MERS-CoV spillover at the camel-human interface

Gytis Dudas; Luiz Max Carvalho; Andrew Rambaut; Trevor Bedford; Ali M. Somily; Mazin Barry; Sarah S. Al Subaie; Abdulaziz A. BinSaeed; Fahad A. Alzamil; Waleed Zaher; Theeb Al Qahtani; Khaldoon Al Jerian; Scott J.N. McNabb; Imad A. Al-Jahdali; Ahmed M. Alotaibi; Nahid A. Batarfi; Matthew Cotten; Simon J. Watson; Spela Binter; Paul Kellam

Here we attempt to investigate MERS-CoV demographic patterns in the camel reservoir. We supplement camel sequence data with a single earliest sequence from each human cluster, treating viral diversity present in humans as a sentinel sample of MERS-CoV diversity circulating in camels. This removes conflicting demographic signals sampled during human outbreaks, where densely sampled closely related sequences from humans could be misconstrued as evidence of demographic crash in the viral population. (Gill et al., 2013) . Three skygrid reconstructions are shown, red and orange for each of the stationary distributions reached by MCMC with the whole genome and a black one where the genome was split into ten partitions. Shaded interval indicates the 95% highest posterior density interval for the product of generation time and effective population size, N e Ï„ . Midline tracks the inferred median of N e Ï„ .