Mosquito-borne arbovirus surveillance at selected sites in diverse ecological zones of Kenya; 2007 - 2012

Abstract

Background: Increased frequency of arbovirus outbreaks in East Africa necessitated the determination of distribution of risk by entomologic arbovirus surveillance. A systematic vector surveillance programme spanning 5 years and covering 11 sites representing seven of the eight provinces in Kenya and located in diverse ecological zones was carried out.

Methods: Mosquitoes were sampled bi-annually during the wet seasons and screened for arboviruses. Mosquitoes were identified to species, pooled by species, collection date and site and screened for arboviruses by isolation in cell culture and/or RT-PCR screening and sequencing.

Results: Over 450,000 mosquitoes in 15,890 pools were screened with 83 viruses being detected/isolated that include members of the alphavirus, flavivirus and orthobunyavirus genera many of which are known to be of significant public health importance in the East African region. These include West Nile, Ndumu, Sindbis, Bunyamwera, Pongola and Usutu viruses detected from diverse sites. Ngari virus, which was associated with hemorrhagic fever in northern Kenya in 1997/98 was isolated from a pool of Anopheles funestus sampled from Tana-delta and from Aedes mcintoshi from Garissa. Insect only flaviviruses previously undescribed in Kenya were also isolated in the coastal site of Rabai. A flavivirus most closely related to the Chaoyang virus, a new virus recently identified in China and two isolates closely related to Quang Binh virus previously unreported in Kenya were also detected.

Conclusion: Active transmission of arboviruses of public health significance continues in various parts of the country with possible undetermined human impact. Arbovirus activity was highest in the pastoralist dominated semi-arid to arid zones sites of the country where 49% of the viruses were isolated suggesting a role of animals as amplifiers and indicating the need for improved arbovirus disease diagnosis among pastoral communities.

Figure 1

Neighbour joining phylogenetic tree of nucleotide sequences of selected Alphavirus isolates and reference sequences. The sequences of the isolates reported in this paper (highlighted in yellow) were compared to other members of the alphavirus genus from Genbank [GenBank: JN989958.1, GenBank: JQ771799.1, GenBank: M69205.1, GenBank: HM147984.1, GenBank: AF369024.2]. The Non structural Protein 4 (NSP4) coding regions of these nucleotide sequences, and those of the selected Alphaviruses in this study were aligned using clustalW and the phylogenetic tree constructed using MEGA v5.05. Numbers on internal branches indicate bootstrap values for 1000 replicates. The results show that the Alphaviruses have grouped into two with one group having the isolates under study (from Kenya) and the other has the reference sequences (from other countries). Within the Kenyan group, the Ndumu virus isolates have clustered separately from the Sindbis and the Sindbis-like viruses. This is due to the diverse nature of Alphaviruses. GSA: Garissa; KSM: Kisumu; NVS: Naivasha; BAR: Baringo. NDUV: Ndumu virus; SINV: Sindbis virus; BBKV: Babanki virus.

Figure 2

Neighbour joining phylogenetic tree of nucleotide sequences of selected Orthobunyavirus isolates and reference sequences. The sequences of the Orthobunyavirus isolates under study (highlighted in yellow) were compared to other Orthobunyaviruses from the database [GenBank: EU564828.1, GenBank: EU564827.1, GenBank: JX857325.1, EMBL: AM709778.1, GenBank: AY729651.1, GenBank: JX846604.1, GenBank: GU206123.1, GenBank: AF362397.1]. The nucleocapsid region of these sequences and those of the selected Orthobunyaviruses under study were aligned using clustalW and the phylogenetic tree constructed using MEGA v5.05. Numbers on internal branches indicate bootstrap values for 1000 replicates. The Orthobunyaviruses from Kenya have clustered together while the reference sequences have also formed a separate clade. Bunyamwera and Ngari viruses have formed a cluster meaning they are closely related while Pongola virus seems to be different from the two viruses. GSA: Garissa; MGD: Magadi; TD: Tana Delta; S: site; PGAV: Pongola virus; BUNV: Bunyamwera virus; NRI: Ngari.

Figure 3

Neighbour joining phylogenetic tree of nucleotide sequences of selected Flavivirus isolates and reference sequences. The sequences of the isolates under study (highlighted in yellow) were compared to other Flaviviruses from database [GenBank: HM147822.1, GenBank: JF834580.1, GenBank: GQ165810.1, GenBank: FJ644291.1, GenBank: AY149905.1, GenBank: JQ068102.1, GenBank: HM582101.1, GenBank: JX898869.1, GenBank: AY632545.2, GenBank: JX236040.1]. The NSP5 coding regions of the sequences and of selected Flaviviruses under study were aligned using clustalW and the phylogenetic tree constructed using MEGA v5.05. Numbers on internal branches indicate bootstrap values for 1000 replicates. The Flaviviruses have originated from a common ancestor. The West Nile viruses isolates under study have all clustered together while the Ntaya virus is an outgroup. The insect flaviviruses seems to have recently emerged as compared to other Flaviviruses and they have formed a clade except Chaoyang virus which has fallen to a different clade. Usutu virus is related to West Nile, Dengue and Yellow Fever viruses. GSA: Garissa; KSM: Kisumu; RAB: Rabai; S: site; CYV: Chaoyang virus; QBV: Quang Bihn virus; CFA: Cell fusing agent; WN: West Nile.

Figure 4

Map of Kenya. The map showing the different provinces in Kenya where the mosquitoes that yielded the isolates reported in this manuscript were collected. The study sites were Marigat, Turkana, Magadi and Naivasha (in Rift Valley province); Budalangi, Busia, (in Western province); Kisumu (in Nyanza province); Rabai, Tana-delta and Garissa (in the Coast and North Eastern provinces respectively); Sukari ranch (on the outskirts of Nairobi city in central province).