Emerg Infect DisEmerging Infect. DisEIDEmerging Infectious Diseases1080-60401080-6059Centers for Disease Control and Prevention22608405335814511-099410.3201/eid1806.110994DispatchDispatchGenome Analysis of Rift Valley Fever Virus, MayotteGenome Analysis of RVFVCêtre-SossahCatherineZellerHervéGrandadamMarcCaroValériePettinelliFrançoisBouloyMichèleCardinaleEricAlbinaEmmanuelCentre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France (C. Cêtre-Sossah, E. Albina);Institut Pasteur, Paris, France (H. Zeller, M. Grandadam, V. Caro, M. Bouloy);Centre Hospitalier de Mayotte, Mayotte (F. Pettinelli);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Sainte-Clotilde, France (E. Cardinale)Address for correspondence: Catherine Cêtre-Sossah, CIRAD, Département Bios, UMR15, TA A-15/G, Campus International de Baillarguet, F-34398 Montpellier Cedex 5, France; email: catherine.cetre-sossah@cirad.fr62012186969971

As further confirmation of a first human case of Rift Valley fever in 2007 in Comoros, we isolated Rift Valley fever virus in suspected human cases. These viruses are genetically closely linked to the 2006–2007 isolates from Kenya.

Keywords: Rift Valley feverRift Valley fever virusarbovirusMayotteviruseszoonosesgenome analysis

Identified during the 1930s in Kenya, Rift Valley fever (RVF) is a zoonotic disease that circulates in many African countries and in the Arabian Peninsula (1,2). RVF virus (RVFV) epizootics are characterized by large sweeping abortion storms and substantial death rates in adult livestock (primarily sheep, goats, and cattle), with the death rate for newborn animals approaching 100% (3). Humans typically are infected by bites of infected mosquitoes or by percutaneous or aerosol exposure to contaminated fluids from infected animals. In most human cases, RVF is characterized by a self-limiting febrile illness (2–5 days), which progresses to more serious complications (hepatitis, encephalitis, blindness, or hemorrhagic syndrome) in only 1%–2% of infected persons (4,5). A large epizootic–epidemic occurred during 2006–2007 on the eastern African mainland, predominantly in Kenya (6) and Madagascar, during 2 successive rainy seasons (7).

In July 2007, a 12-year-old boy with a 2-month history of severe encephalitis was transferred from the Grande Comore, Union of the Comoros, to Mayotte (8,9). RVF infection was confirmed by IgM serologic analysis. Because of the proximity of Comoros and Mayotte, the RVF situation among humans in Mayotte was assessed. In serum samples from 7 humans with dengue-like syndromes, RVFV IgM or RVFV RNA was detected. We report the isolations and full sequence analysis of 2 RVF viral isolates from these serum specimens.

The Study

During January–April 2007, seven patients native to Mayotte were admitted to the hospital for severe dengue-like syndromes. Two patients were RVF seropositive by IgM and IgG, and the other 5 were positive by RVFV-specific reverse transcription PCR (RT-PCR) as detailed in Sissoko et al. (9). As described for other viruses, we used in-house IgM-capture enzyme immunoassays and in-house direct detection for IgG by using microplates coated with RVFV antigen and specific binding by using a peroxidase-labeled goat anti-human IgG conjugate (10).

RVFV isolates were obtained on Vero E6 cells from the serum of 2 hospitalized patients (serum collected on February 21 and March 20, 2008). RNA extracted by using the RNaid Kit (Qbiogene, Carlsbad, CA, USA) was reverse transcribed by PCR and amplified by using SuperScript One-Step RT-PCR with platinum Taq kit (Invitrogen, San Diego, CA, USA) with primers targeting the small, medium, and large segments (adapted from [11]). Overlapping RT-PCR fragments were purified by ultrafiltration. Sequencing reactions were performed by using the Big Dye Terminator v1.1 cycle sequencing kit (Applied Biosystems, Foster City, CA, USA). Sequence chromatograms from both strands were obtained on automated sequence analyzer ABI3730XL (Applied Biosystems). For sequence analysis, contig assemblies and sequence alignments were performed by using BioNumerics version 6.6 (Applied-Maths, Sint-Martens-Latem, Belgium).

