Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts

Abstract

The RNA virus family Picobirnaviridae has traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests that these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing Picobirnavirus genera that we tentatively name ‘Alpha-’, ‘Beta-’, ‘Gamma-’, ‘Delta-’, ‘Epsilon-’, ‘Zeta-’, and ‘Etapicobirnavirus’. A statistical analysis of topological congruence between virus–host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in Picobirnavirus genomes than in the two groups of established RNA bacteriophage—the Leviviricetes and Cystoviridae. Overall, our findings support the hypothesis that the Picobirnaviridae have bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.

Introduction

The analysis of metatranscriptomic data, either sequenced de novo or mined from the Sequence Read Archive, has greatly enhanced our knowledge of the scale, diversity, and composition of the RNA virosphere. As well as documenting huge numbers of novel viruses, this research programme has provided new insights into previously known families of RNA viruses. For example, major changes to taxonomic organisations have been proposed based on updated phylogenetic trees of RNA viruses (Shi et al. 2016; Wolf et al. 2020; Sadiq et al. 2022), and host ranges have been extended when viruses are detected in organisms with which they are not typically associated (Urayama, Takaki, and Nunoura 2016; Bonny et al. 2021; Geoghegan et al. 2021).

Members of the double-stranded RNA virus family Picobirnaviridae (order Durnavirales, class Duplornaviricetes, phylum Pisuviricota) have traditionally been considered opportunistic enteric pathogens of mammals and birds, typically detected in animal faecal samples (Malik et al. 2014), and were recently reported in invertebrate hosts (Delmas et al. 2019). In mammalian and avian species, Picobirnavirus infection has been associated with the disease presenting with diarrhoea or gastroenteritis (Ganesh, Masachessi, and Mladenova 2014; Malik et al. 2014). However, as picobirnaviruses have also been detected in the stool of healthy or asymptomatic animals (Ganesh, Masachessi, and Mladenova 2014), the presence of a Picobirnavirus in the animal gastrointestinal system is not necessarily associated with overt disease. The genomes of these picobirnaviruses are typically bi-segmented, with Segment 1 (2.4–2.7 kb in length) comprising three open reading frames (ORFs). ORF3 is known to code a capsid protein precursor, while recent evidence suggests that ORF1 and ORF2 may encode bacteriolytic proteins (Neri et al. 2022; Gan and Wang 2023). Segment 2 (1.7–1.9 kb) encodes the viral RNA-dependent RNA polymerase (RdRp) that is universal to RNA viruses and hence a powerful phylogenetic marker (Delmas et al. 2019). Picobirnaviruses with non-segmented genomes have also been reported, in which all ORFs are present in a single, monopartite genome (Giannitti et al. 2015; Shi et al. 2016).

The increasing accessibility of metatranscriptomic sequencing has resulted in the identification of huge numbers of Picobirnavirus sequences from both aquatic and terrestrial environmental samples such as wastewater, sewage, permafrost, farmland soils, and forest soils (Adriaenssens et al. 2018; Bell et al. 2020; Guajardo-Leiva et al. 2020; Chen et al. 2022; Neri et al. 2022). As metatranscriptomic sequencing necessarily produces a snapshot of all the RNA expressed in a sample, the host organisms for the majority of recently identified picobirnaviruses cannot be easily determined and characterisation of novel virus species largely relies on phylogenetic placement, often without the presence of complete virus genomes. While the number of Picobirnavirus and picobirna-like sequences available on the National Center for Biotechnology Information (NCBI)/GenBank is now in the thousands and comprises considerable genetic diversity, only a single genus and three species have been formally ratified in the most recent report of the International Committee on Taxonomy of Viruses (ICTV) (Delmas et al. 2019). The Picobirnaviridae are therefore in clear need of further taxonomic assessment and classification. An additional complicating factor is the large number of picobirnaviruses found within individual animal species, which has meant that multiple picobirnaviruses have been assigned the same name. For example, there are 12 viral RdRp sequences designated as ‘bovine picobirnavirus’, 13 as ‘dromedary picobirnavirus’, 16 as ‘human picobirnavirus’, and over 500 as ‘porcine picobirnavirus’ on NCBI/GenBank. Despite their identical names, these sequences are distinct and do not group together in phylogenetic trees (Delmas et al. 2019; Ghosh and Malik 2021).

The remarkably wide range of both animal and non-animal sources in which picobirnaviruses have been detected, combined with an ongoing inability to propagate these viruses in eukaryotic cell lines or detect them in solid tissue samples, has led to the proposal that the Picobirnaviridae are not exclusively animal-associated or that animals may not be the true hosts (Boros et al. 2018; Krishnamurthy and Wang 2018; Yinda et al. 2019; Kleymann et al. 2020; Ghosh and Malik 2021). The closest relative to the Picobirnaviridae is the plant-, fungi-, and protist-infecting family Partitiviridae (Vainio et al. 2018), members of which have also been detected in animal faeces (Chen et al. 2022) and invertebrate samples (Shi et al. 2016; Le Lay et al. 2020), suggesting that they infect components of animal diet rather than the animal themselves. Hence, it is reasonable to propose that the Picobirnaviridae are similarly associated with animal diet and/or commensal gut microflora. Aspects of Picobirnavirus genomes also support the hypothesis that these viruses do not infect animals (at least not exclusively) and may instead be associated with microbial organisms. In particular, the prokaryotic ribosomal binding site (RBS) motif, necessary for the initiation of translation in prokaryotes, is present in the genomes of other RNA bacteriophage such as in the Cystoviridae (Boros et al. 2018; Krishnamurthy and Wang 2018). A high prevalence of RBS motif sequences has been identified upstream of ORFs in both Picobirnavirus genome segments (Boros et al. 2018; Krishnamurthy and Wang 2018), suggesting that the picobirnaviruses, in fact, predominantly represent a family of bacteriophage. In addition, several Picobirnavirus species identified from mammals and invertebrates (Yinda et al. 2019; Kleymann et al. 2020) utilise the mitochondrial genetic code, a characteristic shared by members of the RNA virus family Mitoviridae (phylum Lenarviricota) that replicate in the fungal mitochondria (Cole et al. 2000; Hillman and Cai 2013).

Using a set of 2,286 publicly available Picobirnaviridae RdRp sequences, the majority of which were generated through metatranscriptomic sequencing, we aimed to provide a realistic classification of this important group of viruses, identifying distinct genera, and to reassess their host range. We based our analysis on the extent of congruence between virus and host phylogenetic trees, as well as on features of Picobirnaviridae genomes that may be indicative of bacterial hosts.

Methods

Data set collection and processing for phylogenetic analysis

For all phylogenies generated in this work, the number of sequences included in the data set, the outgroups used, and the lengths (trimmed and untrimmed) of each alignment generated are detailed in Table 1. The labels T1 through T21, where ‘T’ simply stands for ‘tree’, refer to an alignment or phylogeny generated on a particular combination of Picobirnaviridae and outgroup family sequences. The exception is T21, which is a host animal cladogram artificially generated in Newick format and used to assess host associations. The data sets assembled for each tree are detailed later.

As a base Picornaviridae data set, curated in June 2022, we collated all non-redundant Picobirnavirus RdRp sequences available on NCBI/GenBank by searching the protein database for ‘picobirna’. Only sequences with associated hosts or sampling environment metadata were included. Picobirnavirus and picobirna-like sequences described by Neri et al. (2022) were also added to this data set. The majority (89 per cent) of sequences collected were faecal or environmentally sourced picobirnaviruses described in Chen et al. (2022) and Neri et al. (2022). A total of 3,644 sequences clustered at 90–99 per cent amino acid identity using the Cluster Database at High Identity with Tolerance program (Fu et al. 2012). One representative sequence from each cluster was retained. The total number of Picobirnavirus sequences collated in this manner for further analysis was 2,286.

RdRp sequences from families related to the Picobirnaviridae within the order Durnavirales were included in additional alignments as outgroups to provide directionality to the resulting phylogenies: the Amalgaviridae (14 sequences; T2 and T6 in Table 1), Curvulaviridae (8 sequences; T3 and T7), Fusariviridae (32 sequences; T4 and T8), and the Partitiviridae (40, 394, or 2,536 sequences; T9, T10, and T5–8, respectively). A phylogeny of the order Durnavirales was estimated on 4,717 sequences from the families Amalgaviridae, Curvulaviridae, Fusariviridae, Picobirnaviridae, and Partitiviridae (T11). Phylogenetic trees were also estimated based on sequence alignments of each of the proposed Picobirnaviridae genera (T12–18). Finally, sequence alignments were constructed on a subset of 1,269 Picobirnavirus sequences detected in animal (typically faecal) samples, with (T19) and without (T20) an outgroup of 40 partitivirus sequences.

