Ecological Drivers of Virus Evolution: Astrovirus as a Case Study

Abstract

Although RNA viruses exhibit a high frequency of host jumps, major differences exist among the different virus families. Astroviruses infect a wide range of hosts, affecting both public health systems and economic production chains. Here we delineate the ecological and adaptive processes that drive the cross-species transmission of astroviruses. We observe that distinct transmission zones determine the prevailing astrovirus host and virus diversity, which in turn suggests that no single host group (e.g., bats) can be the natural reservoir, as illustrated through our phylogenetic analysis.

FIG 1

Phylogenetic relationship of the RNA-dependent RNA polymerase (RdRp) genes of 1,259 astroviruses. Tree branches are colored based on host ecology to highlight cross-species transmission between and among ecological niches (key), determined by using FigTree (http://tree.bio.ed.ac.uk/software/figtree/). The scale bar indicates nucleotide substitutions per site. The tree was generated based on an alignment of 540 nucleotides of the most conserved region of the RdRp region, which is routinely used for the PCR diagnostics of RNA viruses. This final data set was curated from a preliminary analysis of all publicly available sequence data (∼4,300 sequences deposited in NCBI GenBank) and by picking the most conserved region with the highest numbers of sequences available. The capsid gene had greater representation than the selected RdRp region but was not considered because the genes had greater family-level variation and, hence, could not be unambiguously aligned.

FIG 2

Phylogenetic relationship of mamastroviruses. The mamastrovirus lineage shown in Fig. 1 is enlarged, and tree branches are colored based on host species and group (key) to highlight the relationships between astroviruses isolated from various mammals. Numbers of sequences for severely undersampled hosts (<4 sequences) are shown in parentheses. The scale bar indicates nucleotide substitutions per site.