Molecular Characterization and Phylogenetic Analysis of Dengue Fever Viruses in Three Outbreaks in Tanzania Between 2017 and 2019

Abstract

Background: Dengue is a disease of public health interest, and Tanzania experienced major outbreaks in 2014 and 2019. Here, we report our findings on the molecular characterization of dengue viruses (DENV) that circulated during two smaller outbreaks (2017 and 2018) and one major epidemic (2019) in Tanzania.

Methodology/principal findings: We tested archived serum samples from 1,381 suspected dengue fever patients, with a median age of 29 (IQR:22-40) years, referred to the National Public Health Laboratory for confirmation of DENV infection. DENV serotypes were identified by reverse transcription polymerase chain reaction (RT-PCR), and specific genotypes were identified by sequencing the envelope glycoprotein gene and phylogenetic inference methods. DENV was confirmed in 823 (59.6%) cases. More than half (54.7%) of patients with dengue fever infection were males, and nearly three-quarters (73%) of the infected individuals were living in Kinondoni district, Dar es Salaam. DENV-3 Genotype III caused the two smaller outbreaks in 2017 and 2018, while DENV-1 Genotype V caused the 2019 epidemic. DENV-1 Genotype I was also detected in one patient in 2019.

Conclusion/significance: This study has demonstrated the molecular diversity of dengue viruses circulating in Tanzania. We found that contemporary circulating serotypes did not cause the major epidemic of 2019 but rather due to a serotype shift from DENV-3 (2017/2018) to DENV-1 in 2019. Such a change increases the risk for patients previously infected with a particular serotype to develop severe symptoms upon potential re-infection with a heterologous serotype due to antibody-dependent enhancement of infection. Therefore, the circulation of serotypes emphasizes the need to strengthen the country's dengue surveillance system for better management of patients, early detection of outbreaks, and vaccine development.

Fig 1. Distribution of dengue fever cases in Tanzania from 2017 to 2019.

The map shows 26 Tanzania mainland administrative regions. The five color-coded regions show dengue fever cases distribution between 2017–2019. Map created with QGIS 3.24.1 All shape files are openly available sources (https://www.nbs.go.tz/index.php/en/census-surveys/gis/385-2012-phc-shapefiles-level-one-and-two). The shapefiles were made based on the 2012 population and housing census, but in this study, the shapefile has been modified to capture all the regions and district information.

Fig 2. Genotyping of DENV-3 circulating in Tanzania 2017–2018.

Maximum likelihood phylogenetic tree reconstructed with the 32 DENV-3 sequence generated by this study and 40 additional sequences from GenBank to provide genotype reference and geographic-temporal context. The tree was rooted at midpoint. pink, blue, green, gold and purple represents genotypes V, II, III, I, and IV, respectively. Tanzanian sequences (OM920035—OM920066) are in red. Contextual sequences are labeled with GenBank accession number, country of origin, and year of isolation.

Fig 3. Genotyping of DENV-1 circulating in Tanzania in 2019.

Maximum likelihood phylogenetic tree reconstructed with the 341 sequences generated by this study and 69 additional sequences from GenBank to provide genotype reference and geographic-temporal context. The tree was rooted at midpoint. Genotype I was only detected from one sample in 2019, while genotype V was found widely circulated in the 2019 epidemic. The Tanzanian sequences (OM920075—OM920415) in red. Genotypes are presented with colored highlighted branches; Genotypes IV, III, V, II, and I are highlighted in pink, blue, green, gold, and purple, respectively. Contextual sequences are labeled with GenBank accession number, country of origin, and year of isolation.