Conservation and Variation in Orthopoxvirus Genome Structure

Abstract

Orthopoxvirus DNA from representative strains of rabbitpox, vaccinia, monkeypox, variola, cowpox and ectromelia viruses was analysed by cleavage with restriction endonucleases HindIII, Xho1 or Sma1. Genome mol. wt. vary from about 120 × 10⁶ for rabbitpox to about 145 × 10⁶ for cowpox. Physical maps of cleavage sites are similar and characteristic for strains of the same Orthopoxvirus type. The distribution of HindIII sites suggests that an internal region of mol. wt. about 30 × 10⁶ is highly conserved between Orthopoxvirus genomes although some type-specific differences occur within this region, especially with strains of ectromelia virus. Conservation of internal sequences is less marked following analysis with Xho1 although cleavages within this central region of particular genomes appear to represent a subset of preferred sites. Endonuclease Sma1 cleaves exceptionally infrequently and distinguishes variola, monkeypox, vaccinia, cowpox or ectromelia viruses. Type specific differences result largely from extensive, near terminal variations in length and sequence.