High genetic divergence and recombination in Arenaviruses from the Americas

Abstract

The rodent-borne Arenaviruses are divided into two major antigenic groups: the Old World and New World complexes. Of the 15 known New World arenaviruses, four (Junin, Machupo, Sabia, and Guanarito) have been associated with hemorrhagic fever in humans. It has been difficult to assess the pathogenic or epidemic potential of the remaining viruses and the threat of emerging disease. We obtained full-length small (S) segment sequence data, encoding the nucleoprotein (NP) and glycoprotein precursor (GPC), from all American arenaviruses to predict their evolutionary and functional relationships. Phylogenetic analysis of NP or GPC amino acid sequences from all New World arenaviruses revealed three lineages and that Tamiami and Whitewater Arroyo viruses were probably derived from a single recombinant progenitor. The results imply that arenaviruses have been evolving independently for a very long time, leading to very diverse groupings that do not correlate with geography, rodent host, or human epidemic potential.

FIG. 1

Phylogenetic relationships among New World arenaviruses based on maximum parsimony analysis of the amino acid sequences of the complete glycoprotein precursor (GPC) gene (561 characters) and the complete nucleoprotein (NP) gene (581 characters). The numbers above the nodes indicate bootstrap support for branching patterns to the right. Scale indicates 50 changes. Lineages are indicated by A, B, or C.

FIG. 2

RNA secondary structure predicted using RNASTAR for the intergenic nucleotides of Tamiami virus (TAMV), 182 nucleotides, and Whitewater Arroyo virus (WWAV), 71 nucleotides. Sequences were analyzed with the 100 flanking nucleotides on either side of the intergenic region for context.