The New Age of Virus Discovery: Genomic Analysis of a Novel Human Betacoronavirus Isolated from a Fatal Case of Pneumonia

Holmes, Kathryn V.; Dominguez, Samuel R.

How does the genomic analysis of HCoV-EMC expedite further research on this new human virus? As soon as partial nucleotide sequences of HCoV-EMC were available, sensitive RT-PCR tests were developed to specifically detect RNA of this virus in tissues and body fluids of humans and animals. These tests are being used to screen for HCoV-EMC RNA in patients with severe respiratory disease of unknown etiology and in wildlife surveillance. Based on the predicted amino acid sequences of the HCoV-EMC proteins, plasmids can be engineered to express the proteins for structural, antigenic, and functional studies. Recombinant viral proteins are being used in enzyme-linked immunosorbent assays (ELISAs) to detect HCoV-EMC-specific antibodies in sera. HCoV-EMC spike protein in retrovirus pseudotypes can be used to identify the virus receptor and study virus entry. Antisera raised against the recombinant HCoV-EMC proteins can detect viral antigens in infected cell cultures and infected tissues of humans or animals for studies on virus tissue tropism and pathogenesis. The viral genome can now be reconstructed by synthetic biology to create a manipulable cDNA copy that can be mutated for analysis of virus replication, pathogenesis, virulence factors, host range, and vaccines. When additional virus isolates from other patients or animal reservoirs become available, genomic analysis can be used to analyze variants to detect amino acid substitutions in the spike or other proteins that are associated with adaptation to cell culture or changes in antigenicity, host range, and virulence.