Sequence alignment and phylogenetic analysis

All sequences were aligned using MAFFT (v7.487) (Katoh and Standley 2013) and trimmed using trimAL (v1.4.1) (Capella-Gutierrez, Silla-Martinez, and Gabaldon 2009) to retain the most conserved amino acid positions. Trimmed alignments were manually inspected in Geneious Prime 2022.2.1 to identify and remove any ambiguously aligned regions, resulting in trimmed alignments ranging between 691 and 757 positions in length used to generate phylogenetic trees.

The best-fit amino acid substitution model for all data sets was found to be the Le–Gascuel (LG) model, established using ModelFinder within IQ-TREE (v1.6.2). Due to the consistently very high number of amino acid changes per position, a gamma distribution of among-site rate variation was not used to estimate the full Durnavirales phylogeny (T11 in Table 1). Maximum likelihood phylogenetic trees were then estimated on each data set using IQ-TREE (v1.6.2) (Nguyen et al. 2015), with node support evaluated using the SH-like approximate likelihood ratio test (SH-aLRT), with 1,000 replicates. Trees were visualised in FigTree (v1.4.4) (Rambaut 2018), as well as in R (v4.1.0) using the packages ‘ape’ (v5.5) (Paradis, Schliep, and Schwartz 2019) and ggtree (v3.0.2) (Yu et al. 2017).

Classification of the Picobirnaviridae

Ten phylogenies (T1–T10; see Table 1) were used for determining potential genera within the Picobirnaviridae. Four large and three small defined clusters were identified in the midpoint-rooted tree (T1 in Table 1), defined by relatively long branch lengths to their respective common ancestor node and ≥80 per cent SH-aLRT support. Sequences within each cluster were annotated as ‘clade 1’ through ‘clade 7’. These clusters or ‘draft genera’ were then annotated in all other trees. Any sequences not clustering within their assigned ‘draft genus’ with ≥80 per cent SH-aLRT node support in any of the ten trees were excluded. The remaining sequences that consistently grouped within the same clade in every tree were considered the ‘core’ sequences of each proposed genus. Sequence alignments were constructed on each set of core sequences, and subsequent genus-level phylogenetic trees were estimated as described earlier.

Analysis of phylogenetic incongruence

Prior to analysis, Picobirnaviridae sequences were grouped by assigned host (animals) or sampling source (environments and microbial communities). Hosts and sampling sources were categorised in two ways (Table 2). The first focused on specific animal hosts, with non-animal sources simply reflected in a joint ‘microbial/environmental’ category, while mammals were further categorised into lower taxonomic levels. The second grouped animal hosts more broadly as ‘mammalian’, ‘avian’, ‘fish’, ‘reptile’, and ‘invertebrate’, with non-animal sources similarly expanded into ‘aquatic’, ‘terrestrial’, and ‘engineered’ environments and microbial communities. Aquatic sources included bodies of water and sediments, while terrestrial environments included various soils and plant matter (Chen et al. 2022; Neri et al. 2022). Engineered sources included wastewater, food fermentation processes, and laboratory cultures (Neri et al. 2022).

A cladogram of relevant ‘host’ animals (as listed in Table 2) was constructed based on the evolutionary relationships demonstrated in the current literature on vertebrate and invertebrate evolution (Lindblad-Toh et al. 2005; Fong et al. 2012; Song et al. 2012; Shen et al. 2014; Prum et al. 2015; Zhou, Wang, and Ma 2017; Zurano et al. 2019). The eMPRess program (v1.2.1) (Santichaivekin et al. 2021) was used to reconcile topologies of the animal-associated Picobirnavirus (T20 in Table 1) and host animal (T21 in Table 1) phylogenies to determine the event likelihoods of co-divergence, cross-species transmission, duplication, and extinction. Event costs were defined as 0 for co-divergence and 1 for cross-species transmission, duplication, and extinction. The R package ‘NELSI’ (v0.21) (Ho, Duchêne, and Duchêne 2015) was used to calculate the normalised PH85 (nPH85) distance for the Picobirnaviridae. The nPH85 distance is based on Penny and Hendy distance metric and describes the topological distance between the virus and host phylogenies (Geoghegan, Duchêne, and Holmes 2017). An nPH85 distance of 0 indicates complete co-divergence between virus and host, whereas an nPH85 of 1 indicates complete cross-species transmission.

