Detection of dengue virus serotypes 1, 2 and 3 in selected regions of Kenya: 2011-2014

Abstract

Background: Dengue fever, a mosquito-borne disease, is associated with illness of varying severity in countries in the tropics and sub tropics. Dengue cases continue to be detected more frequently and its geographic range continues to expand. We report the largest documented laboratory confirmed circulation of dengue virus in parts of Kenya since 1982.

Methods: From September 2011 to December 2014, 868 samples from febrile patients were received from hospitals in Nairobi, northern and coastal Kenya. The immunoglobulin M enzyme linked immunosorbent assay (IgM ELISA) was used to test for the presence of IgM antibodies against dengue, yellow fever, West Nile and Zika. Reverse transcription polymerase chain reaction (RT-PCR) utilizing flavivirus family, yellow fever, West Nile, consensus and sero type dengue primers were used to detect acute arbovirus infections and determine the infecting serotypes. Representative samples of PCR positive samples for each of the three dengue serotypes detected were sequenced to confirm circulation of the various dengue serotypes.

Results: Forty percent (345/868) of the samples tested positive for dengue by either IgM ELISA (14.6 %) or by RT-PCR (25.1 %). Three dengue serotypes 1-3 (DENV1-3) were detected by serotype specific RT-PCR and sequencing with their numbers varying from year to year and by region. The overall predominant serotype detected from 2011-2014 was DENV1 accounting for 44 % (96/218) of all the serotypes detected, followed by DENV2 accounting for 38.5 % (84/218) and then DENV3 which accounted for 17.4 % (38/218). Yellow fever, West Nile and Zika was not detected in any of the samples tested.

Conclusion: From 2011-2014 serotypes 1, 2 and 3 were detected in the Northern and Coastal parts of Kenya. This confirmed the occurrence of cases and active circulation of dengue in parts of Kenya. These results have documented three circulating serotypes and highlight the need for the establishment of active dengue surveillance to continuously detect cases, circulating serotypes, and determine dengue fever disease burden in the country and region.

Keywords: Dengue; Kenya; Serotypes 1, 2 and 3.

Fig. 1

Map of Kenya showing locations from which dengue cases were detected, 2011–2014. Map of Kenya showing the regions and number of samples received from different parts of Kenya. Samples were received from 7 regions of Kenya and from neighboring Somalia. Dengue serotypes 1–3 represented in different colours in the map were detected in various regions as shown in the pie charts. Only sites from which dengue cases were detected are shown on this map

Fig. 2

Number of dengue cases per region in Kenya, 2011–2014. Distribution of DENV serotypes in various regions in Kenya varied from 2011 to 2014. Overall, DENV1 was the most dominant serotype followed by DENV2 and 3 respectively. The colour green, purple, blue and orange represent the number of DENV-1, DENV-2, DENV-3 and IgM cases detected respectively

Fig. 3

Maximum Likelihood tree of Dengue virus capsid sequences. Phylogenetic relationships of Kenyan isolates of DENV-1, DENV-2 and DENV-3 as inferred by using the Maximum Likelihood method based on the Tamura-Nei model. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap values above 80 % are highlighted. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 34 nucleotide sequences. There were a total of 200 positions in the final dataset. Evolutionary analyses were conducted in MEGA7