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

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.

Phenotypic and genetic characterization of MERS coronaviruses from Africa to understand their zoonotic potential.

Coronaviruses are pathogens of pandemic potential. Middle East respiratory syndrome coronavirus (MERS-CoV) causes a zoonotic respiratory disease of global public health concern, and dromedary camels are the only proven source of zoonotic infection. More than 70% of MERS-CoV-infected dromedaries are found in East, North, and West Africa, but zoonotic MERS disease is only reported from the Arabian Peninsula. We compared viral replication competence of clade A and B viruses from the Arabian Peninsula with genetically diverse clade C viruses found in East (Egypt, Kenya, and Ethiopia), North (Morocco), and West (Nigeria and Burkina Faso) Africa. Viruses from Africa had lower replication competence in ex vivo cultures of the human lung and in lungs of experimentally infected human-DPP4 (hDPP4) knockin mice. We used lentivirus pseudotypes expressing MERS-CoV spike from Saudi Arabian clade A prototype strain (EMC) or African clade C1.1 viruses and demonstrated that clade C1.1 spike was associated with reduced virus entry into the respiratory epithelial cell line Calu-3. Isogenic EMC viruses with spike protein from EMC or clade C1.1 generated by reverse genetics showed that the clade C1.1 spike was associated with reduced virus replication competence in Calu-3 cells in vitro, in ex vivo human bronchus, and in lungs of hDPP4 knockin mice in vivo. These findings may explain why zoonotic MERS disease has not been reported from Africa so far, despite exposure to and infection with MERS-CoV.

Camel production systems in Ethiopia: a review of literature with notes on MERS-CoV risk factors.

Camels are the most adapted species to the harsh conditions of arid/semi-arid rangelands of Ethiopia where pastoralism is the dominant mode of life and mobility is an inherent strategy to efficiently utilize the spatially and temporally distributed pasture and water resources. Usually, large numbers of camels and other domestic animals from many different herds/flocks congregate at watering sites, and this may create a perfect condition for disease transmission and spread among animals. The same water sources are also shared by multitudes of wild animals. Camel herd sizes per household range from few heads (five to ten) to several hundreds. Female camels account for more than 75% of the herd. Male camels are usually sold early as pack animals or for slaughter. Female camels may remain fertile up to 25 years, during which time they produce eight to ten calves. Camels are herded during daytime on communal rangelands. During night, they are kept in traditional kraals around homesteads. Breeding time is short and seasonal and is affected by rainfall patterns and feed availability. Usually, only men milk camels. Milking frequency ranges from two to five times per day. Washing of hands, milking vessels, the udder and teats is not practised by many prior to milking the camels. Besides, the milking area is generally full of dust and dung and without shade. This affects the quality and safety of the produced milk. Pathogens and diseases of camelids are less well known; however, they are suspected as zoonotic sources for the human infection with the Middle East respiratory syndrome coronavirus. There is an increasing need to determine whether camels are clinically susceptible, act as potential reservoirs and maintenance or bridge hosts, to viral pathogens.

Prioritizing zoonotic diseases in Ethiopia using a one health approach.

BACKGROUND: Ethiopia has the second largest human population in Africa and the largest livestock population on the continent. About 80% of Ethiopians are dependent on agriculture and have direct contact with livestock or other domestic animals. As a result, the country is vulnerable to the spread of zoonotic diseases. As the first step of the country's engagement in the Global Health Security Agenda, a zoonotic disease prioritization workshop was held to identify significant zoonotic diseases of mutual concern for animal and human health agencies. METHODS: A semi-quantitative tool developed by the US CDC was used for prioritization of zoonotic diseases. Workshop participants representing human, animal, and environmental health ministries were selected as core decision-making participants. Over 300 articles describing the zoonotic diseases considered at the workshop were reviewed for disease specific information on prevalence, morbidity, mortality, and DALYs for Ethiopia or the East Africa region. Committee members individually ranked the importance of each criterion to generate a final group weight for each criterion. RESULTS: Forty-three zoonotic diseases were evaluated. Criteria selected in order of importance were: 1)severity of disease in humans, 2)proportion of human disease attributed to animal exposure, 3)burden of animal disease, 4)availability of interventions, and 5)existing inter-sectoral collaboration. Based on the results from the decision tree analysis and subsequent discussion, participants identified the following five priority zoonotic diseases: rabies, anthrax, brucellosis, leptospirosis, and echinococcosis. DISCUSSION: Multi-sectoral collaborations strengthen disease surveillance system development in humans and animals, enhance laboratory capacity, and support implementation of prevention and control strategies. To facilitate this, the creation of a One Health-focused Zoonotic Disease Unit is recommended. Enhancement of public health and veterinary laboratories, joint outbreak and surveillance activities, and intersectoral linkages created to tackle the prioritized zoonotic diseases will undoubtedly prepare the country to effectively address newly emerging zoonotic diseases.