Species Are Shaped by Recombination and Can Be Reliably Distinguished in ORF1b Genome Region

Astroviruses are a diverse group of small non-enveloped positive sense single-stranded RNA viruses that infect animals and birds. More than half of all known genome sequences of mammalian astroviruses are not assigned to provisional species, and the biological mechanisms that could support segregation of astroviruses into species are not well understood. The systematic analysis of recombination in genomes available in GenBank was done to identify mechanisms providing genetic distinction between astroviruses. Recombination breakpoints were present in all genome regions, but occurred most commonly at the ORF1b/ORF2 junction. Recombination was ubiquitous within, but never between established and putative new species, and may be suggested as an additional species criterion. The current species criterion for the genus based on ORF2 amino acid sequence p-distances did not reliably distinguish several established species and was of limited use to identify distinct groups among unclassified astroviruses that were isolated recently, predominantly from cattle and pigs. A 17% nucleotide sequence distance cut-off in ORF1b fairly distinguished the established species and several groups among the unclassified viruses, providing better correspondence between phylogenetic grouping, reproductive isolation and the virus hosts. Sequence distance criteria (17% in nucleotide sequence of ORF1b and 25% in amino acid sequence of ORF2) and the recombination pattern corresponded fairly well as species criteria, but all had minor exclusions among mammalian astroviruses. A combination of these taxonomic criteria supported the established species and suggested redefining a few provisional species that were proposed earlier and introducing at least six novel species among recently submitted rat and bovine astroviruses.