Rice yellow mottle virus in Madagascar and in the Zanzibar Archipelago; island systems and evolutionary time scale to study virus emergence.

Rice yellow mottle virus (RYMV), of the genus Sobemovirus, is a major threat to rice cultivation in Africa. Long range transmission of RYMV, difficult to study experimentally, is inferred from a detailed analysis of the molecular diversity of the virus in Madagascar and in the Zanzibar Archipelago (Zanzibar and Pemba Islands; Tanzania) compared with that found elsewhere in Africa. A unique successful introduction of RYMV to Madagascar, which is ca. 400 km from mainland Africa, contrasted with recurrent introductions of the virus to the Zanzibar Archipelago, ca. 40 km from the East African coast. Accordingly, RYMV dispersal over distances of hundreds of kilometers is rare whereas spread of the virus over distances of tens of kilometers is relatively frequent. The dates of introduction of RYMV to Madagascar and to Pemba Island were estimated from three sets of ORF4 sequences of virus isolates collected between 1966 and 2011. They were compared with the dates of the first field detection in Madagascar (1989) and in Pemba Island (1990). The estimates did not depend substantially on the data set used or on the evolutionary model applied and their credible intervals were narrow. The estimated dates are recent - 1978 (1969-1986) and 1985 (1977-1993) in Madagascar and in Pemba Island, respectively - compared to the early diversification of RYMV in East Africa ca. 200 years ago. They predated by 5-10 years the first field detections in these islands. The interplay between virus sources, rice cultivation and long range dispersal which led to RYMV emergence and spread is enlightened.