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

The observation that ORF4b, ORF4a, and ORF3 deletions appear to arise independently in clade B and C viruses and that ORF4b deletions are fixed in MERS-CoV from dromedaries West Africa may suggest that the virus is not yet fully adapted to camels and the presence of these genes is either neutral or slightly deleterious to virus growth in these settings. Given the propensity of viruses to discard unnecessary genetic information, these results suggest that these accessory proteins are advantageous in some other reservoir host species, perhaps bats. The time to most recent common ancestor (TMRCA) for MERS-CoV, the >99% nucleotide homology of viruses across a wide geographic area, the genetic instability of the virus in dromedaries, and the lack of endemic infection in dromedaries in parts of the Virus titers in culture supernatants were determined by the TCID 50 assay. Means and SEM of three biological replicates are shown. The horizontal dotted line denotes the limit of detection in the TCID 50 assay. (B and C) Calu-3 cells were infected at an MOI of 2 with MERS-CoVs rgEMC-WT and rgEMCΔ4b; mock-infected cells served as negative controls. RNA expression of viral gene UpE (B) and mRNA expression of IFN-β and IFN-λ1 (C) is shown as the mean and the SEM of three biological replicates. The detection limit of each gene was 20 copies. Each experiment was repeated once, and a representative experiment is shown. Statistical significance was determined by two-way ANOVA with Bonferroni's comparisons: *P < 0.05; **P < 0.01; ***P < 0.001.