Circulation, reassortment and transmission of Ngari and Bunyamwera viruses in Northen Kenya

Abstract

Kenya has experienced severe arboviral outbreaks of public health concern in the recent past, including yellow fever (YF), Crimean Congo hemorrhagic fever (CCHF), chikungunya, and Rift Valley fever (RVF) among others. Most of these infections are under diagnosed and hence neglected due to non-specific nature of their symptoms. Often they are mistaken for endemic tropical diseases such as malaria and typhoid infections and are only recognized during major outbreaks which result in adverse public health and economic consequences to the affected communities. Ongoing inter-epidemic surveillance in RVF virus hotspots in Kenya has indicated continued intense transmission of Bunyamwera virus (BUNV) in the absence or under low level activity of RVF virus. BUNV belongs to the genus Orthobunyavirus of the family Bunyaviridae. These are segmented RNA viruses whose members have the potential for genetic reassotment and/or drift. Recently, Ngari virus (NRIV), a natural reassortant virus associated with hemorrhagic fever was documented to have emerged from BUNV, which previously was not associated with such symptoms. However, the vectors that are involved in the maintenance and transmission of BUNV and NRIV are diverse and their role in virus maintenance/dynamics is poorly known. It is thus important to investigate the dynamics of BUNV and NRIV in selected transmission foci in an effort to understand their circulation better in order to be able to control and predict outbreaks. In this study, we determined the evolutionary and phenotypic diversity of BUNV and NRIV isolates previously obtained from vectors in parts of Kenya. We have provided genetic sequences of two BUNV and three NRIV isolates which contribute to addressing paucity of genetic sequences associated with this group of viruses. Phylogenetic analysis of these sequences in addition to other sequences in GenBank revealed evidence of geographic/temporal clustering that requires further investigation. Next, we demonstrated that plaque purified phenotypes of selected BUNV and NRIV isolates differ in in vivo growth kinetics and pathogenicity in mice, possibly related to specific mutations within the genome. The phenotypic changes and identification of mutations possibly associated with these changes support further investigation of specific mutations using site directed mutagenesis. In addition, we determined the competence of some of the mosquito species implicated in their transmission, Anopheles gambiae, Aedes aegypti and Culex quinquefaciatus and evaluated the dynamics of their transmission in these vectors. We conclude that Anopheles gambiae is likely a more competent vector for NRIV than Aedes aegypti and is a moderately competent vector for BUNV, which has implications for animal movement in malaria endemic areas where the vector is present. We also report evidence of BUNV transovarial transmission in both Aedes aegypti and Anopheles gambiae with the prevalence of transmission related to the ovarian cycle. Finally, we determined the level of human exposure to these viruses in the transmission foci. Orthobunyavirus-specific antibodies were detected by plaque reduction neutralization test in 89 (25.8%) of 345 persons tested. Multivariable analysis revealed age and residence in North Eastern Kenya as risk factors. In conclusion, we propose that acute febrile disease surveillance needs to be implemented in North Eastern Kenya. This study helps identify the virus strains/populations and the vector species that play a critical role in sustenance and transmission of BUNV and NRIV in different ecosystems in the country. All these are important in understanding virus circulation, potential for emergence and risk to populations in areas of circulation, and will help in making decisions for intervention and management. Generated sequence data in this study contributes to global phylogenetic characterization of Orthobunyaviruses worldwide and their molecular epidemiology. The study also shed light/improve our knowledge on the genetic stability or diversity and evolutionary trends of Orthobunyavirus strains in Kenya.