A phylogenetically distinct Middle East respiratory syndrome coronavirus detected in a dromedary calf from a closed dairy herd in Dubai with rising seroprevalence with age

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) was detected by monoclonal antibody-based nucleocapsid protein-capture enzyme-linked immunosorbent assay (ELISA), RNA detection, and viral culture from the nasal sample of a 1-month-old dromedary calf in Dubai with sudden death. Whole genome phylogeny showed that this MERS-CoV strain did not cluster with the other MERS-CoV strains from Dubai that we reported recently. Instead, it formed a unique branch more closely related to other MERS-CoV strains from patients in Qatar and Hafr-Al-Batin in Saudi Arabia, as well as the MERS-CoV strains from patients in the recent Korean outbreak, in which the index patient acquired the infection during travel in the eastern part of the Arabian Peninsula. Non-synonymous mutations, resulting in 11 unique amino acid differences, were observed between the MERS-CoV genome from the present study and all the other available MERS-CoV genomes. Among these 11 unique amino acid differences, four were found in ORF1ab, three were found in the S1 domain of the spike protein, and one each was found in the proteins encoded by ORF4b, ORF5, envelope gene, and ORF8. MERS-CoV detection for all other 254 dromedaries in this closed dairy herd was negative by nucleocapsid protein-capture ELISA and RNA detection. MERS-CoV IgG sero-positivity gradually increased in dromedary calves with increasing age, with positivity rates of 75% at zero to three months, 79% at four months, 89% at five to six months, and 90% at seven to twelve months. The development of a rapid antigen detection kit for instantaneous diagnosis is warranted.Emerging Microbes & Infections (2015) 4, e74; doi:10.1038/emi.2015.74; published online 2 December 2015.

Figure 1

Sero-positivity of the 254 dromedaries in the herd tested in the present study.

Figure 2

(A) Maximum likelihood phylogeny based on complete concatenated coding sequences of 68 available human MERS-CoV and 18 camel MERS-CoV genomes. A general time-reversible model of nucleotide substitution with estimated base frequencies, a proportion of invariant sites, and a gamma distribution of rates across sites was applied to conduct maximum likelihood analysis. Bootstrap values (1000 replicates) are shown next to the branches. A scale bar indicates the number of nucleotide substitutions per site. The MERS-CoV strain from the present study is shown in blue, those from eastern and western Saudi Arabia are in magenta and green, respectively, other strains from the United Arab Emirates are in orange, and those from the recent Korean outbreak are in purple. (B) Map of the Arabian Peninsula, with the colors of different geographical regions corresponding to those in panel A.

Figure 3

Map of unique mutations in the camel MERS-CoV genome, with the nucleotide positions shown on the scale above it. Blue arrows indicate unique mutations observed in the MERS-CoV genome. Amino acid changes are shown above the arrows.