Functional comparison of MERS-coronavirus lineages reveals increased replicative fitness of the recombinant lineage 5

Simon Schroeder 1, Christin Mache 2, Hannah Kleine-Weber 3, Victor M Corman 1 4, Doreen Muth 1, Anja Richter 1, Diana Fatykhova 5, Ziad A Memish 6 7 8, Megan L Stanifer 9, Steeve Boulant 10 11, Mitra Gultom 12 13 14 15, Ronald Dijkman 12 13 14, Stephan Eggeling 16, Andreas Hocke 5, Stefan Hippenstiel 5, Volker Thiel 12 13, Stefan Pöhlmann 3, Thorsten Wolff 2, Marcel A Müller 1 4 17, Christian Drosten 18 19

Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels across the Middle East and Africa. Virus-induced pneumonia in humans results from animal contact, with a potential for limited onward transmission. Phenotypic changes have been suspected after a novel recombinant clade (lineage 5) caused large nosocomial outbreaks in Saudi Arabia and South Korea in 2016. However, there has been no functional assessment. Here we perform a comprehensive in vitro and ex vivo comparison of viruses from parental and recombinant virus lineages (lineage 3, n = 7; lineage 4, n = 8; lineage 5, n = 9 viruses) from Saudi Arabia, isolated immediately before and after the shift toward lineage 5. Replication of lineage 5 viruses is significantly increased. Transcriptional profiling finds reduced induction of immune genes IFNB1, CCL5, and IFNL1 in lung cells infected with lineage 5 strains. Phenotypic differences may be determined by IFN antagonism based on experiments using IFN receptor knock out and signaling inhibition. Additionally, lineage 5 is more resilient against IFN pre-treatment of Calu-3 cells (ca. 10-fold difference in replication). This phenotypic change associated with lineage 5 has remained undiscovered by viral sequence surveillance, but may be a relevant indicator of pandemic potential.