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

Badr Al-Shomrani,Majed Nassar,Mussad Altammami,Muhammed Bakhrebah,Manee Manee,Sultan Alharbi,Mohamed Al-Fageeh,Manal Alshehri

doi:10.3390/v12060611

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.

Highlights

Coronaviruses are a family of single-stranded, positive-sense RNA genomes that range from 26,000 to 32,000 basepairs in length
Middle East respiratory syndrome (MERS)-CoV is a zoonotic virus for which ongoing studies indicate major roles in transmission for direct contact with live camels and with humans having symptomatic MERS [27,28,29], with dromedary camels being considered intermediate hosts that are the main source of human infections
The second largest outbreak to date occurred in Saudi Arabia, and MERS-CoV is widespread among humans and camels in the Gulf countries [30], where it remains a potential hazard to regional and global health and welfare

Summary

Introduction

Coronaviruses are a family of single-stranded, positive-sense RNA genomes that range from 26,000 to 32,000 basepairs in length. This family can infect both humans and animals, and has been found in many mammal hosts, including bats, camels, and pigs [1]. Coronaviruses are known to have high genetic diversity influenced by mutation and recombination, which can lead to the development of new viruses. Before 2003, human coronaviruses were primarily known for causing common colds. In 2003, severe acute respiratory syndrome coronavirus (SARS-CoV) was first diagnosed in southern. In 2012, another novel and deadly human coronavirus emerged, named the Middle East respiratory syndrome coronavirus (MERS-CoV); it infected more

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