inter-outbreak inferred evolutionary relationships. (A) Maximum likelihood phylogenetic tree for all available full-length SUDV sequences. The tree is midpoint rooted, and the outbreak locations (Sudan vs Uganda) are indicated by color. Bootstrap support values (gray) greater than 70% are indicated at nodes (n = 1,000 replicates). (B) Divergence from root vs time demonstrates the clock-like nature of the Orthoebolavirus sudanense species substitution rate (dotted line). The confidence interval is shaded gray. (C) Substitution rate estimates compared across different Bayesian models, the root-to-tip analysis from (B), and the historic analysis from Carroll et al.

Fig 3

Sudan virus, Mubende variant intra-outbreak inferred evolutionary relationships. (A) Time-scaled phylogeny with leaves colored according to residence district. Nodes with posterior support greater than 0.6 are labeled in red. Node age estimates with 95% HPD intervals are at selected internal nodes (black). (B) Divergence from root vs time demonstrates the clock-like nature of the Mubende variant substitution rate (dotted line). The confidence interval is shaded gray. Root age was estimated at 1 November 2021.

Fig 4

The prevalence of nucleotide and amino acid mutations during the SUDV, Mubende variant outbreak. Mutations are relative to the inferred root ancestral sequence, and entropy is a count of the observed and inferred mutations relative to the total number of sequences in the tree. (A) Entropy of nucleotide mutations from Mubende variant sequences (n = 120). A red asterisk indicates the location of the UVRI SUDV qRT-PCR diagnostic assay primer and probe binding sites. (B) Entropy of non-silent amino acid mutations from Mubende variant sequences (n = 120).

Fig 5

Combining epidemiological and phylogenetic networks provides a wide-scale view of the Mubende SUDV outbreak. Circular nodes represent single individuals, are located a symptom onset dates (x-axis), and are colored according to residence district. Shading in boxes (green to orange) indicates genetic distance relative to the earliest sequence in the outbreak. Inset demonstrates a contact tracing chain consisting of three individuals. Numbers next to nodes indicate the number of raw nucleotide differences relative to the C069 sequence.