A study of nucleotide sequence homology between the nucleic acids of different alphaviruses

Abstract

Base sequence homologies have been analyzed between the virus-specific nucleic acids of the four different alphaviruses, Semliki Forest (SF) virus, Sindbis (SIN) virus, Chikungunya (CHIK) virus, and O'nyong-nyong (ONN) virus and between different strains of these viruses by RNA-RNA hybridization experiments and by two-dimensional gel electrophoretic analyses of the oligonucleotides generated by RNase T 1 digestion. The following results were obtained: (1) Similar to earlier findings in SIN and SF virus-infected cells two species of single-stranded virus-specific RNA sedimenting at about 42 S and 26 S on sucrose density gradients, respectively, are synthesized in ONN and CHIK virus-infected cells and the 26 S RNA molecules are subgenomic RNA species. (2) Different oligonucleotide patterns were obtained for the genome RNA molecules of the different viruses and none of the oligonucleotides characterized was present in more than one of the viruses. (3) Besides a large number of common oligonucleotides, differences were found in the oligonucleotide patterns of different strains of the same virus, which allowed the identification of the virus strain from the oligonucleotide pattern of its genome RNA. (4) A 13% base sequence homology was detected between CHIK virus and ONN virus by RNA-RNA hybridization, whereas only small sequence homologies of about 1% or less were detected between the other viruses.