MERS coronaviruses in dromedary camels, Egypt

Abstract

We identified the near-full-genome sequence (29,908 nt, >99%) of Middle East respiratory syndrome coronavirus (MERS-CoV) from a nasal swab specimen from a dromedary camel in Egypt. We found that viruses genetically very similar to human MERS-CoV are infecting dromedaries beyond the Arabian Peninsula, where human MERS-CoV infections have not yet been detected.

Keywords: Egypt; MERS; MERS-CoV; Middle East respiratory syndrome; camel; coronaviruses; dromedary; genomics; phylogeny; pneumonia; viruses; zoonosis.

Figure 1

Phylogenetic analyses of a partial RNA-dependent RNA polymerase (RdRp) sequence determined from samples from dromedary camels (Camelus dromedarius) NRCE-HKU205 and NRCE-HKU270 that were positive for Middle East respiratory syndrome coronavirus (MERS-CoV). The viral RdRp region analyzed is a highly conserved region of the genome (covering motif B of RdRp) in nonstructural protein 12, at position 15202–15582 of MERS-CoV genome. The partial RdRp sequence of NRCE-HKU205 (GenBank accession no. KJ477102) and NRCE-HKU270 (GenBank accession no. KJ477103) was aligned with human MERS-CoVs (GenBank accession nos. KF600652, KF600630, KF600651, KF186567, KF600627, KF186564, KF600634, KF600632, KF600644, KF600647, KF600645, KF186565, KF186566, KF745068, KF600620, KF600612, KC667074, KC164505, KF192507, KF600613, KF600628, KF961222, KF961221, KC776174, and JX869059) and other representative animal betacoroanviruses (GenBank accession nos. HKU5–1, EF065509; BtCoV/PML/Neo cf. zul/RSA/2011, KC869678). Bat CoV HKU5–1 and bat CoV/PML/Neo cf. zul/RSA/2011 were included in the analysis as outgroups because they are phylogenetically closest to MERS-CoV. Phylogenetic trees were constructed by using MEGA5 (14) with neighbor-joining method. Numbers at nodes indicate bootstrap values determined by 500 replicates. Only bootstrap values >70 are denoted. Bold type indicates MERS-CoV identified in the current study. Scale bars indicate the estimated genetic distance of these viruses.

Figure 2

Phylogenetic analyses of Middle East respiratory syndrome coronavirus (MERS-CoV) from dromedary camels. Genomic (A), spike (B), and nucleocapsid (C) sequences of the dromedary camel MERS-CoV NRCE-HKU205 (GenBank accession no. KJ477102) were aligned with the corresponding human MERS-CoV (N = 25) sequences retrieved from GenBank (accession nos. as in Figure 1 legend). Phylogenetic trees were constructed by using MEGA5 (14) with neighbor-joining method. Numbers at nodes indicate bootstrap values determined by 500 replicates. Only bootstrap values >70 are denoted. Bold type indicates MERS-CoV identified in the current study. Scale bars indicate the estimated genetic distance of these viruses.