CHARACTERIZATION OF ARENAVIRUSES USING A FAMILY-SPECIFIC PRIMER SET FOR RT-PCR AMPLIFICATION AND RFLP ANALYSIS - ITS POTENTIAL USE FOR DETECTION OF UNCHARACTERIZED ARENAVIRUSES

Arenaviruses are enveloped viruses with a genome composed of two ssRNA species, designated L and S. The arenaviruses were divided in two maj or groups (Old World and New World), based on serological properties a nd genetic data, as well as geographic distribution. A sequence alignm ent analysis of all reported arenavirus S RNAs yielded 17 conserved re gions in addition to a reported conserved region at the end of both RN As. The consensus sequences of these regions were used to design gener alized primers suitable for RT-PCR amplification of a set of overlappi ng nucleotide sequence fragments comprising the complete S RNA of any arenavirus. A restriction analysis (RFLP) was designed to rapidly typi fy the amplified fragments. This RT-PCR-RFLP approach was tested with Old World (LCM) and New World (Junin and Tacaribe) arenaviruses. Furth ermore, using this procedure the whole S RNA of a novel arenavirus iso late obtained from a rodent trapped in central Argentina, was amplifie d and characterized. Partial nucleotide sequence data were used for ph ylogenetic analyses that showed the relationships between this arenavi rus and the rest of the members of the family. This relatively simple methodology will be useful both in basic studies and epidemiological s urvey programs. (C) 1997 Elsevier Science B.V.