Within-host Evolution of Segments Ratio for the Tripartite Genome of Alfalfa Mosaic Virus

Abstract

One of the most intriguing questions in evolutionary virology is why multipartite viruses exist. Several hypotheses suggest benefits that outweigh the obvious costs associated with encapsidating each genomic segment into a different viral particle: reduced transmission efficiency and segregation of coadapted genes. These putative advantages range from increasing genome size despite high mutation rates (i.e., escaping from Eigen paradox), faster replication, more efficient selection resulting from segment reassortment during mixed infections, or enhanced virion stability and cell-to-cell movement. However, empirical support for these hypotheses is scarce. A more recent hypothesis is that segmentation represents a simple and robust mechanism to regulate gene copy number and, thereby, gene expression. According to this hypothesis, the ratio at which different segments exist during infection of individual hosts should represent a stable situation and would respond to the varying necessities of viral components during infection. Here we report the results of experiments designed to test whether an evolutionary stable equilibrium exists for the three RNAs that constitute the genome of Alfalfa mosaic virus (AMV). Starting infections with many different combinations of the three segments, we found that, as infection progresses, the abundance of each genome segment always evolves towards a constant ratio. Population genetic analyses show that the segments ratio at this equilibrium is determined by frequency-dependent selection; indeed, it represents an evolutionary stable solution. The replication of RNAs 1 and 2 was coupled and collaborative, whereas the replication of RNA 3 interfered with the replication of the other two. We found that the equilibrium solution is slightly different for the total amounts of RNA produced and encapsidated, suggesting that competition exists between all RNAs during encapsidation. Finally, we found that the observed equilibrium appears to be host-species dependent.