Emerging Microbes and Infections (Jan 2016)

Polyphyletic origin of MERS coronaviruses and isolation of a novel clade A strain from dromedary camels in the United Arab Emirates

  • Susanna K P Lau,
  • Renate Wernery,
  • Emily Y M Wong,
  • Sunitha Joseph,
  • Alan K L Tsang,
  • Nissy Annie Georgy Patteril,
  • Shyna K Elizabeth,
  • Kwok-Hung Chan,
  • Rubeena Muhammed,
  • Jöerg Kinne,
  • Kwok-Yung Yuen,
  • Ulrich Wernery,
  • Patrick C Y Woo

DOI
https://doi.org/10.1038/emi.2016.129
Journal volume & issue
Vol. 5, no. 1
pp. 1 – 9

Abstract

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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.

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