Retrospective Genomic Characterization of a 2017 Dengue Virus Outbreak, Burkina Faso

Abstract

Knowledge of contemporary genetic composition of dengue virus (DENV) in Africa is lacking. By using next-generation sequencing of samples from the 2017 DENV outbreak in Burkina Faso, we isolated 29 DENV genomes (5 serotype 1, 16 serotype 2 [DENV-2], and 8 serotype 3). Phylogenetic analysis demonstrated the endemic nature of DENV-2 in Burkina Faso. We noted discordant diagnostic results, probably related to genetic divergence between these genomes and the Trioplex PCR. Forward and reverse1 primers had a single mismatch when mapped to the DENV-2 genomes, probably explaining the insensitivity of the molecular test. Although we observed considerable homogeneity between the Dengvaxia and TetraVax-DV-TV003 vaccine strains as well as B cell epitopes compared with these genomes, we noted unique divergence. Continual surveillance of dengue virus in Africa is needed to clarify the ongoing novel evolutionary dynamics of circulating virus populations and support the development of effective diagnostic, therapeutic, and preventive countermeasures.

Keywords: Africa; Burkina Faso; RT-PCR; dengue virus; diagnostics; mosquito-borne diseases; next-generation sequencing; outbreak; phylogenetics; vector-borne infections; viruses.

Figure 1

Phylogenetic trees of dengue virus (DENV) serotypes 1 (A), 2 (B), and 3 (C), inferred from an alignment of the 2017 Burkina Faso dengue virus outbreak genomes (boldface) and all other complete genomes from US National Institutes of Health National Institute of Allergy and Infectious Diseases Virus Pathogen Database and Analysis Resource (http://www.viprbrc.org) and pruned to representative genotypes. The Burkina Faso genomes were DENV-1 genotype V, DENV-2 genotype Cosmopolitan, and DENV-3 genotype III. GenBank accession numbers are provided for reference genomes.

Figure 2

Time-calibrated phylogenetic trees of a subset of global dengue virus 1 genomes and 2017 Burkina Faso dengue virus outbreak genomes (boldface). Colored circles indicate geographic origin. Dates indicate the most recent common ancestor for the 2017 Burkina Faso dengue virus outbreak and all genomes from Africa. Posterior probabilities are indicated at major nodes. GenBank accession numbers are provided for reference genomes.

Figure 3

Time-calibrated phylogenetic trees of a subset of global dengue virus 2 genomes and 2017 Burkina Faso dengue virus outbreak genomes (boldface). Colored circles indicate geographic origin. Dates indicate the most recent common ancestor for the 2017 Burkina Faso dengue virus outbreak and all genomes from Africa. Posterior probabilities are indicated at major nodes. GenBank accession numbers are provided for reference genomes.

Figure 4

Time-calibrated phylogenetic trees of a subset of global dengue virus 3 genomes and 2017 Burkina Faso dengue virus outbreak genomes indicated (boldface). Colored circles indicate geographic origin. Dates indicate the most recent common ancestor for the 2017 Burkina Faso dengue virus outbreak and all genomes from Africa. Posterior probabilities are indicated at major nodes. GenBank accession numbers are provided for reference genomes.

Figure 5

Nucleotide identity between dengue virus molecular diagnostics and all sequenced DENV genomes from the 2017 Burkina Faso dengue outbreak. The map indicates the proportion of genomes from each country with >1 mismatches against the Trioplex PCR forward primer (A), probe (B), and reverse1 primer (C). Countries in gray have no data. DENV-1 and DENV-3 have concordant nucleotide identity to the primers and probe, but most DENV-2 forward primer and reverse1 primer in sequences from Africa have a high proportion of genomes with >1 mismatches to the Trioplex PCR’s primers and probe. DENV-1, dengue virus serotype 1; DENV-2, dengue virus serotype 2; DENV-3, dengue virus serotype 3

Figure 6

Dengue virus prM and E protein sequence alignments of Dengvaxia and TetraVax-DV-TV003 vaccine strains (boldface) and 2017 Burkina Faso dengue virus outbreak genomes for serotypes 1, 2, and 3. Only amino acid positions with disagreements are shown; single-point disagreements are highlighted. For clarity, prM protein sequences are shaded in red. Numerals represent the prM and E protein amino acid position. CYD, Dengvaxia vaccine; DENV-1, dengue virus serotype 1; DENV-2, dengue virus serotype 2; DENV-3, dengue virus serotype 3; E, envelope; prM, premembrane; TV003, TetraVax-DV-TV003 vaccine.

Figure 7

Amino acid mismatch comparison between 2017 Burkina Faso dengue virus outbreak genomes and virus neutralizing human mAbs for the 3 dengue virus serotypes. The amino acid changes presented are expected to disrupt binding between the envelope protein and heavy chain of the monoclonal antibodies. Dengvaxia vaccine amino acid included for comparison. Asterisk indicates all of the 2017 Burkina Faso dengue virus outbreak genomes share the same amino acid at that position. Numerals represent the E protein amino acid position. CYD, Dengvaxia vaccine; DENV-1, dengue virus serotype 1; DENV-2, dengue virus serotype 2; DENV-3, dengue virus serotype 3; E, envelope; mAb, monoclonal antibody.