Presence of bacterial RBSs

A sequence alignment was generated using MAFFT (v7.487) comprising all available non-redundant and annotated nucleotide sequences of Segment 1 of the Picobirnavirus genome that contained at least 24 nucleotides of a 5ʹ untranslated region (UTR), totalling 352 sequences. Sequences were aligned to assist in locating the start codons of ORFs, upstream of which the RBS motifs are potentially located. Similarly, an alignment was constructed comprising all available Segment 2 Picobirnaviridae sequences using the same criteria, for a total of 984 sequences. The twenty-four nucleotides upstream of the start codon of each annotated ORF were annotated and extracted using Geneious Prime 2022.2.1. Occurrences of the ‘AGGAGG’ hexamer, ‘AGGAG’ or ‘GGAGG’ 5-mers, or ‘AGGA’, ‘GGAG’ or ‘GAGG’ 4-mers within each extracted 24-nucleotide region were identified and annotated using Geneious Prime 2022.2.1, as these likely represented a bacterial RBS motif and hence are evidence of a bacterial host. The frequency of RBS occurrence for each segment was calculated as a proportion of the total number of annotated ORFs in the set of sequences for that segment. To compare the frequencies of RBS presence between the Picobirnaviridae and established RNA bacteriophage families, this process was repeated on 1,040 Leviviricetes genomes and 17, 11, and 38 Cystoviridae S, M, and L segments, respectively.

Results

Classification of the Picobirnaviridae

We observed seven major well-supported clusters of RdRp sequences within the Picobirnaviridae that were consistently present across ten phylogenies inferred using different outgroups and rooting methods (Fig. 1, Table 1). Each of the seven clades were defined by relatively long branches to their respective common ancestral node with >80 per cent SH-aLRT node support in each of the ten phylogenies (Fig. 1). We propose that these groups are candidates for novel genera with the Picobirnaviridae, tentatively named: ‘Alphapicobirnavirus’ (421 sequences, containing Orthopicobirnavirus equi), ‘Betapicobirnavirus’ (802 sequences, containing Orthopicobirnavirus hominis), ‘Gammapicobirnavirus’ (418 sequences, containing Orthopicobirnavirus beihaiense), ‘Deltapicobirnavirus’ (311 sequences), ‘Epsilonpicobirnavirus’ (36 sequences), ‘Zetapicobirnavirus’ (67 sequences), and ‘Etapicobirnavirus’ (70 sequences), in line with the nomenclature for other multi-genus families within the Durnavirales. While these are ‘proposed’ or ‘candidate genera’ only and will not be italicised following ICTV convention, for simplicity they will be hereafter referred to directly as ‘genera’. Sequences consistently clustering within one of these clades in each of the ten trees were considered the ‘core’ members comprising each genus. Those sequences whose phylogenetic position was inconsistent remained as ‘unclassified’ Picobirnaviridae. Using this approach, we were able to assign 2,125 non-redundant picobirnaviruses to a proposed genus (Supplementary Table 1). Genus-level phylogenies of each proposed genus are shown in Supplementary Figures 1–7.

The only currently accepted genus in the Picobirnaviridae—Orthopicobirnavirus—contains three species: Orthopicobirnavirus hominis, Orthopicobirnavirus equi, and Orthopicobirnavirus beihaiense, isolated from human (Wakuda, Pongsuwanna, and Taniguchi 2005), horse (Giannitti et al. 2015), and peanut worms (Shi et al. 2016), respectively. Each of these species appear in a different proposed genus described here (Supplementary Figures 1–3), limiting our ability to clearly determine which most closely resembles the genus Orthopicobirnavirus.

There were no common topologies for the proposed Picobirnaviridae genera across all ten phylogenetic trees. As a consequence, exact evolutionary relationships among genera cannot be safely determined. However, the genera ‘Deltapicobirnavirus’ and ‘Etapicobirnavirus’ formed sister clades in seven of the ten phylogenies (Fig. 1A–D, F, H, J). In the remaining three trees (Fig. 1E, G, I), one genus fell directly basal to the other, but which genus was basal to the other was inconsistent among trees. In six phylogenies, ‘Alphapicobirnavirus’ and ‘Epsilonpicobirnavirus’ formed sister clades (Fig. 1B, C, E, G, I, J), suggesting that these genera are more closely related to each other. In eight trees, the two largest genera, ‘Alphapicobirnavirus’ and ‘Betapicobirnavirus’, either grouped together (Fig. 1D–I) or one fell directly basal to the other (Fig. 1A, C). Furthermore, in four of the trees where ‘Alphapicobirnavirus’ and ‘Betapicobirnavirus’ genera clustered together, ‘Epsilonpicobirnavirus’ was also part of the group as a sister clade to ‘Alphapicobirnavirus’ (Fig. 1C, E, G, I). Based on these topological patterns, we further suggest that subfamilies may also eventually be defined, likely one comprising ‘Alpha-’, ‘Beta-’, and ‘Epsilonpicobirnavirus’, with another comprising ‘Delta-’ and ‘Etapicobirnavirus’. However, more sequences are required to achieve a more consistent topology before such subfamilies can be confidently defined.

