title: Analysis of intrahost variation in Venezuelan equine encephalitis virus reveals repeated deletions in the 6-kilodalton protein gene.
abstract: RNA viruses exist as a spectrum of mutants that is generated and maintained during replication within the host. Consensus sequencing overlooks minority genotypes present in the viral sample that may impact the population's phenotype. In-depth sequencing of an original field isolate of subtype IE Venezuelan equine encephalitis virus (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.
authors.affiliation: Institute for Human Infections and Immunity, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA.
authors.forename: N L
authors.initials: NL
authors.lastname: Forrester
authors.forename: M
authors.initials: M
authors.lastname: Guerbois
authors.forename: A P
authors.initials: AP
authors.lastname: Adams
authors.forename: X
authors.initials: X
authors.lastname: Liang
authors.forename: S C
authors.initials: SC
authors.lastname: Weaver
mesh_terms: D000818:Animals; D002460:Cell Line; D006224:Cricetinae; D004195:Disease Models, Animal; D004666:Encephalitis Virus, Venezuelan Equine / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D004685:Encephalomyelitis, Venezuelan Equine / Q000821:virology*; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D008647:Mesocricetus; D050296:Microbial Viability; D012367:RNA, Viral / Q000235:genetics; D017384:Sequence Deletion; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins