Abstract:
The first description of a disease resembling dengue fever (DF) was in the 15
century
slave trade era by Spanish sailors visiting the Tanzania coast. The disease, then associated
with evil spirits is now known to be caused by four serotypes of dengue virus (DENV1-4) that
are transmitted by Aedes mosquitoes. Kenya has experienced multiple outbreaks, mostly
associated with DENV-2. In this study, plasma samples obtained from 37 febrile patients
during a DF outbreak at Kenya’s south coast in March 2019 were screened for DENV. Total
RNA was extracted and screened for the alpha- and flavi-viruses by real-time polymerase
chain reaction (qPCR). DENV-3 was the only virus detected. Shotgun metagenomics and
targeted sequencing were used to obtain DENV whole genomes and the complete envelope
genes (E gene) respectively. Sequences were used to infer phylogenies and time-scaled
genealogies. Following Maximum likelihood and Bayesian phylogenetic analysis, two
DENV-3 genotypes (III, n = 15 and V, n = 2) were found. We determined that the two genotypes
had been in circulation since 2015, and that both had been introduced independently.
Genotype III’s origin was estimated to have been from Pakistan. Although the origin of genotype
V could not be ascertained due to rarity of these sequences globally, it was most related
to a 2006 Brazilian isolate. Unlike genotype III that has been described in East and West
Africa multiple times, this was the second description of genotype V in Kenya. Of note, there
was marked amino acid variances in the E gene between study samples and the Thailand
DENV-3 strain used in the approved Dengvaxia vaccine. It remains to be seen whether
these variances negatively impact the efficacy of the Dengvaxia or future vaccines.
