Analysis of Intrahost Variation in Venezuelan Equine Encephalitis Virus Reveals Repeated Deletions in the 6-Kilodalton Protein Gene

(VEEV) demonstrated the presence of multiple deletions within the 6,000-molecular-weight (6K) protein gene. Using in vitro and in vivo experiments, similar deletions were generated in an additional VEEV strain originating from an infectious cDNA clone. Time course experiments demonstrated that the deletions are produced during acute infection although not until 24 h postinfection. Molecular clones containing some of these deletions were generated, and although the larger deletions appear to be noninfectious, viruses with the smaller deletions were viable and formed small plaques. Serial passages provided no evidence that these deletion mutants function as defective interfering particles. Furthermore, since wild-type infections generally occur at a low multiplicity of infection, it is unlikely that these deletions are propagated in natural transmission cycles. However, they could affect pathogenesis at later stages of infection. Because they are ubiquitously generated both in vivo and in vitro, further investigation is warranted to understand the generation of these deletions and their significance for disease. Alphaviruses such as Venezuelan equine encephalitis (VEE) virus (VEEV) are positive-stranded RNA viruses belonging to the family Togaviridae. Their genomes are approximately 11 kb in length and encode two open reading frames (ORF), with