RNA virus discovery in Australian camelids reveals divergent picornaviruses and the convergent evolution of upstream ORFs

Abstract

Invasive species can impact viral ecology, evolution and emergence by acquiring and disseminating viruses absent from native hosts. However, the extent to which invasive species harbour previously unrecognized RNA viruses and transmit these to native species is uncertain. We performed metatranscriptomic sequencing of invasive camelids in Australia and identified several previously undescribed vertebrate-associated RNA viruses, including an astrovirus closely related to avian-associated viruses suggesting a recent host jump. We also identified highly divergent picornaviruses that differed sufficiently from recognized taxa in genome organization and polyprotein phylogeny to establish a new genus. Notably, one virus encoded a putative upstream ORF (uORF) in the 5' genomic region. Across the Picornaviridae, putative uORF gain and loss appear to have occurred multiple times independently. In addition, although most of these uORF-encoded proteins exhibited little to no amino acid sequence homology, a subset showed overlapping ranges of secondary structure composition and intrinsic disorder, and when heterologously expressed, these proteins were translated and triggered reproducible transcriptional responses in a cell line. While no single pathway was uniformly affected across all uORFs, distinct uORFs from divergent lineages consistently perturbed overlapping sets of cellular pathways, supporting broadly analogous functional effects despite a lack of sequence homology. These findings demonstrate that uORFs represent a recurrent and selectable functional module within RNA virus genomes, suggest that the upstream genomic position itself constitutes a "hotspot" for the repeated acquisition of a functional module, and provide experimental evidence that their functional properties have converged across evolutionarily independent lineages. Author SummaryRNA viruses evolve under strong genomic constraints, forcing them to repeatedly adopt similar solutions to common challenges posed by their host environment. Invasive species can impact viral ecology, evolution and emergence by acquiring and disseminating non-native viruses. By characterizing RNA viruses infecting invasive camelids in Australia, we discovered previously unrecognized RNA viruses and recurrent patterns of genome evolution. Notably, we identified a small additional gene located at the 5' genomic region, known as an upstream open reading frame (uORF). uORFs were independently acquired and lost across multiple viral lineages, revealing that the same genomic region can be repeatedly exploited to acquire new functions. Although uORF-encoded proteins share little or no amino acid sequence homology, some of the encoded proteins showed comparable secondary structure composition and induce overlapping host cellular responses when expressed in cells. Hence, RNA viruses that have followed different evolutionary paths can converge on similar functional strategies.