We next sought to give these proposed genera evolutionary context by placing them in a tree with multiple related families of RNA viruses. An unrooted phylogeny was estimated on 4,717 RdRp sequences from the order Durnavirales, including the Picobirnaviridae, Partitiviridae, Amalgaviridae, Curvulaviridae, and Fusariviridae (Fig. 2). Sequences from the family Hypoviridae were too divergent to reliably align and were therefore excluded. Importantly, the Picobirnaviridae formed a monophyletic group that was phylogenetically distinct from the other families in the order. Certain trends in tree topology frequently observed in Fig. 1 were repeated here, such as ‘Deltapicobirnavirus’ and ‘Etapicobirnavirus’ forming sister clades, as well as ‘Alphapicobirnavirus’ and ‘Epsilonpicobirnavirus’ forming sister clades that clustered with ‘Betapicobirnavirus’ (Fig. 2). The proposed genera also remained mostly intact despite the high level of diversity in the alignment. The only exception was a group of seven divergent deltapicobirnaviruses that fell as a small sister clade to the zetapicobirnaviruses (Fig. 2, denoted by a star).

Distribution of apparent hosts or environmental source of picobirnaviruses in each proposed genus

The genus ‘Alphapicobirnavirus’ (Fig. 3A, Supplementary Figure 1) predominantly comprised mammalian and avian picobirnaviruses, as well as those sampled from some invertebrate species. In the most basal clade of this genus, the majority of sequences were identified in microbial communities, although a small number of mammalian, avian, invertebrate, and environmentally sourced picobirnaviruses also fell in this group. The genus ‘Betapicobirnavirus’ (Fig. 3B, Supplementary Figure 2) was similarly dominated by picobirnaviruses from mammalian and avian sources. This genus also contained the divergent species identified in fish (AVM87403 Beihai goldsaddle goldfish Picobirnavirus) and lizards (AVM87436 Guangdong Chinese water skink Picobirnavirus and UCS96434 Picobirnaviridae sp.). There were fewer microbial/environmental-sourced viruses in the betapicobirnaviruses and none formed large, monophyletic clusters as seen in the basal ‘Alphapicobirnavirus’ group.

In contrast to the predominantly animal-associated genera described earlier, the ‘Gammapicobirnavirus’ (Fig. 3E, Supplementary Figure 3) and ‘Deltapicobirnavirus’ (Fig. 3F, Supplementary Figure 4) genera were almost entirely composed of sequences detected in microbial communities and environmental samples. Some invertebrate-associated picobirnaviruses (namely, from Cnidara, Porifera, crustaceans, and molluscs) clustered within the ‘Gammapicobirnavirus’ (Supplementary Figure 3), as well as two picobirnaviruses from vertebrate faecal samples (USE08169 Picobirnavirus sp. from pig faeces and QUS52969 mute swan faeces associated Picobirnavirus 3). However, most viruses from this genus were sampled in environmental or microbial samples, particularly aquatic sources.

Viruses in the genus ‘Deltapicobirnavirus’ were predominantly sourced from terrestrial microbe communities and environments (Fig. 3F, Supplementary Figure 4). The most recently diverged clade had a more even distribution of viruses sampled from aquatic and terrestrial environments and microbes (Supplementary Figure 4). Again, two picobirnaviruses sourced from animals were present in this genus—ND_241614 and ND_192065—from cattle and sheep, respectively. However, these sequences were mined from animal rumen microbiome sequence data (Neri et al. 2022), thereby making ‘Deltapicobirnavirus’ the only genus containing entirely microbe-associated or environmentally sourced viruses.

The remaining genera were considerably smaller. All but one of the thirty-six viruses falling into the genus ‘Epsilonpicobirnavirus’ were sourced from vertebrate faeces, the majority of which were mammalian (cattle and porcine) (Fig. 3C, Supplementary Figure 5). The genus ‘Zetapicobirnavirus’ also featured a similar range of sampling sources, with the majority being cattle and porcine samples, along with one avian- and one primate-sourced Picobirnavirus. This phylogeny included a notable divergent clade of five arthropod-associated zetapicobirnaviruses (Fig. 3D, Supplementary Figure 6). Finally, despite only comprising seventy sequences, the genus ‘Etapicobirnavirus’ had a broader ‘host’ range across the two sister clades observed within this group. One predominantly comprised vertebrate etapicobirnaviruses, as well as one sequence identified in a termite that is likely associated with its bacterial symbionts (Fig. 3G, Supplementary Figure 7). The other clade included another 15 etapicobirnaviruses identified in termite samples, with the basal lineages largely viruses sourced from microbial and aquatic environmental samples (Supplementary Figure 7).

