The phylogenetic analysis shown in Fig. 1 was done using the maximum-likelihood method (PhyML) (24 (link)). Other phylogenetic methods are detailed in Supporting Information. Dromedary virus BF785 and Nig1657 viruses isolated as part of this study were chosen for comparison with the prototype human MERS-CoV strain EMC (clade A) provided by R. A. M. Fouchier (Erasmus University Medical Center, Rotterdam, The Netherlands) and a dromedary camel virus, dromedary/Al-Hasa-KFU-HKU13/2013 (AH13) (clade B), isolated in the Kingdom of Saudi Arabia (25 (link)). Viruses were isolated and grown in Vero cells, aliquoted, and stored at −80 °C until used. The passage history of these viruses is shown in Dataset S1. Antigenic comparison also included dromedary/Egypt NRCE-HKU-270 (15 (link)). Phenotypic comparison of viruses in Calu-3 cells and ex vivo cultures of human lung and bronchus were carried out as described in Supporting Information. The procedure for transducing mice with an adenovirus vector expressing human DPP4 has been previously described (14 (link)) and is detailed in Supporting Information.
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Chu D.K., Hui K.P., Perera R.A., Miguel E., Niemeyer D., Zhao J., Channappanavar R., Dudas G., Oladipo J.O., Traoré A., Fassi-Fihri O., Ali A., Demissié G.F., Muth D., Chan M.C., Nicholls J.M., Meyerholz D.K., Kuranga S.A., Mamo G., Zhou Z., So R.T., Hemida M.G., Webby R.J., Roger F., Rambaut A., Poon L.L., Perlman S., Drosten C., Chevalier V, & Peiris M. (2018). MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity. Proceedings of the National Academy of Sciences of the United States of America, 115(12), 3144-3149.
Other organizations :
University of Hong Kong, Animal, Santé, Territoires, Risques et Ecosystèmes, Université de Montpellier, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Charité - Universitätsmedizin Berlin, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, University of Iowa, First Affiliated Hospital of Guangzhou Medical University, Cancer Research Center, Fred Hutch Cancer Center, University of Ilorin, Centre National de la Recherche Scientifique et Technologique, Institut Agronomique et Vétérinaire Hassan II, Ethiopian Public Health Institute, Haramaya University, Addis Ababa University, King Faisal University, Kafrelsheikh University, St. Jude Children's Research Hospital, Kasetsart University, National Institutes of Health, University of Edinburgh, Fogarty International Center, Institut Pasteur du Cambodge
Viruses used for comparison (dromedary virus BF785, Nig1657, prototype human MERS-CoV strain EMC, dromedary/Al-Hasa-KFU-HKU13/2013 (AH13), dromedary/Egypt NRCE-HKU-270)
dependent variables
Phylogenetic relationships of the viruses
Phenotypic comparison of viruses in Calu-3 cells and ex vivo cultures of human lung and bronchus
control variables
Passage history of the viruses
Conditions for virus isolation, growth, aliquoting, and storage
controls
Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned
Annotations
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