The Betacoronavirus genus includes two viruses, SARS-CoV and MERS-CoV that emerged from animal reservoirs to produce severe pulmonary disease in man in 2002, and 2012, respectively. In this application we propose to study the RNA secondary structure of MERS-CoV and two related coronaviruses, mouse hepatitis virus (MHV) and bovine coronavirus (BCoV) with the goal of identifying and functionally characterizing novel conserved RNA secondary structures in the genomes of these viruses.
In aim one we will employ a state-of- the-art, high throughput approach, SHAPE-MaP, to generate biochemical data that allows the creation of highly accurate models of RNA secondary structures of large RNAs, such as coronavirus genomes. Through comparison of the RNA secondary structures of the genomes of MHV, BCoV, and MERS-CoV we will seek previously undiscovered phylogenetically conserved RNA secondary structures that are strong candidates to play a functional role in viral replication.
In aim 2 we will employ reverse genetic approaches to characterize the functional role in MHV and MERS-CoV replication of conserved secondary structures identified in aim 1.
Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) are both caused by viruses originating in animals and producing severe lung disease with 10-35% mortality rate in man. Both of these viruses (SARS-CoV and MERS-CoV) are members of the Betacoronavirus genus, as are two related Betacoronaviruses, mouse hepatitis virus (MHV) and bovine coronavirus (BCoV). This proposal will use a new high throughput method to look for novel RNA secondary structures (foldings) that are conserved amongst MHV, BCoV, and MERS-CoV, and thus are likely to be important for virus replication. Reverse genetic mutational studies will confirm their functional role in virus growth. Identificatin of functionally important conserved structural features in the genomes of these viruses has the potential to ultimately reveal potential new therapeutic targets for antiviral therapies.
