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

All MERS-CoV sequences were downloaded from GenBank and accession numbers are given in Table S1 . Sequences without accessions were kindly shared by 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, and Paul Kellam prior to publication. Fragments of some strains submitted to GenBank as separate accessions were assembled into a single sequence. Only sequences covering at least 50% of MERS-CoV genome were kept, to facilitate later analyses where the alignment is split into two parts in order to account for effects of recombination (Dudas and Rambaut, 2016) . Sequences were annotated with available collection dates and hosts, designated as camel or human, aligned with MAFFT (Katoh and Standley, 2013), and edited manually. Protein coding sequences were extracted and concatenated, reducing alignment length from 30130 down to 29364, which allowed for codon-partitioned substitution models to be used. The final dataset consisted of 174 genomes from human infections and 100 genomes from camel infections (Table S1 ).