Origin and evolution of dengue virus type 2 causing outbreaks in Kenya: Evidence of circulation of two cosmopolitan genotype lineages

Abstract

Dengue fever (DF) is an arboviral disease caused by dengue virus serotypes 1-4 (DENV 1-4). Globally, DF incidence and disease burden have increased in the recent past. Initially implicated in a 1982 outbreak, DENV-2 recently reemerged in Kenya causing outbreaks between 2011 and 2014 and more recently 2017–8. The origin and the evolutionary patterns that may explain the epidemiological expansion and increasing impact of DENV-2 in Kenya remain poorly understood. Using whole-genome sequencing, samples collected during the 2011–4 and 2017–8 dengue outbreaks were analyzed. Additional DENV-2 genomes were downloaded and pooled together with the fourteen genomes generated in this study. Bioinformatic methods were used to analyze phylogenetic relationships and evolutionary patterns of DENV-2 causing outbreaks in Kenya. The findings from this study have shown the first evidence of circulation of two different Cosmopolitan genotype lineages of DENV-2; Cosmopolitan-I (C-I) and Cosmopolitan-II (C-II), in Kenya. Our results put the origin location of C-I lineage in India in 2011, and C-II lineage in Burkina Faso between 1979 and 2013. C-I lineage was the most isolated during recent outbreaks, thus showing the contribution of this newly emerged strain to the increased DENV epidemics in the region. Our findings, backed by evidence of recent local epidemics that have been associated with C-I in Kenya and C-II in Burkina Faso, add to the growing evidence of expanding circulation and the impact of multiple strains of DENV in the region as well as globally. Thus, continued surveillance efforts on DENV activity and its evolutionary trends in the region, would contribute toward effective control and the current vaccine development efforts.

Evolution, heterogeneity and global dispersal of cosmopolitan genotype of Dengue virus type 2

“…The BSSVS findings reflected the epidemiological reality of cosmopolitan genotype’s presence in a wide geographical scale 20 , 33 , 54 – 61 . The most intense virus activity was visible in Southeast Asia, mainly in two epicenters; first, an area covering Singapore, Malaysia and Indonesia and the second centered on Taiwan and China in the Far East.…”

Evolution, heterogeneity and global dispersal of cosmopolitan genotype: The most widespread genotype of Dengue Virus type 2

“…The BSSVS ndings re ected the epidemiological reality of cosmopolitan genotype's presence in a wide geographical scale [20,33,[52][53][54][55][56][57][58][59]. The most intense virus activity was visible in Southeast Asia, mainly in two epicenters; rst, an area covering Singapore, Malaysia and Indonesia and the second centered on Taiwan and China in the Far East.…”

Clinical and epidemiologic characteristics associated with dengue fever in Mombasa, Kenya

“…In our study covering 2016–2017, DENV-2 was the predominant serotype both before and during the outbreak ( Figure 3 ). A study of febrile patients in CPGH from January 2014 to March 2015 also reported DENV-2 as the predominant serotype, followed by DENV-3 and DENV-1 ( Munyuga et al, 2016 ), as did a study of the outbreaks in 2013–2014 and 2017 based on sequencing results ( Langat et al, 2020 ). Although not observed in this study, outbreaks may coincide with a shift in dengue serotypes ( Bennett et al, 2010 , Gubler, 1998 , Saha et al, 2016 ), and earlier reports, covering the times prior to DENV-2 in circulation, support DENV-1 to be the prevalent serotype in Kenya.…”