title: Polyphyletic origin of MERS coronaviruses and isolation of a novel clade A strain from dromedary camels in the United Arab Emirates.
abstract: Little is known regarding the molecular epidemiology of Middle East respiratory syndrome coronavirus (MERS-CoV) circulating in dromedaries outside Saudi Arabia. To address this knowledge gap, we sequenced 10 complete genomes of MERS-CoVs isolated from 2 live and 8 dead dromedaries from different regions in the United Arab Emirates (UAE). Phylogenetic analysis revealed one novel clade A strain, the first detected in the UAE, and nine clade B strains. Strain D998/15 had a distinct phylogenetic position within clade A, being more closely related to the dromedary isolate NRCE-HKU205 from Egypt than to the human isolates EMC/2012 and Jordan-N3/2012. A comparison of predicted protein sequences also demonstrated the existence of two clade A lineages with unique amino acid substitutions, A1 (EMC/2012 and Jordan-N3/2012) and A2 (D998/15 and NRCE-HKU205), circulating in humans and camels, respectively. The nine clade B isolates belong to three distinct lineages: B1, B3 and B5. Two B3 strains, D1271/15 and D1189.1/15, showed evidence of recombination between lineages B4 and B5 in ORF1ab. Molecular clock analysis dated the time of the most recent common ancestor (tMRCA) of clade A to March 2011 and that of clade B to November 2011. Our data support a polyphyletic origin of MERS-CoV in dromedaries and the co-circulation of diverse MERS-CoVs including recombinant strains in the UAE.
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China.|State Key Laboratory of Emerging Infectious Diseases, Research Centre of Infection and Immunology, Carol Yu Centre for Infection, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
authors.forename: Susanna K P
authors.initials: SK
authors.lastname: Lau
authors.affiliation: Central Veterinary Research Laboratory, PO Box 597, Dubai, UAE.
authors.forename: Renate
authors.initials: R
authors.lastname: Wernery
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China.
authors.forename: Emily Y M
authors.initials: EY
authors.lastname: Wong
authors.affiliation: Central Veterinary Research Laboratory, PO Box 597, Dubai, UAE.
authors.forename: Sunitha
authors.initials: S
authors.lastname: Joseph
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China.
authors.forename: Alan K L
authors.initials: AK
authors.lastname: Tsang
authors.affiliation: Central Veterinary Research Laboratory, PO Box 597, Dubai, UAE.
authors.forename: Nissy Annie Georgy
authors.initials: NA
authors.lastname: Patteril
authors.affiliation: Central Veterinary Research Laboratory, PO Box 597, Dubai, UAE.
authors.forename: Shyna K
authors.initials: SK
authors.lastname: Elizabeth
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China.
authors.forename: Kwok-Hung
authors.initials: KH
authors.lastname: Chan
authors.affiliation: Central Veterinary Research Laboratory, PO Box 597, Dubai, UAE.
authors.forename: Rubeena
authors.initials: R
authors.lastname: Muhammed
authors.affiliation: Central Veterinary Research Laboratory, PO Box 597, Dubai, UAE.
authors.forename: Jöerg
authors.initials: J
authors.lastname: Kinne
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China.|State Key Laboratory of Emerging Infectious Diseases, Research Centre of Infection and Immunology, Carol Yu Centre for Infection, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
authors.affiliation: Central Veterinary Research Laboratory, PO Box 597, Dubai, UAE.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Wernery
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China.|State Key Laboratory of Emerging Infectious Diseases, Research Centre of Infection and Immunology, Carol Yu Centre for Infection, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
authors.forename: Patrick C Y
authors.initials: PC
authors.lastname: Woo
mesh_terms: D000818:Animals; D002162:Camelus / Q000821:virology*; D016000:Cluster Analysis; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D065207:Middle East Respiratory Syndrome Coronavirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D017720:Molecular Epidemiology; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014479:United Arab Emirates / Q000453:epidemiology