High-resolution functional mapping of the venezuelan equine encephalitis virus genome by insertional mutagenesis and massively parallel sequencing

• Published in: PLoS pathogens 2010-10, Vol.6 (10), p.e1001146
• Main Authors: Beitzel, Brett F, Bakken, Russell R, Smith, Jeffrey M, Schmaljohn, Connie S
• Format: Article
• Language: English
• Subjects: Alphavirus; Animals; Arboviruses; Biotechnology; Cells, Cultured; Cercopithecus aethiops; Chromosome mapping; Chromosome Mapping - methods; DNA sequencing; Encephalitis Virus, Venezuelan Equine - genetics; Encephalitis Virus, Venezuelan Equine - physiology; Experiments; Genetic aspects; Genetics and Genomics; Genome, Viral - genetics; Genomes; High-Throughput Nucleotide Sequencing - methods; Immunology/Immunity to Infections; Infectious Diseases/Viral Infections; Methods; Mice; Mice, Inbred BALB C; Microbiology; Molecular weight; Mutagenesis; Mutagenesis, Insertional - methods; Mutation; Nucleotide sequencing; Proteins; RNA polymerase; Sequence Analysis, DNA - methods; Sequence Homology, Nucleic Acid; Studies; Venezuelan equine encephalitis virus; Vero Cells; Virology/Vaccines; Virulence - genetics; Virus Replication - genetics; Viruses
• ISSN: 1553-7374; 1553-7366; 1553-7374
• DOI: 10.1371/journal.ppat.1001146

We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus (VEEV) genome. We initially used a capillary electrophoresis method to gain insight into the role of the VEEV nonstructural protein 3 (nsP3) in viral replication. We identified several regions in nsP3 that are intolerant to small (15 bp) insertions, and thus are presumably functionally important. We also identified nine separate regions in nsP3 that will tolerate small insertions at low temperatures (30°C), but not at higher temperatures (37°C, and 40°C). Because we found this method to be extremely effective at identifying temperature sensitive (ts) mutations, but limited by capillary electrophoresis capacity, we replaced the capillary electrophoresis with massively parallel sequencing and used the improved method to generate a functional map of the entire VEEV genome. We identified several hundred potential ts mutations throughout the genome and we validated several of the mutations in nsP2, nsP3, E3, E2, E1 and capsid using single-cycle growth curve experiments with virus generated through reverse genetics. We further demonstrated that two of the nsP3 ts mutants were attenuated for virulence in mice but could elicit protective immunity against challenge with wild-type VEEV. The recombinant ts mutants will be valuable tools for further studies of VEEV replication and virulence. Moreover, the method that we developed is applicable for generating such tools for any virus with a robust reverse genetics system.