Surveillance and phenotyping East African camel MERS-CoV and role of the spike protein on the phenotype of clade C MERS-CoV

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012 in Saudi Arabia, has infected more than 2500 people with a fatality rate of 34.4% to date, and remains a threat of the global public health concern. MERS-CoV is enzootic in camels in Africa and the Arabian Peninsula. Camel-to-human transmissions occur in the Arabian Peninsula. Although over 80% of the global population of dromedary camels is found in Africa and there is high seroprevalence in these camels, zoonotic disease has not been reported in Africa.

In this thesis, MERS-CoV surveillance studies were carried out in camels in Ethiopia, East Africa, to understand the transmission dynamics within camel populations. The viral RNA prevalence of MERS-CoV in nasal swabs was 3.47%. Age, type of collection site (e.g., herd vs. slaughterhouse), and seasonality were identified as risk factors for MERS-CoV infection in this study. Viruses detected were genetically characterized by sequencing and phylogenetic analysis. MERS-CoVs from Ethiopia were found to be clade C2 viruses. A virus isolate was obtained and characterized phenotypically for virus replication competence in comparison with other clade C viruses from Kenya and Burkina Faso, and clade A and B viruses from Saudi Arabia. In comparison to clade A and B viruses from Saudi Arabia, clade C2 viruses (Ethiopia and Kenya) and a clade C1.1 virus (Burkina Faso) had lower replication competence in Calu-3 cells, ex vivo cultures of human bronchus, and in lungs of hDPP4 knock-in mice. The viral genetic determinants were then investigated for this low replication phenotype difference. Lentiviruses pseudotyped with the spike of African clade C1.1 viruses were associated with reduced cell entry in comparison to a Saudi Arabian clade A (strain EMC) in Calu-3 cells, the human lung epithelial cell line. Isogenic EMC viruses with spike protein from EMC or clade C1.1 virus demonstrated that the clade C1.1 spike was associated with reduced virus replication competence in Calu-3 cells, ex vivo cultures of human lungs, and in lungs of hDPP4 knock-in mice. In summary, the reduced replication competence of African camel MERS-CoVs may explain why zoonotic MERS-CoV is rarely reported in Africa, even though MERS-CoV is enzootic in camels in Africa. Our findings suggest that the virus spike protein is one key factor contributing to the reduced replication competence of clade C MERS-CoVs in Africa. These findings highlight the importance of MERS-CoV surveillance in Africa.