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. 2020 Jun 3;12(6):611.
doi: 10.3390/v12060611.

Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia

Badr M Al-Shomrani  1 , Manee M Manee  1   2 , Sultan N Alharbi  1 , Mussad A Altammami  1 , Manal A Alshehri  1 , Majed S Nassar  1 , Muhammed A Bakhrebah  1 , Mohamed B Al-Fageeh  1
Affiliations

Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia

Badr M Al-Shomrani et al. Viruses. .

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe respiratory illness in humans; the second-largest and most deadly outbreak to date occurred in Saudi Arabia. The dromedary camel is considered a possible host of the virus and also to act as a reservoir, transmitting the virus to humans. Here, we studied evolutionary relationships for 31 complete genomes of betacoronaviruses, including eight newly sequenced MERS-CoV genomes isolated from dromedary camels in Saudi Arabia. Through bioinformatics tools, we also used available sequences and 3D structure of MERS-CoV spike glycoprotein to predict MERS-CoV epitopes and assess antibody binding affinity. Phylogenetic analysis showed the eight new sequences have close relationships with existing strains detected in camels and humans in Arabian Gulf countries. The 2019-nCov strain appears to have higher homology to both bat coronavirus and SARS-CoV than to MERS-CoV strains. The spike protein tree exhibited clustering of MERS-CoV sequences similar to the complete genome tree, except for one sequence from Qatar (KF961222). B cell epitope analysis determined that the MERS-CoV spike protein has 24 total discontinuous regions from which just six epitopes were selected with score values of >80%. Our results suggest that the virus circulates by way of camels crossing the borders of Arabian Gulf countries. This study contributes to finding more effective vaccines in order to provide long-term protection against MERS-CoV and identifying neutralizing antibodies.

Keywords: 2019-nCov; MERS-CoV; dromedary camel; phylogenetic analysis; vaccine design.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Phylogenetic analysis of the complete genomes of our eight MERS-CoV isolates and representative viruses of the genus Betacoronavirus. The new eight isolates are in blue, other MERS-CoV strains in green, and 2019-nCoV in red. The numbers at nodes represent the posterior probabilities of their clustering.
Figure 2
Figure 2
Phylogenetic analysis of spike proteins of our eight MERS-CoV isolates and representative viruses of the genus Betacoronavirus. The new eight isolates are in blue, other MERS-CoV strains in green, and 2019-nCoV in red. The numbers at nodes represent the posterior probabilities of their clustering.
Figure 3
Figure 3
Three-dimensional locations of discontinuous epitopes (a–f) predicted in the MERS-CoV spike protein. The epitopes are shown in yellow, with the bulk of the MERS-CoV spike protein as grey sticks.
Figure 4
Figure 4
Geographical distribution of dromedaries in Saudi Arabia infected with MERS-CoV viruses that were isolated in the present study. The number of dromedaries corresponds to the number of isolates from the sampling location.
See this image and copyright information in PMC

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