Approaches in Identification of Putative Reservoirs/Hosts of Rift Valley Fever Virus (RVF) in Kenya

Background: Rift Valley Fever (RVF) is a mosquito borne viral zoonosis, first reported in the Rift Valley of Kenya in 1931. In the last major outbreak of 2006/2007 in Kenya, Baringo, Garissa, and Kilifi districts were major hotspots with mortality of approximately 300 human and 40,000 livestock. Methodology: Blood fed mosquitoes sampled during the outbreak were cryopreserved. Heads and abdomens of single cryopreserved blood fed mosquitoes (n = 213) (Aedes, Culex, Anopheles and Mansonia genera) were screened for RVF virus by cell culture, and RT-PCR. Putative vertebrate hosts of the virus were determined by amplification and sequencing of blood meal cytochrome c oxidase I (COI). The resultant sequences were annotated through a bioinformatic pipeline suite comprising of 1) BioEdit for initial cleaning and development of consensus sequences 2) Basic Local Alignment Search Tool (BLAST) searches against GenBank nr database to identify putative homologues of the sequences and 3) Barcode of Life Data Systems (BOLD) for COI. Results: The results of the in silico analyses implicated 3 species in 2 genera as putative vectors of the virus. Among 12 blood meal samples positive for RVFV 6 were drawn from Garissa samples and implicated goats, human and donkey while the rest were from Baringo and implicated sheep and goats as putative hosts. Conclusion: The analyses demonstrate the potential application of bioinformatics approaches when integrated to wet lab tools as accurate and effective in identification of the vertebrate hosts of RVF, with potential application in public health initiatives in understanding vector borne pathogen epidemiology, and enabling control

Rift Valley Fever Virus Epidemic in Kenya, 2006/2007: The Entomologic Investigations

In December 2006, Rift Valley fever (RVF) was diagnosed in humans in Garissa Hospital, Kenya and an outbreak reported affecting 11 districts. Entomologic surveillance was performed in four districts to determine the epidemic/epizootic vectors of RVF virus (RVFV). Approximately 297,000 mosquitoes were collected, 164,626 identified to species, 72,058 sorted into 3,003 pools and tested for RVFV by reverse transcription-polymerase chain reaction. Seventy-seven pools representing 10 species tested positive for RVFV, including Aedes mcintoshi/circumluteolus (26 pools), Aedes ochraceus (23 pools), Mansonia uniformis (15 pools); Culex poicilipes, Culex bitaeniorhynchus (3 pools each); Anopheles squamosus, Mansonia africana (2 pools each); Culex quinquefasciatus, Culex univittatus, Aedes pembaensis (1 pool each). Positive Ae. pembaensis, Cx. univittatus, and Cx. bitaeniorhynchus was a first time observation. Species composition, densities, and infection varied among districts supporting hypothesis that different mosquito species serve as epizootic/epidemic vectors of RVFV in diverse ecologies, creating a complex epidemiologic pattern in East Africa

Dual African Origins of Global <i>Aedes aegypti</i> s.l. Populations Revealed by Mitochondrial DNA

<div><p>Background</p><p><i>Aedes aegypti</i> is the primary global vector to humans of yellow fever and dengue flaviviruses. Over the past 50 years, many population genetic studies have documented large genetic differences among global populations of this species. These studies initially used morphological polymorphisms, followed later by allozymes, and most recently various molecular genetic markers including microsatellites and mitochondrial markers. In particular, since 2000, fourteen publications and four unpublished datasets have used sequence data from the NADH dehydrogenase subunit 4 mitochondrial gene to compare <i>Ae. aegypti</i> collections and collectively 95 unique mtDNA haplotypes have been found. Phylogenetic analyses in these many studies consistently resolved two clades but no comprehensive study of mtDNA haplotypes have been made in Africa, the continent in which the species originated.</p><p>Methods and Findings</p><p>ND4 haplotypes were sequenced in 426 <i>Ae. aegypti</i> s.l. from Senegal, West Africa and Kenya, East Africa. In Senegal 15 and in Kenya 7 new haplotypes were discovered. When added to the 95 published haplotypes and including 6 African <i>Aedes</i> species as outgroups, phylogenetic analyses showed that all but one Senegal haplotype occurred in a basal clade while most East African haplotypes occurred in a second clade arising from the basal clade. Globally distributed haplotypes occurred in both clades demonstrating that populations outside Africa consist of mixtures of mosquitoes from both clades.</p><p>Conclusions</p><p>Populations of <i>Ae. aegypti</i> outside Africa consist of mosquitoes arising from one of two ancestral clades. One clade is basal and primarily associated with West Africa while the second arises from the first and contains primarily mosquitoes from East Africa</p></div

Fourteen publications and 3 unpublished (GenBank) databases of <i>Aedes aegypti sl</i> mitochondrial ND4 sequences.

a<p>– data only appears in GenBank, GB1 = Costa,M.C.V., Paduan,K.S., Ribolla,P.E.M. and Lourenco-de-Oliveira,R., GB2 = Bona,A.C.D., Twerdochlib,A.L., Leandro,A.S., Kafka,R. and Nararro-Silva,M.A. GB3 = Twerdochlib,A.L., Bona,A.C.D. and Navarro-Silva,M.A. GenBank Accession numbers appear in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002175#pntd.0002175.s003" target="_blank">Table S1</a>.</p>b<p>– Tamura-Nei genetic distance/Neighbor-Joining in the original publication.</p>c<p>– Tamura-Nei genetic distance/Neighbor-Joining applied in the present study.</p>d<p>– Maximum Parsimony phylogenetic analyses.</p>e<p>– Maximum Likelihood/Bayesian phylogenetic analyses.</p>f<p>– first value is the number of ND4 haplotypes followed by the number of COI haplotypes.</p>g<p>– clade credibility scores.</p

Location and samples sizes of <i>Aedes aegypti s.l.</i> from 10 collections in Senegal and 7 locations in Kenya^*.

*<p>Entomological gathering was not done on private land or in private residences.</p

Maximum likelihood tree of the 34 mtDNA ND4 <i>Ae. aegypti</i> haplotypes found to date in Africa and outgroups.

<p>These were comprised of the 15 new unique Senegal haplotypes from the present study and one Senegal haplotype collected in Dakar in a previous study (labeled in red). Seven novel haplotypes from Kenya and one from Uganda (in blue), three from Cameroon (in black) and seven haplotypes (in large green font) that appeared in collections from Africa and other global locations in various other studies (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002175#pntd.0002175.s003" target="_blank">Table S1</a>). Branches with bootstrap support values >50% are labeled with % support. These support values are followed by clade credibility values in parentheses from MrBayes analysis.</p