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

Primary analysis, structured coalescent estimates four parameters: rate of coalescence in human viruses, rate of coalescence in camel viruses, rate of migration from the human deme to the camel deme and rate of migration from the camel deme to the human deme. Analyses were run on codon position partitioned data with two separate HKY+Γ 4 (Hasegawa et al., 1985; Yang, 1994) nucleotide substitution models specified for codon positions 1+2 and 3. A relaxed molecular clock with branch rates drawn from a lognormal distribution (Drummond et al., 2006) was used to infer the evolutionary rate from date calibrated tips. Default priors were used for all parameters except for migration rates between demes for which an exponential prior with mean 1.0 was used. All analyses were run for 200 million steps across ten independent Markov chains (MCMC runs) and states were sampled every 20 000 steps. Due to the complexity of multitype tree parameter space 50% of states from every analysis were discarded as burn-in, convergence assessed in Tracer v1.6 and states combined using LogCombiner distributed with BEAST v2.4.3 (Bouckaert et al., 2014) . Three chains out of ten did not converge and were discarded altogether. This left 70 000 states on which to base posterior inference. Posterior sets of typed (where migrating branches from structured coalescent are collapsed, and migration information is left as a switch in state between parent and descendant nodes) trees were summarised using TreeAnnotator v2.4.3 with the common ancestor heights option (Heled and Bouckaert, 2013) . A maximum likelihood phylogeny showing just the genetic relationships between MERS-CoV genomes from camels and humans was recovered using PhyML (Guindon et al., 2003) under a HKY+Γ 4 (Hasegawa et al., 1985; Yang, 1994) nucleotide substitution model and is shown in Figure S14 .