According to published information, picobirnaviruses utilising an alternative genetic code appeared in the ‘Alphapicobirnavirus’ (one sequence), ‘Betapicobirnavirus’ (six sequences), ‘Gammapicobirnavirus’ (one sequence), and ‘Zetapicobirnavirus’ (six sequences) proposed genera. Of the six betapicobirnaviruses, one utilised the flatworm mitochondrial code (translation table 14), while the remainder used the ciliate code (translation table 6), although none of these sequences clustered together (Supplementary Figure 2). This is in contrast to the zetapicobirnaviruses, where all viruses utilising alternative genetic codes fell in the basal lineages (Supplementary Figure 6). One used the ciliate genetic code, while the other five were all arthropod-associated picobirnaviruses using the invertebrate mitochondrial code (translation table 5) and formed a monophyletic group. The single sequences within ‘Alpha-’ and ‘Gammapicobirnavirus’ that utilised an alternative genetic code shared only 48 per cent and 40 per cent amino acid identity with their nearest relatives, respectively. This suggests a large amount of missing diversity within these clades and that many more picobirnaviruses utilising alternative genetic codes may be identified in future studies.

Accuracy of host assignments based on phylogenetic position

To visualise the extent of apparent cross-species transmission within the Picobirnaviridae based on assigned hosts/sample source, we estimated a phylogeny of only the animal-sourced picobirnaviruses (Fig. 4A, T19 in Table 1) and a complete Picobirnavirus phylogeny (Fig. 4B, T9 in Table 1). Both trees were rooted by a set of forty partitiviruses as they represent the most closely related family to the Picobirnaviridae. The diverse distribution of assigned host species across the phylogeny, as demonstrated in Fig. 4A and B where tips are coloured by host, revealed a lack of consistent clustering by assigned host. Even at the order level within the Mammalia, closely related virus sequences had assigned hosts spanning diverse groups of mammals. Picobirnaviruses from birds did not form any large monophyletic groups, and instead clustered with species from cattle, pigs, felines, canines, primates, and marsupials (Fig. 4A, C). This was also clearly observable within the predominantly animal-associated genera ‘Alphapicobirnavirus’, ‘Betapicobirnavirus’, ‘Epsilonpicobirnavirus’, and ‘Zetapicobirnavirus’ (Fig. 3A–D, Supplementary Figures 1–4). Although microbial/environmentally sourced viruses tended to group together in clades distinct from the animal-sourced picobirnaviruses, there were several invertebrate-, primate-, cattle-, pig-, and avian-associated species present in the environmental/microbial clades (Fig. 4B, D). Notably, representatives from all subcategories of microbial and environmental picobirnaviruses were present in animal-associated clades with the exception of those sourced from terrestrial microbes (Fig. 4D). Rectangular, midpoint-rooted versions of the trees shown in Fig. 4 with tip labels including accession numbers and virus names are shown in Supplementary Figures 8–11. The distribution of assigned hosts and sampling sources across each genus is shown in Supplementary Figure 12.

A phylogeny of animal-associated picobirnaviruses (T20 in Table 1) was compared to a host phylogeny (Supplementary Figure 13, T21 in Table 1) using NELSI (Ho, Duchêne, and Duchêne 2015) to estimate the frequency of cross-species transmission (assuming assigned hosts are the true hosts) by calculating the nPH85 metric that describes the topological distance between the two phylogenies. The nPH85 distance between the unrooted animal-associated Picobirnaviridae tree and host taxa tree was 0.998 (Fig. 5A), suggesting almost complete cross-species transmission and very little occurrence of co-divergence among the animal-associated members of this family. Similarly, the nPH85 distance for the genus ‘Alphapicobirnavirus’ was 0.994 and 1 for both the ‘Betapicobirnavirus’ and ‘Epsilonpicobirnavirus’. The genus ‘Zetapicobirnavirus’ had a comparatively higher, yet still low, level of co-divergence with an nPH85 distance of 0.921 (Fig. 5A). eMPRess (Santichaivekin et al. 2021) was utilised to determine the respective likelihoods of co-divergence, cross-species transmission, duplication, or extinction in the reconciled virus–host co-phylogeny. The event likelihoods are shown in Fig. 5B–F and reveal that cross-species transmission was far more frequent than any other event (68 per cent of events, Fig. 5B) for the entire family as well as for each individual genus (45–68 per cent of events, Fig. 5C–F). In contrast, only low levels of apparent virus–host co-divergence were observed, especially at the level of the entire Picobirnaviriade (1–23 per cent of events, Fig. 5B–F).

