MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity

Chu, Daniel K. W.; Hui, Kenrie P. Y.; Perera, Ranawaka A. P. M.; Miguel, Eve; Niemeyer, Daniela; Zhao, Jincun; Channappanavar, Rudragouda; Dudas, Gytis; Oladipo, Jamiu O.; Traoré, Amadou; Fassi-Fihri, Ouafaa; Ali, Abraham; Demissié, Getnet F.; Muth, Doreen; Chan, Michael C. W.; Nicholls, John M.; Meyerholz, David K.; Kuranga, Sulyman A.; Mamo, Gezahegne; Zhou, Ziqi; So, Ray T. Y.; Hemida, Maged G.; Webby, Richard J.; Roger, Francois; Rambaut, Andrew; Poon, Leo L. M.; Perlman, Stanley; Drosten, Christian; Chevalier, Veronique; Peiris, Malik

Studies of MERS-CoV in dromedaries in Burkina Faso (West Africa), Nigeria (West Africa), Morocco (North Africa), and Ethiopia (East Africa) showed that virus circulation was as extensive and viral shedding as common as previously reported in the Arabian Peninsula (7) . However, while zoonotic MERS has been repeatedly reported from the Arabian Peninsula, zoonotic human disease has not so far been reported in Africa. There are, however, little viral genetic data from MERS-CoV in Africa. To begin to address this knowledge gap, we genetically characterized MERS-CoV from Burkina Faso, Nigeria, Morocco, and Ethiopia. We found that MERS-CoV circulating in dromedaries in Africa are phylogenetically distinct from viruses in the Arabian Peninsula. There are no homoplasies (convergent mutations) shared between the African and Saudi clades, suggesting no recombination between these lineages (consistent with a single or just a few introductions into the Kingdom of Saudi Arabia and limited further contact between the lineages). MERS-CoV from North and West Africa form a distinct subclade (clade C1) within those from Africa, and they have characteristic deletions in ORF4b, an accessory gene that has been previously reported to be an IFN antagonist (10, 11) . Some of these viruses also have partial deletions of ORF3. The biological function of ORF3 still remains unclear. Dromedary camel movements in Africa occur more in the north-south direction with movements between countries such as Morocco, Burkina Faso, and Nigeria being more much likely than east-west movements, i.e., between West Africa and Ethiopia or Egypt (17) . This may explain the observed separate phylogenetic clustering of viruses from West and North Africa as clade C1, which were also the viruses that have the ORF4b gene deletions. Although genetically distinct, MERS-CoV from West Africa were antigenically similar to the prototype EMC virus (clade A), AH13 (clade B), and Egypt NRCE-HKU270 (clade C, nonclade C1) viruses in microneutralization tests. Thus, it is likely that neutralizing antibodies elicited by the prototype strain EMC in putative vaccines are likely to be cross-protective against these genetically diverse African strains.