Conservation of a packaging signal and the viral genome RNA packaging mechanism in alphavirus evolution.

Academic Article


  • Alphaviruses are a group of small, enveloped viruses which are widely distributed on all continents. In infected cells, alphaviruses display remarkable specificity in RNA packaging by encapsidating only their genomic RNA while avoiding packaging of the more abundant viral subgenomic (SG), cellular messenger and transfer RNAs into released virions. In this work, we demonstrate that in spite of evolution in geographically isolated areas and accumulation of considerable diversity in the nonstructural and structural genes, many alphaviruses belonging to different serocomplexes harbor RNA packaging signals (PSs) which contain the same structural and functional elements. Their characteristic features are as follows. (i) Sindbis, eastern, western, and Venezuelan equine encephalitis and most likely many other alphaviruses, except those belonging to the Semliki Forest virus (SFV) clade, have PSs which can be recognized by the capsid proteins of heterologous alphaviruses. (ii) The PS consists of 4 to 6 stem-loop RNA structures bearing conserved GGG sequences located at the base of the loop. These short motifs are integral elements of the PS and can function even in the artificially designed PS. (iii) Mutagenesis of the entire PS or simply the GGG sequences has strong negative effects on viral genome packaging and leads to release of viral particles containing mostly SG RNAs. (iv) Packaging of RNA appears to be determined to some extent by the number of GGG-containing stem-loops, and more than one stem-loop is required for efficient RNA encapsidation. (v) Viruses of the SFV clade are the exception to the general rule. They contain PSs in the nsP2 gene, but their capsid protein retains the ability to use the nsP1-specific PS of other alphaviruses. These new discoveries regarding alphavirus PS structure and function provide an opportunity for the development of virus variants, which are irreversibly attenuated in terms of production of infectious virus but release high levels of genome-free virions.
  • Published In


  • Animals, Base Composition, Capsid Proteins, Chikungunya virus, Chlorocebus aethiops, Cricetinae, Culicidae, Encephalitis Virus, Eastern Equine, Encephalitis Virus, Venezuelan Equine, Evolution, Molecular, Genome, Viral, Inverted Repeat Sequences, RNA, Viral, Signal Transduction, Sindbis Virus, Vero Cells, Virus Assembly
  • Digital Object Identifier (doi)

    Author List

  • Kim DY; Firth AE; Atasheva S; Frolova EI; Frolov I
  • Start Page

  • 8022
  • End Page

  • 8036
  • Volume

  • 85
  • Issue

  • 16