Evidence for an ancient aquatic origin of the RNA viral order Articulavirales

Abstract

The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes the emergence of viruses in new hosts. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the RNA virus order Articulavirales, which includes the influenza viruses. We identified instances of Articulavirales in the invertebrate phylum Cnidaria (including corals), constituting a novel and divergent family that we provisionally named the "Cnidenomoviridae." We further extended the evolutionary history of the influenza virus lineage by identifying four divergent, fish-associated influenza-like viruses, thereby supporting the hypothesis that fish were among the first hosts of influenza viruses. In addition, we substantially expanded the phylogenetic diversity of quaranjaviruses and proposed that this genus be reclassified as a family-the "Quaranjaviridae." Within this putative family, we identified a novel arachnid-infecting genus, provisionally named "Cheliceravirus." Notably, we observed a close phylogenetic relationship between the Crustacea- and Chelicerata-infecting "Quaranjaviridae" that is inconsistent with virus-host codivergence. Together, these data suggest that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of the Articulavirales was likely shaped by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.

Keywords: Articulavirales; Cnidaria; evolution; influenza; virosphere.

Fig. 1.

Expanding the known diversity of the Articulavirales. (A) Overrepresentation of influenza A and B viruses in publicly available genomic data. Distribution of 99.7% of publicly available PB1 segments on NCBI Virus as of January 2023 by virus species. Those virus species not shown each comprise <0.05% of available data. (B) PB1 segments of novel Articulavirales identified in Cnidaria hosts. Heliopora-associated virus 1 was identified through sequencing while Heliopora-associated virus 2 was identified through data mining. (C) Distribution of host species and classes associated with the Articulavirales detected through total RNA sequencing and data mining.

Fig. 2.

Phylogenetic evidence for four virus families within the order Articulavirales. (A) Unrooted maximum likelihood tree of the Articulavirales PB1 segment, with branch lengths scaled to the number of amino acid substitutions per site. *Novel viruses identified in this study. The red arrow marks Salmon isavirus while the gold arrow marks an aquatic amnoon-like virus clade associated with Mollusca and fish hosts (“Metamyxovirus”). (B) PB1 maximum likelihood tree rooted on basal invertebrate family “Cnidenomoviridae”. (C) PB1 maximum likelihood tree rooted on the Amnoonviridae. In all cases, branch lengths are scaled to the number of amino acid substitutions per site.

Fig. 3.

Characterization of a divergent influenza-like viruses identified in a flounder, seahorse, carp, and sturgeon. (A) Conserved motifs of the PB1 segment of flounder-, seahorse-, sturgeon-, carp-, and hagfish-associated influenza-like viruses. Maximum likelihood phylogenetic trees of the influenza virus PB1 (B), PB2 (C), and PB3 (D) segments. Putative aquatic hosts are indicated with icons. Segments from viruses identified in this study are shown in red. All trees were rooted using the “Quaranjaviridae” as outgroups with branch lengths scaled to the number of amino acid substitutions per site.

Fig. 4.

Evolution of the “Quaranjaviridae” is shaped by virus–host codivergence and cross-species transmission. (A–E) Maximum likelihood phylogenies of the “Quaranjaviridae” rooted with Thogotovirus. “Cheliceravirus” are denoted by a spider icon. (A), PB2 (B), PB3 (C), NP (D), and HA (E). Branch color indicates putative host. Due to limitations in data availability differing numbers of segment were used for each tree (PB1: n = 208; PB2: n = 144; PB3: n = 168; NP: n = 149; HA: n = 128) (A) Mosquito-borne viruses are denoted with a mosquito icon. Host phylogeny adapted from Thomas et al. (38) *Novel viruses identified in this study. Branch lengths are scaled according to the number of amino acid substitutions per site.