We used 2 methods for phylogenetic reconstruction: maximum likelihood and the Bayesian inference. The best models of nucleotide substitution for each dataset were selected from the uncorrected and corrected Akaike Information Criterion, the Hannan and Quinn performance-based decision theory and Bayesian Information Criterion of Jmodeltest version 0.1 and TREEFINDER version October 2008 (Munich, Germany, distributed by its author at www.treefinder.de). The consensus substitution models proposed by the different software packages were selected for further analyses. Comparison of the maximum-likelihood method implemented by the TREEFINDER program with others was performed on the small, medium, and large segments by using the neighbor-joining and maximum parsimony methods from Mega5 software and the Bayesian approach by using MrBayes version 3.0B4 for phylogenetic reconstruction with random starting trees and run for 2,000,000 generations, sampling the Markov chains at intervals of 100 generations (12,13). Branch support values were obtained by using nonparametric bootstrapping with 1,000 resampling for PhyML and TREEFINDER and the posterior probabilities for the Bayesian approach estimated on 10,000 samples (sample frequency set to every 100th generation by using the Markov Chain Monte Carlo sampling). We compared topologies of the maximum-likelihood and Bayesian trees obtained for the different segments.

The complete genome sequences performed on 2 human RVFV isolates from Mayotte referenced as 2008/00099 and 2008/00101 (deposited in GenBank/EMBL under accession nos. HE687302–HE687307) are embedded within the larger 2006–2007 East African clade, specifically within the lineage previously termed Kenya-1 (Table A1). The Kenya-1 virus lineage includes 18 isolates, 8 human isolates (035/07Baringo Kenya 2007, SPU10315 Kenya 2007, Garissa 004/006 Kenya 2006, Dod002/007Tanzania 2007, 3162 Madagascar 2008, 3163 Madagascar 2008, 3164 Madagascar 2008, 3165 Madagascar 2008), 2 mosquito isolates (KLFMsq091/07 Kenya 2007, 131B04/06Garissa Kenya 2006), and 8 livestock isolates (1602Mombassa Kenya 2007, 2820Garissa Kenya 2007, 3644Baringo Kenya 2007, 473Kajaido Kenya 2007, 0611Kenya 2007, 3168 Madagascar 2008, 3169 Madagascar 2008, 3170 Madagascar 2008). The Kenya 2 virus lineage comprises 3 human isolates (1811Garissa Kenya 2006, 0094 Kenya 2007, Tan001/007 Tanzania 2007).

Because maximum-likelihood and Bayesian tree topologies obtained for the 3 segments were similar, only the small segment is presented. The Figure shows the Bayesian tree topology based on all RVFV small segments, with the HB29 phlebovirus from the People’s Republic of China as an outgroup. Tree topologies are consistent with those generated in previous work (7,11). The reliability of the phylogenetic trees was confirmed by performing bootstrap analysis. The Kenya 1 and Kenya 2 lineages clustered together with an overall bootstrap value of 92% but with sublineage bootstrap values of 56%–100%.

Fifty-two complete sequences of Rift Valley fever virus small genome segments aligned and analyzed by the Bayesian program (MrBayes). Scale bar indicates nucleotide substitutions per site.

Conclusions

The work of Sissoko et al. (9) suggested the indigenous transmission of RVFV in humans in Mayotte. The geographic distribution of the 10 human serum samples found positive for RVFV in 2007 and 2008 was not spatially delimited. All case-patients were native to the island and resided in the following districts: Mamoudzou (3), Brandaboua (2), Dembeni (1), Sada (1), Chirongui (2), and Boueni (1). None reported travel into countries where RVF is endemic (9). The genomic analysis of the Mayotte isolates placed them within the 2006–2007 eastern African Kenya-1 lineage. RVF activity in Mayotte appears to be an expansion of the eastern African mainland 2007–2008 outbreak. It illustrates the risk for introduction in Mayotte or other Comorian islands of infectious agents involved in outbreaks in neighboring eastern African coastal countries, the major source being livestock importation from the African mainland or Madagascar.

The recent data published on RVFV Malagasy strains (7,14) support an epidemic cycle with introduction of the virus from outbreaks on mainland eastern Africa rather than an enzootic cycle in Madagascar. RVFV has been isolated from at least 40 species of mosquitoes in 8 genera. Recent experimental RVFV infections on African mosquito species revealed that 8 species—Aedes palpalis (Newstead), Ae. mcintoshi Huang, Ae. circumluteolus (Theobald), Ae. calceatus Edwards, Ae. aegypti (L), Culex antennatus (Becker), Cx. pipiens (L), and Cx. quinquefasciatus Say—are susceptible to infection, and that all except Ae. calceatus, Ae. aegypti, and Cx. quinquefasciatus transmitted RVFV by bite after oral exposure (15). In Mayotte, a preliminary study has shown that 4 species—Ae. circumluteolus, Cx. antennatus, Cx. quinquefasciatus, and Ae. aegypti—are present (T. Balenghien, V. Robert, pers. comm.).