Genetic evidence of Picobirnaviridae in non-animal hosts

We next searched for bacterial RBS motifs in a data set of 1,336 Picobirnavirus, 1,040 Levivirus, and 64 Cystovirus genome segments. The detection of an ‘AGGAGG’ hexamer up to twenty-four nucleotides upstream of the start codon of an annotated ORF was considered to indicate the presence of a full RBS motif. Partial RBS motifs included the 4-mers AGGA, GGAG, and GAGG, and the 5-mers AGGAG and GGAGG. There were 687 annotated ORFs across the 352 Picobirnavirus Segment 1 nucleotide sequences and 782 annotated ORFs across the 984 Picobirnavirus Segment 2 sequences. The number of Segment 1 and Segment 2 ORFs preceded by a full or partial RBS motif was 571 (83.1 per cent) and 667 (85.3 per cent), respectively (Table 3). Strikingly, this was a higher proportion of RBS motif enrichment than observed in the confirmed RNA bacteriophage groups of Leviviricetes (1901 of 3251 ORFs; 58.5 per cent) and Cystoviridae (169 of 294 ORFs; 57.1 per cent) (Table 3). This difference was most prominent with respect to the frequency of a complete RBS motif: 52.8 per cent and 69.3 per cent of ORFs in Picobirnaviridae genome Segments 1 and 2, respectively, were preceded by the ‘AGGAGG’ motif, compared to 0–6.4 per cent of ORFs in Cystoviridae or Leviviricetes sequences. In contrast, Picobirnaviridae genomes segments had much lower frequencies of 4-mer partial RBS motifs (5.4–5.8 per cent) compared to 13.7–33.5 per cent of Cystoviridae or Leviviricetes ORFs (Table 3).

Discussion

The Picobirnaviridae are a family of RNA viruses traditionally associated with opportunistic gastroenteritis in humans and other animals that have dramatically increased in size and diversity in recent years due to metatranscriptomic sequencing. Despite this marked increase in diversity, picobirnaviruses remain largely unclassified beyond the family level, with only three divergent species comprising a single genus having been formally accepted by the ICTV (Delmas et al. 2019). The central aim of this study was to provide a taxonomic structure for this family by identifying distinct clades within the Picobirnaviridae that may represent genera (while noting that all such definitions are arbitrary). To this end, multiple outgroups and rooting schemes were utilised in an expansive phylogenetic analysis. From this, we identified seven clusters of sequences that consistently appeared across ten different phylogenies, which we propose be considered as distinct genera: ‘Alphapicobirnavirus’, ‘Betapicobirnavirus’, ‘Gammapicobirnavirus’, ‘Deltapicobirnavirus’, ‘Epsilonpicobirnavirus’, ‘Zetapicobirnavirus’, and ‘Etapicobirnavirus’. In addition, these seven proposed genera remained mostly intact and together formed a monophyletic, phylogenetically distinct group within the order Durnavirales. No genera shared greater than an average of 19 per cent amino acid identity in the RdRp with any other genera, which is in line with the <24 per cent amino acid identity shared between genera of the related Partitiviridae (Vainio et al. 2018).

Correctly assigning host organisms to novel virus species is a major limitation of the meta-transcriptomic approach to virus discovery. While the Picobirnaviridae have historically been associated with humans and other animals, there is mounting evidence that animals may not be the true hosts (Ghosh and Malik 2021). As a consequence, we asked whether the Picobirnaviridae were a true animal-infecting family of RNA viruses or one that infect microbiota themselves associated with animal hosts, i.e. that they are bacteriophage or other microbe-infecting viruses. The marked lack of topological congruence between phylogenies of the animal-associated picobirnaviruses and their apparent animal hosts indicates that the evolutionary history of the Picobirnaviridae has been characterised by extensive host-jumping, with statistical tests revealing near complete cross-species transmission. Notably, the nPH85 distance for animal-associated picobirnaviruses (0.998) is higher than the average for RNA virus families (0.95) and indeed higher than Rhabdoviridae (0.989), the family with the highest nPH85 distance of those analysed in Geoghegan, Duchêne, and Holmes (2017). This supports previous suggestions that animal-associated picobirnaviruses do not cluster according to their ‘host’ of sampling (Duraisamy et al. 2018; Woo et al. 2019; Mahar et al. 2020), although the current study uses a much larger data set. The complete lack of apparent host and viral phylogenetic congruence points towards an error in host assignment rather than the less biologically likely alternative of near complete cross-species transmission at a rate not seen in any other RNA virus family.

