Molecular and Structural Characterisation of the MERS-Coronavirus Polymerase

MERS-CoV (Middle East respiratory syndrome coronavirus) belongs to the Betacoronavirus genus, which also includes SARS-CoV-2, the causative agent of the COVID-19 pandemic. MERS-CoV is the pathogen responsible for Middle East Respiratory Syndrome (MERS), a respiratory disease with a 36.5% case fatality rate. Given the capacity of coronaviruses for genetic recombination and mutation, MERS-CoV remains a pathogen of significant pandemic potential, with viral evolution potentially facilitating enhanced adaptation and transmission in humans. There are no approved treatments for MERS-CoV infection. The MERS-CoV replication-transcription complex (RTC), a multimeric protein complex key to genome amplification, has no cellular analogues and a highly conserved sequence, making it a useful target for antiviral compounds; however, structural and biochemical characterisation of the MERS-CoV RTC is limited. Here, we characterise the minimal MERS-CoV RTC using in vitro and single-molecule assays and show that it is susceptible to the RNA-dependent-RNA-polymerase inhibitor suramin. We present a structure of the minimal MERS-CoV RTC in complex with an RNA duplex, which shows strong structural similarity to the SARS-CoV-2 RTC. We use cross-subunit swapping experiments to show that the MERS-CoV NSP12 core can efficiently utilise SARS-CoV-2 cofactors NSP7 and NSP8, whereas SARS-CoV-2 NSP12 exhibits reduced in vitro activity with the MERS-CoV NSP8. This asymmetric cross-species compatibility highlights both the evolutionary conservation and virus-specific adaptation of coronavirus polymerase-cofactor interactions. Together, these findings provide a structural and mechanistic framework for understanding MERS-CoV RNA synthesis and establish its conserved RTC as a potential target for the development of broadly acting coronavirus antivirals.