Genetic diversity and molecular epidemiology of Middle East Respiratory Syndrome Coronavirus in dromedaries in Ethiopia, 2017–2020

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels and causes zoonotic infection and disease in humans. Although over 80% of the global population of infected dromedary camels are found in Africa, zoonotic disease had only been reported in the Arabia Peninsula and travel-associated disease has been reported elsewhere. In this study, genetic diversity and molecular epidemiology of MERS-CoV in dromedary camels in Ethiopia were investigated during 2017–2020. Of 1766 nasal swab samples collected, 61 (3.5%) were detected positive for MERS-CoV RNA. Of 484 turbinate swab samples collected, 10 (2.1%) were detected positive for MERS-CoV RNA. Twenty-five whole genome sequences were obtained from these MERS-CoV positive samples. Phylogenetically, these Ethiopian camel-originated MERS-CoV belonged to clade C2, clustering with other East African camel strains. Virus sequences from camel herds clustered geographically while in an abattoir, two distinct phylogenetic clusters of MERS-CoVs were observed in two sequential sampling collections, which indicates the greater genetic diversity of MERS-CoV in abattoirs. In contrast to clade A and B viruses from the Arabian Peninsula, clade C camel-originated MERS-CoV from Ethiopia had various nucleotide insertions and deletions in non-structural gene nsp3, accessory genes ORF3 and ORF5 and structural gene N. This study demonstrates the genetic instability of MERS-CoV in dromedaries in East Africa, which indicates that the virus is still actively adapting to its camel host. The impact of the observed nucleotide insertions and deletions on virus evolution, viral fitness, and zoonotic potential deserves further study.

Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses

“…Recently, the whole genome of MERS-CoV isolated from humans and camels was used for a global analysis of genetic diversity, and the results showed that three clades (A, B, and C) were generated in the software, and it was concluded that MERS-CoV and its new variants are circulating in camels [22]. Additionally, one more study from Ethiopia reported that the MERS-CoV infecting Ethiopian camels phylogenetically belongs to clade C2 and forms closed clusters with East African strains [36]. Due to their continuous exposure to infected animals, animal handlers can facilitate the transmission and introduction of moderately to highly virulent HCoVs in a specific geographic location.…”

“…Based on recently analyzed samples from Uganda, it was observed that there were many amino acid substitutions in the RBD and recombination in the S1 sub-unit of the S protein gene, which may have facilitated the emergence of MERS-CoV and caused human disease [29,32]. Several significant variations have been identified in the non-structural and structural genes of MERS-CoV among humans and camels, which have significantly impacted virus transmission, disease spread, and the evolution of the virus in various geographical locations, resulting in the emergence of recombinant viruses [6,22,[33][34][35][36].…”

Biphasic MERS-CoV Incidence in Nomadic Dromedaries with Putative Transmission to Humans, Kenya, 2022–2023

“…For 9/36 MERS-CoV–positive samples, we obtained ORF1ab sequences and performed phylogenetic analysis. The 9 ORF1ab sequences were highly similar (>99.93% nucleotide identity) and had 99.75%–99.78% nucleotide identity with the closest MERS-CoV relative identified in Akaki, Ethiopia, in 2019 ( 9 ). Phylogenetic analysis showed that the 9 sequences clustered as a monophyletic group within clade C2.2, which encompasses East Africa strains initially detected in Kenya in 2018 ( 10 ) ( Appendix Figure 2).…”

The Threat of Impending Pandemics: A Proactive Approach

“…The zoonosis, with dromedary camels as the source of infection, has been reported in the Arabian Peninsula. Outbreaks of non-sustained human-to-human transmission affecting more than 100 individuals occur, with occasional importations recurrent and outbreaks in healthcare settings in the Arabian Peninsula and the Republic of Korea [ 13 , 14 ]. Currently, there are numerous knowledge gaps regarding the transmission of MERS-CoV, its evolution, probable disease pathogenesis, the absence of any efficacious therapeutic options, and vaccine prospects.…”