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.

中文翻译：

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导致肯尼亚爆发的 2 型登革热病毒的起源和进化：两个世界性基因型谱系传播的证据

摘要 登革热 (DF) 是一种由登革病毒血清型 1-4 (DENV 1-4) 引起的虫媒病毒病。在全球范围内，近年来 DF 的发病率和疾病负担有所增加。DENV-2 最初与 1982 年的爆发有关，最近在肯尼亚重新出现，导致 2011 年至 2014 年以及最近的 2017-8 年爆发。可能解释 DENV-2 在肯尼亚的流行病学扩张和影响越来越大的起源和进化模式仍然知之甚少。使用全基因组测序，分析了 2011-4 年和 2017-8 年登革热爆发期间收集的样本。额外的 DENV-2 基因组被下载并与本研究中生成的 14 个基因组合并在一起。使用生物信息学方法分析导致肯尼亚爆发的 DENV-2 的系统发育关系和进化模式。这项研究的结果显示了 DENV-2 的两种不同 Cosmopolitan 基因型谱系流通的第一个证据；Cosmopolitan-I (CI) 和 Cosmopolitan-II (C-II)，在肯尼亚。我们的结果将 2011 年 CI 谱系的起源位置放在印度，以及 1979 年至 2013 年间布基纳法索的 C-II 谱系。CI 谱系在最近的爆发中是最孤立的，因此显示了这种新出现的菌株对增加的 DENV 的贡献该地区的流行病。我们的研究结果得到了最近与肯尼亚 CI 和布基纳法索 C-II 相关的当地流行病的证据的支持，增加了越来越多的证据，表明该地区以及全球 DENV 的多种毒株正在扩大传播和影响。因此，继续对 DENV 活动及其在该地区的演变趋势进行监测，