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

Despite lack of convergence, neither of the two demographic reconstructions show evidence of fluctuations in the relative genetic diversity (N e Ï„ ) of MERS-CoV over time ( Figure 5 ). We recover a similar demographic trajectory when estimating N e Ï„ over time with a skygrid tree prior across the genome split into ten fragments with independent phylogenetic trees to account for confounding effects of recombination (Figures 5, S13). However, we do note that coalescence rate estimates are high relative to the sampling time period, with a mean estimate of N e Ï„ at 3.49 years (95% HPD: 2.71-4.38), and consequently MERS-CoV phylogeny resembles a ladder, as often seen in human influenza A virus phylogenies (Bedford et al., 2011) .