Middle East respiratory syndrome coronavirus (MERS-CoV) in West Africa : phylogenetics, human infection and viral determinants of interspecies transmission

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012 and is a zoonotic pathogen that can cause severe respiratory disease. Dromedary camels are the source of zoonotic infection. While over 80% of the global camel population is located in Africa and these camels also are infected with MERS-CoV, zoonotic MERS disease has not been reported in Africa. This enigma motivated our investigation of the viral genetic diversity and zoonotic potential of MERS-CoV from Africa. We studied dromedary camels and humans at a camel abattoir in Kano, Nigeria where 3666 camel nasal swabs were screened and 84 (2.3%) MERS-CoV positive swabs identified. Phylogenetic analysis showed Nigerian MERS-CoV clustered with other sequences from West Africa Burkina Faso and Morocco to form a subclade C1.1. Deletions in ORF3 and a 360-nucleotide deletion in ORF4b were characteristic of this subclade. Comparative analysis of the evolutionary rates between African and the Middle East MERS-CoV did not show significant differences.

We found very high levels of human exposure to camels and camel products such as consuming fresh camel milk, medicinal use of camel urine, and unprotected exposure to camels. Of a total of 404 workers recruited in a sero-epidemiological study in 2016 and 2019, 334 (83%) of them had direct camel exposure. However, none of them showed MERS-CoV neutralizing antibodies. This observation was in contrast with the higher seroprevalence observed in camel workers from Arabian Peninsula. A Nigeria MERS-CoV culture isolate (Nig1657) was biologically characterised in comparison with other MERS-CoV strains to compare putative zoonotic potential. Nig1657, together with other clade C African strains, had lower replication kinetics and elicited lower innate immune responses in the lungs of human DPP4 knockin mice. Taken together with other studies showing viral replication competence in ex vivo human respiratory tissues, these data suggested the West African MERS-CoV may have reduced zoonotic potential to cause recognizable human disease.

Additionally, we used plasmid-based reverse genetics to investigate the biological role of a potentially a human adaptive mutation in nsp6 of MERS-CoV repeatedly observed in human MERS-CoV in Saudi Arabia but not in camel viruses from the Middle East or Africa. This nsp L232F amino acid substitution was shown to modulate higher viral replication in ex vivo human respiratory tissues and the lungs of human DPP4 knockin mice. The higher replication phenotype was associated with higher induction of innate immune responses. These findings provide a genetic signature that could inform an increased viral fitness in human.

Finally, we characterised the genetic diversity of another betacoronavirus DcCoV HKU23, an Embecovirus that was shown to cocirculate in African camels to provide possible insights into the emergence and evolution of MERS-CoV. We showed evidence of recombination between Embecovirus species but not with MERS-CoV. The findings provided insights into the evolution and emergence of MERS-CoV.