High Dengue Burden and Circulation of 4 Virus Serotypes among Children with Undifferentiated Fever, Kenya, 2014-2017

Abstract

Little is known about the extent and serotypes of dengue viruses circulating in Africa. We evaluated the presence of dengue viremia during 4 years of surveillance (2014-2017) among children with febrile illness in Kenya. Acutely ill febrile children were recruited from 4 clinical sites in western and coastal Kenya, and 1,022 participant samples were tested by using a highly sensitive real-time reverse transcription PCR. A complete case analysis with genomic sequencing and phylogenetic analyses was conducted to characterize the presence of dengue viremia among participants during 2014-2017. Dengue viremia was detected in 41.9% (361/862) of outpatient children who had undifferentiated febrile illness in Kenya. Of children with confirmed dengue viremia, 51.5% (150/291) had malaria parasitemia. All 4 dengue virus serotypes were detected, and phylogenetic analyses showed several viruses from novel lineages. Our results suggests high levels of dengue virus infection among children with undifferentiated febrile illness in Kenya.

Keywords: Kenya; arboviruses; children; circulation; dengue; dengue virus; disease burden; serotypes; undifferentiated fever; viruses; zoonoses.

Figure 1

Countries in Africa (indicated by colors) for which dengue virus (DENV) sequences isolated from humans are available in GenBank. A) DENV-1, B) DENV-2, C) DENV-3, D) DENV-4. Further details on search strategy used for this map are available in Appendix Table.

Figure 2

Study recruitment sites (black dots) for high dengue burden and circulation of 4 virus serotypes among children with undifferentiated fever, Kenya, 2014–2017. Inset map shows location of Kenya in Africa.

Figure 3

Dengue virus serotypes detected over time for children tested during a medical visit for fever, Kenya, 2014–2017. Data from 4 sites are included. DENV, dengue virus.

Figure 4

Maximum-likelihood phylogenetic tree for DENV-1 sequences from children with undifferentiated fever in Kenya, 2014–2017 (red), and reference sequences from other locations in Africa (blue) and elsewhere. Numbers at nodes represent bootstrap support values based on maximum-likelihood replicates. Genotypes are indicated at right. Scale bar indicates nucleotide substitutions per site. DENV, dengue virus.

Figure 5

Maximum-likelihood phylogenetic tree for DENV-2 sequences from children with undifferentiated fever in Kenya, 2014–2017 (red), and reference sequences from other locations in Africa (blue) and elsewhere. Numbers at nodes represent bootstrap support values based on maximum-likelihood replicates. Genotypes are indicated at right. Scale bar indicates nucleotide substitutions per site. DENV, dengue virus.

Figure 6

Maximum-likelihood phylogenetic tree for DENV-3 sequences from children with undifferentiated fever in Kenya, 2014–2017 (red), and reference sequences from other locations in Africa (blue) and elsewhere. Numbers at nodes represent bootstrap support values based on maximum-likelihood replicates. Genotypes are indicated at right. Scale bar indicates nucleotide substitutions per site. DENV, dengue virus.

Figure 7

Maximum-likelihood phylogenetic tree for DENV-4 sequences from children with undifferentiated fever in Kenya, 2014–2017 (red), and reference sequences from other locations in Africa (blue) and elsewhere. Numbers at nodes represent bootstrap support values based on maximum-likelihood replicates. Genotypes are indicated at right. Scale bar indicates nucleotide substitutions per site. DENV, dengue virus.