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Rice yellow mottle virus (RYMV, sobemovirus) is a stable and highly concentrated plant virus transmitted during cultural practices, by beetles (under a non-persistent mode), by other biotic means but not through seeds. The spatio-temporal dynamics of RYMV within East Africa and towards West Africa and Madagascar was reconstructed using Bayesian inference under a single relaxed continuous dispersal model. The choice of the coat protein gene sequences for the phylogeographic studies was validated after phylogenetic reconstructions based on complete genome sequences and after analysis of the insertion-deletion polymorphism in the sobemovirus genus. The patterns of dispersion were visualized by Evolaps (Chevenet et al., 2021), and interpreted at the light of historical and agronomical information on rice in Africa.The contrasted spatio-temporal dynamics of the three strains of RYMV in East Africa (S4, S5, S6) revealed by the phylogeographic analyses lead to following epidemiological scenario.

RYMV originated in the southern part of the Eastern Arc Mountains (South-East of Tanzania), one of word biodiversity hotspot. Transfer from the (unknown) original hosts to rice occurred at the end of the 19^th century, possibly throughout the (documented) slash-and-burnt agriculture practiced in these mountains for rice and eleusine (another host of RYMV). The S6 and later the S5 strains infected the large adjacent rice-growing Kilombero Valley. The S4 strain rapidly spread inland East Africa through infected rice residues associated to seeds (husks, leaves…) carried along the caravan routes. RYMV further spreads throughout East Africa in parallel to the increase in rice cultivation. RYMV dispersal from East Africa towards West Africa and Madagascar at the beginning and at the end of the 20^th century, respectively, is consistent with what is known on rice seed transfers for agronomic improvement. Incidentally, it provides an explanation of the origins of the recombinant strain of Madagascar. The role of beetles in the short-range and recent spread was assessed in the large and intensive rice plantation KPL located in the Kilombero Valley. Altogether, this study unveils the multiplicity of dissemination modes, their changing roles among regions and across periods, and reverses the ideas on the respective impacts of insects and humans in the epidemiology of an economically important plant virus.

Chevenet et al. 2021. EvoLaps: a web interface to visualize continuous phylogeographic reconstructions. BMC Bioinformatics  22, 463