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 use an explicit model of metapopulation structure and migration between discrete subpopulations, referred to here as demes (Vaughan et al., 2014) , derived from the structured coalescent (Notohara, 1990) . Unlike approaches that model host species as a discrete phylogenetic trait of the virus using continuous-time Markov processes (or simpler, parsimony based, approaches) Lycett et al., 2016) , population structure models explicitly incorporate contrasts in deme effective population sizes and migration between demes. By estimating independent coalescence rates for MERS-CoV in humans and camels, as well as migration patterns between the two demes, we show that long-term viral evolution of MERS-CoV occurs exclusively in camels. Our results suggest that spillover events into humans are seasonal and might be associated with the calving season in camels. However, we find that MERS-CoV, once introduced into humans, follows transient transmission chains that soon abate. Using Monte Carlo simulations we show that R 0 for MERS-CoV circulating in humans is much lower than the epidemic threshold of 1.0 and that correspondingly the virus has been introduced into humans hundreds of times.