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

Genetic Characterization. The epidemiological aspects of field studies of dromedary camels in Morocco, Burkina Faso, Ethiopia, and Nigeria, including seroprevalence and RT-PCR detection of virus from nasal swabs, have been reported previously (6, 7) . An additional 102 nasal swabs were collected in the Afar region of Ethiopia in 2017. Of 173 RT-PCR-positive specimens detected in these studies, those with high viral load were selected, attempting to maximize diversity in geography and sampling dates, for full viral genome sequencing directly from the clinical specimen and for virus isolation (Dataset S1). Three viruses from Burkina Faso, one from Morocco, nine from Nigeria, and three from Ethiopia were fully sequenced, and an additional virus from Ethiopia was sequenced from the S2 gene region to the 3′ end of the genome (5,126 nt) . Genetic nucleotide identity was 99.17% within African camel virus genomes, >99.26% within human and camel MERS-CoV from the Middle East, and 99. .58% between viruses from the Middle East and Africa (GenBank accession nos: MG923465-MG923481).