Abstract
Rift Valley fever virus (RVFV), a mosquito-borne phlebovirus, has been detected in Madagascar since 1979 with occasional outbreaks. In 2008-2009, a large RVFV outbreak was detected in Malagasy livestock and humans during two successive rainy seasons. To determine whether cases were due to enzootic maintenance of virus within Madagascar or importation from the East African mainland, nine RVFV whole genomic sequences were generated for viruses from the 1991 and 2008 Malagasy outbreaks. Bayesian coalescent analyses of available whole S, M, and L segment sequences were used to estimate the time to most recent common ancestor for the RVFVs. The 1979 Madagascar isolate shared a common ancestor with strains on the mainland around 1972. The 1991 Madagascar isolates were in a clade distinct from the 1979 isolate and shared a common ancestor around 1987. Finally, the 2008 Madagascar viruses were embedded within a large clade of RVFVs from the 2006-2007 outbreak in East Africa and shared a common ancestor around 2003-2004. These results suggest that the most recent Madagascar outbreak was caused by a virus likely arriving in country sometime between 2003 and 2008 and may be an extension of the 2006-2007 East African outbreak. Clustering of the Malagasy sequences into sub-clades indicates that the viruses have continued to evolve during their short term circulation within the country. These data are consistent with RVFV outbreaks in Madagascar resulting not from emergence from enzootic cycles within country, but from recurrent virus introductions from the East African mainland.