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

Phylogenetic analysis of these and other relevant viruses is shown in Fig. 1 . The tree was rooted against a MERS-CoVrelated bat coronavirus Neoromicia/PML-PHE/RSA/2011 (8) . Viruses from Nigeria, Burkina Faso, Morocco, and Ethiopia formed a monophyletic clade together with previously sequenced viruses from Egypt, which we now provisionally designate as virus "clade C." A time-resolved phylogeny of currently available MERS-CoV sequences, including those generated in this study from diverse parts of Africa, is shown in Fig. S1 . An analysis of synapomorphies (mutations inferred to have occurred once in the tree), homoplasies (repeat mutations), and reversions within available MERS-CoV full-genome sequences is shown in Fig. S2 . Viruses from Burkina Faso (n = 3), Morocco (n = 1), and Nigeria (n = 9) had signature deletions in the ORF4b and/or ORF3 gene regions ( Fig. S3 ) and are designated "clade C1" (Fig. 1 ). Clade C viruses from Ethiopia (n = 4) and Egypt (n = 3) did not have such gene deletions, nor do the majority of viruses from the Arabian Peninsula. However, sequences of two clade B human viruses detected in 2012 (Riyadh_1_2012 and Bisha_1_2012) available in public databases also have short (17-nt) deletions in the ORF4b region in a similar, although not identical, region as the African isolates (Fig. S3 ). Targeted sequencing of the ORF3/4b gene region was done on additional African camel viruses from which full genomes could not be obtained because viral load was too low. Overall, all 10 additional viruses from Burkina Faso carried these same signature deletions, frame shift mutations, or premature stop-codons that markedly reduced the size of the ORF4b, but none of the 10 additional viruses from Ethiopia did so (Fig. S3 ). Clade C1 viruses with ORF4b deletions appear to share a common ancestor, with a 6-nt and a 360-nt deletion in ORF4b denoted as the "ancestral type i ORF4b deletion" in the phylogenetic tree ( Fig. 1 ) and in the schematic of the deletion (Fig. S3 ). This deletion has been added to progressively, and these deletions are denoted as "ii," "iii," "iv," and "v" along the branches of the phylogenetic tree ( Fig. 1 ) and the schematic (Fig. S3 ). Some of these viruses (Nigeria/HKU NV1657-like and Burkina Faso/CIRAD-HKU697-like) have also acquired deletions in ORF3. Notably, the Ethiopian and Egyptian viruses encoded a full-length ORF3.