Picobirnaviruses have been detected in a large range of animal species, including those from terrestrial and aquatic habitats, invertebrates and vertebrates and those with herbivorous, carnivorous and omnivorous diets. This raises the question of how picobirnaviruses are able to overcome the geographical and biological barriers between animals with remarkably different habitats, lifestyles, and gastrointestinal systems, if they truly infect the hosts being sampled. Broad host ranges spanning vertebrates and invertebrates have been observed in several RNA virus orders, such as the Articulavirales, Nidovirales, Reovirales, and Mononegevirales, with the latter two also carrying fungi-infecting species. At a family level, the Orthomyxoviridae, Rhabdoviridae, and Spinareoviridae also infect a wide variety of hosts, including mammals, birds, insects, and other arthropods, along with fish in the case of the Orthomyxoviridae, plants in the Rhabdoviridae, and fungi in the Spinareoviridae. There are, however, clear phylogenetic distinctions between genera infecting vastly different hosts, and host ranges are generally limited at a genus level. Genera with cross-phylum or cross-kingdom host ranges are typically characterised by well-established transmission routes between arthropod vectors and animal or plant hosts. For example, arboviruses in the genera Orthoflavivirus, Alphavirus, Coltivirus, and Orbivirus replicate in their vertebrate hosts as well as the arthropod vectors that transmit them (Huang et al. 2023). Similarly, plant-infecting genera in the families Tospoviridae, Tymoviridae (Marafivirus), Rhabdoviridae, and order Reovirales also replicate in their arthropod vectors (Gray and Banerjee 1999). While it is plausible that members of the Picobirnaviridae are capable of extensive host-jumping, their remarkably wide host range raises the possibility that the picobirnaviruses are in fact associated with gut microflora or dietary components present in and excreted by these animals (Krishnamurthy and Wang 2018). This would also explain why non-environmental picobirnaviruses are detected almost exclusively in animal faeces and are still unable to be cultured in any eukaryotic cell lines (Ghosh and Malik 2021).

The presence of a bacterial RBS motif is well established in bacteriophage genomes. Krishnamurthy and Wang (2018) noted that the ‘AGGAGG’ RBS hexamer is enriched in the genomes of both RNA and DNA bacteriophage and appears at much lower frequency in eukaryote-infecting virus genomes. In our expansive data set, we detected an RBS motif in 83–85 per cent of ORFs in Picobirnavirus genomes, such that this marker is substantially more enriched than in confirmed RNA bacteriophages Leviviricetes and Cystoviridae. This constitutes further evidence that the Picobirnaviridae indeed have bacterial hosts.

The host range of virus species within each of the seven proposed Picobirnaviridae genera appeared to comprise either predominantly animal-associated picobirnaviruses (‘Alphapicobirnavirus’, ‘Betapicobirnavirus’, ‘Epsilonpicobirnavirus’, and ‘Zetapicobirnavirus’) or those identified in microbial or environmental samples (‘Gammapicobirnavirus’, ‘Deltapicobirnavirus’, and ‘Etapicobirnavirus’). However, the four genera comprising predominantly animal-associated viruses did not group together to the exclusion of the three genera comprising mainly microbe/environmentally sourced viruses. As such, this broad host-associated clustering may reflect the different microbial community compositions in terrestrial, aquatic, and engineered environments compared to those of mammals, birds, and invertebrates. Picobirnaviruses may infect different microbial organisms that play roles in food webs linking vertebrates, invertebrates, and their diets and habitats. This would facilitate the extensive ‘host-jumping’ observed within the animal-dominated genera. Hence, future metagenomic studies on the viromes of animal (particularly faecal) or environmental samples should also include community composition analyses of the microorganisms present. Determining if the microbial community composition of a sampled animal or environment is indeed driving the phylogenetic patterns of the Picobirnaviridae may elucidate the true host range of Picobirnavirus genera.

Supplementary data

Supplementary data is available at VEVOLU Journal online.

Acknowledgements

This work was funded by a National Health and Medical Research Council Investigator award (GNT201719) to E.C.H. and by AIR@InnoHK administered by the Innovation and Technology Commission, Hong Kong Special Administrative Region, China.

Conflict of interest:

None declared.

References

Author notes