Occurrence and diversity of tick-borne viruses in the pastoral eco-zone of Ijara District, North Eastern Province of Kenya

Abstract

Most arbovirus isolations in East Africa have been recorded from mosquitoes but less information is available about tick-borne viruses including Crimean-Congo hemorrhagic fever virus (CCHFV), which is prevalent in Africa with a mortality rate of up to 40%. The study envisioned gaining an in-depth understanding of the circulation, transmission and diversity of tick-borne viruses in Ijara District of North Eastern Kenya, a pastoral ecozone with a defined population size of 19,259 that are served by 8 health facilities where arbovirus activity among mosquitoes, animals and humans is frequently reported. The study aimed at determining the prevalence of CCHF antibodies in humans that attend selected health facilities in Ijara District, identify tick-borne viruses among tick vectors and genetic diversity of the tick-borne viruses circulating among ticks and/or their host animals. A total of 517 human serum samples were screened for the presence of IgG and IgM antibodies to CCHF using CCHF-IgG and IgM ELISA test kits (VectoCrimean-CHF-IgG and IgM ELISA; Vector-Best, Novosibirsk, Russia). A multivariable logistic regression model was used to investigate the exposure to CCHFV in patients enrolled in this study. In this first part of the study, a single patient tested positive for anti-CCHF IgM, while 96 were positive for anti-CCHF IgG, suggesting an overall seroprevalence of CCHFV in Ijara District of 19%. The results indicate the possibility of acute CCHFV infections occurring without being detected in this population. A total of 10,488 ticks were also sampled from livestock and wild animal hosts and processed in 1,520 pools of upto 8 ticks per pool. The sampled ticks were classified to species, processed for virus screening by cell culture using Vero cells, RT-PCR, and sequencing. Bunyamwera (BUN), Dugbe (DUG), Ndumu (NDU), Semliki forest (SF), Thogoto (THO), and West Nile (WN) virus strains were isolated and identified. Phylogenetic analysis based on nucleotide sequences showed that the Kenyan isolates clustered closely to their respective reference strains. Semliki forest virus (SFV) isolate (ATH00510) sequence obtained by 454 sequencing, clustered closely to the Kenyan strains (HQ848388 and JF972635) isolated from mosquitoes sampled in North Eastern Province of Kenya. Ndumu virus (NDUV) (ATH002166) was similar to the Ugandan strain (JN989958). All BUNV strains isolated in the study clustered distinctively on a tree branching comprising viruses of Bunyamwera serogroup. The two Dugbe viruses detected in this study were highly similar to each other and formed a cluster with the United Kingdom (NC004159 and U15018) strains. Thogoto virus was divergent from strains obtained from Germany, Senegal, Turkey, USA and Vietnam. WNV strains isolated in Kenya clustered relatively close to viruses isolated in Russia, Europe and the United States belonging to lineage 1 of WNV. The identification of WNV Lineage 1 in Ijara District brings in to light the ability of this virus to spread across wide geographical regions taking into consideration that this virus lineage is also found in Europe, America, India and the Middle East. These study findings provide additional evidence on the potential role of ticks and animals (both livestock and wildlife) in the circulation of tick-borne viruses as well as viruses previously known to be mosquito-borne. It also provides a basis in understanding the genetic diversity of arboviruses circulating in Ijara District.