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

We believe that the small number of inferred human-to-camel migrations are induced by the migration rate prior, while some are derived from phylogenetic proximity of human sequences to the apparent "backbone" of the phylogenetic tree. This is most apparent in lineages in early-mid 2013 that lead up to sequences comprising the MERS-CoV clade dominant in 2015, where owing to poor sampling of MERS-CoV genetic diversity from camels the model cannot completely dismiss humans as a potential alternative host. The first sequences of MERS-CoV from camels do not appear in our data until November 2013. Our finding of negligible human-to-camel transmission is robust to choice of prior ( Figure S2 ). The vast majority of MERS-CoV evolution is inferred to occur in camels (orange) with human outbreaks (blue) representing evolutionary dead-ends for the virus. Confidence in host assignment is depicted as a colour gradient, with increased uncertainty in host assignment (posterior probabilities close to 0.5) shown as grey. While large clusters of human cases are apparent in the tree, significant contributions to human outbreaks are made by singleton sequences, likely representing recent cross-species transmissions that were caught early.