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

The structured coalescent approach we employ (see Methods) identifies camels as a reservoir host where most of MERS-CoV evolution takes place (Figure 1 ), while human MERS outbreaks are transient and terminal with respect to long-term evolution of the virus ( Figure S1 ). Across 174 MERS-CoV genomes collected from humans, we estimate a median of 56 separate camel-to-human cross-species transmissions (95% highest posterior density (HPD): 48-63). While we estimate a median of 3 (95% HPD: 0-12) humanto-camel migrations, the 95% HPD interval includes zero and we find that no such migrations are found in the maximum clade credibility tree ( Figure 1 ). Correspondingly, we observe substantially higher camel-to-human migration rate estimates than human-tocamel migration rate estimates ( Figure S2 ). This inference derives from the tree structure wherein human viruses appear as clusters of highly related sequences nested within the diversity seen in camel viruses, which themselves show significantly higher diversity and less clustering. This manifests as different rates of coalescence with camel viruses showing a scaled effective population size N e Ï„ of 3.49 years (95% HPD: 2.71-4.38) and human viruses showing a scaled effective population of 0.24 years (95% HPD: 0.14-0.34).