Even if mosquito transmission might have occurred among some of the 7 reported RVF case-patients, contact with imported ruminants is the predominant means of exposure among these reported case-patients. However, further entomologic studies need to be conducted to identify all potential vector species in the island and animal surveys need to be conducted to help detect RVF at early stages to gain a better understanding of the ecologic and climatic factors that favor RVFV dissemination. These assessments will help in the development of appropriate control measures to better predict and respond to potential RVF outbreaks.

Suggested citation for this article: Cêtre-Sossah C, Zeller H, Grandadam M, Caro V, Pettinelli F, Bouloy M, et al. Genome analysis of Rift Valley fever virus, Mayotte. Emerg Infect Dis [serial on the Internet]. 2012 Jun [date cited]. http://dx.doi.org/10.3201/eid1806.110994

Acknowledgment

We thank Vincent Michaud for his steadfast support.

Strains analyzed in study of the genome analysis of Rift Valley fever virus, Mayotte
Source of isolateVirus strainCountry of originYear isolatedGenBank accession no. for small segment
Bovine763/70Zimbabwe1970DQ380174
Bovine1260/78Zimbabwe1978DQ380164
Bovine1853/78Zimbabwe1978DQ380168
Bovine2250/74Zimbabwe1974DQ380143
Bovine2269/74Zimbabwe1974DQ380173
Bovine2373/74Zimbabwe1974DQ380159
Human73HB1230Central African Republic1973DQ380172
Human73HB1449Central African Republic1973DQ380162
Human74HB59Central African Republic1974DQ380163
Aedes cuminsi mosquitoArD38388Burkina Faso1983DQ380181
Hipposideros caffer batANK3837Guinea1981DQ380165
Micropterus pusillus batANK6087Guinea1984DQ380166
HumanCARR1622Central African Republic1985DQ380160
Eretmapodites sp. mosquitoEntebbeUganda1944DQ380156
HumanHvB375Central African Republic1985DQ380161
BovineKenyaIB8Kenya1965DQ380176
Ae. macintoshi mosquitoKenya21445Kenya1983DQ380171
HumanKenya00523Kenya1998DQ380169
HumanMgH824Madagascar1979DQ380144
HumanOS1Mauritania1987DQ380180
HumanOS3Mauritania1987DQ380178
HumanOS8Mauritania1987DQ380177
HumanOS9Mauritania1987DQ380179
OvineSA51South Africa1951DQ380158
HumanSA75South Africa1975DQ380175
HumanSaudi10911Saudi Arabia2000DQ380170
BovineZC3349Egypt1978DQ380152
HumanZH501Egypt1977DQ380149
HumanZH548Egypt1977DQ380151
HumanZH1776Egypt1978DQ380153
MosquitoZM657Egypt1978DQ380146
OvineZS6365Egypt1979DQ380145
HumanZingaCentral African Republic1969DQ380167
Bovine0611MeruSouthKenya2007EU574078
Bovine0094GarissaKenya2007EU574086
Buffalo2820GarissaKenya2007EU574061
Human2008/00099Mayotte2008HE687302
Human2008/00101Mayotte2008HE687307
BovineAn1000Madagascar1991EU312108
Human3162Madagascar2008JF311386
Human3163Madagascar2008JF311387
Human3164Madagascar2008JF311388
Human3165Madagascar2008JF311389
Bovine3168Madagascar2008JF311392
Bovine3169Madagascar2008JF311393
Bovine3170Madagascar2008JF311394
HumanSPU10315Kenya2007EU312147
HumanSPU384001Kenya1997EU312128
HumanB1143Kenya1977EU312119
Goat1811GarissaKenya2006EU574068
Bovine1602MombassaKenya2007EU574071
Ovine473KajaidoKenya2007EU574080
Ovine3644BaringoKenya2007EU574059
Human004/006GarissaKenya2006HM586975
Human035/07BarissaKenya2007HM586980
Aedes sp. mosquito131B04/06GarissaKenya2006HM586983
Aedes sp. mosquitoKLF091/07Kenya2007HM586984
HumanTanga001/007Tanzania2007HM586981
HumanDodoma002/07Tanzania2007HM586982
HumanHB29 PhlebovirusChina2010HM745932

Mrs Cêtre-Sossah is a virologist at the Unit Control of Animal and Exotic Diseases at Centre de Coopération Internationale en Recherche Agronomique pour le Développement in Montpellier. Her research interests include the diagnosis and control of communicable and noncommunicable diseases, especially Rift Valley fever, and those caused by poxviruses and bluetongue viruses.

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