Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris

Abstract

Background: Trypanosomatids are parasitic flagellates well known because of some representatives infecting humans, domestic animals, and cultural plants. Many trypanosomatid species bear RNA viruses, which, in the case of human pathogens Leishmania spp., influence the course of the disease. One of the close relatives of leishmaniae, Leptomonas pyrrhocoris, has been previously shown to harbor viruses of the groups not documented in other trypanosomatids. At the same time, this species has a worldwide distribution and high prevalence in the natural populations of its cosmopolitan firebug host. It therefore represents an attractive model to study the diversity of RNA viruses.

Results: We surveyed 106 axenic cultures of L. pyrrhocoris and found that 64 (60%) of these displayed 2-12 double-stranded RNA fragments. The analysis of next-generation sequencing data revealed four viral groups with seven species, of which up to five were simultaneously detected in a single trypanosomatid isolate. Only two of these species, a tombus-like virus and an Ostravirus, were earlier documented in L. pyrrhocoris. In addition, there were four new species of Leishbuviridae, the family encompassing trypanosomatid-specific viruses, and a new species of Qinviridae, the family previously known only from metatranscriptomes of invertebrates. Currently, this is the only qinvirus with an unambiguously determined host. Our phylogenetic inferences suggest reassortment in the tombus-like virus owing to the interaction of different trypanosomatid strains. Two of the new Leishbuviridae members branch early on the phylogenetic tree of this family and display intermediate stages of genomic segment reduction between insect Phenuiviridae and crown Leishbuviridae.

Conclusions: The unprecedented wide range of viruses in one protist species and the simultaneous presence of up to five viral species in a single Leptomonas pyrrhocoris isolate indicate the uniqueness of this flagellate. This is likely determined by the peculiarity of its firebug host, a highly abundant cosmopolitan species with several habits ensuring wide distribution and profuseness of L. pyrrhocoris, as well as its exposure to a wider spectrum of viruses compared to other trypanosomatids combined with a limited ability to transmit these viruses to its relatives. Thus, L. pyrrhocoris represents a suitable model to study the adoption of new viruses and their relationships with a protist host.

Keywords: Leishbuviridae; Ostravirus; Pyrrhocoris apterus; Qinviridae; Tombus-like viruses.

Fig. 1

Tombus-like virus of Leptomonas pyrrhocoris. A ML phylogenetic tree based on RDRP amino acid sequences. Numbers at the branches indicate Bayesian posterior probability (PP) and ML bootstrap supports (BS). Only supports PP ≥ 0.8 and BS ≥ 50 are shown, lower values replaced with dashes (-). Circles correspond to maximal statistical support by both methods. The scale bar indicates the number of substitutions per site. Outgroups are shown in gray. Inversed font and background colors indicate the strains studied in this work. B Schemes of the genomic organization of LeppyrTLV1 and chronic bee paralysis virus, the closest available reference species

Fig. 2

ML phylogenetic trees of the three ORFs of LeppyrTLV1 strains based on nucleotide sequences. Numbers at the branches indicate Bayesian posterior probability (PP) and ML bootstrap supports (BS). Only supports PP ≥ 0.8 and BS ≥ 50 are shown, lower values are replaced with dashes. Circles correspond to maximal statistical support by both methods. The scale bar indicates the number of substitutions per site. Some groups are highlighted for easier comparison of topologies

Fig. 3

Ostravirus of Leptomonas pyrrhocoris. A Genomic organization of LeppyrOV1. B ML phylogenetic tree of LeppyrOV1 based on the concatenated nucleotide sequences of the seven ORFs. Circles correspond to maximal Bayesian posterior probability and ML bootstrap supports. The scale bar indicates the number of substitutions per site. Inversed font and background colors indicate the strains studied in this work

Fig. 4

ML phylogenetic tree of Leishbuviridae based on RDRP amino acid sequences. Numbers at the branches indicate Bayesian posterior probability (PP) and ML bootstrap supports (BS). Only supports PP ≥ 0.8 and BS ≥ 50 are shown, lower values are replaced with dashes. Circles correspond to maximal statistical support by both methods. The scale bar indicates the number of substitutions per site. The double-crossed branch is at 50% of the original length. Outgroup is shown in gray. Inversed font and background colors indicate the strains studied in this work. Single asterisk marks viruses detected in trypanosomatid cultures, and two asterisks indicate viruses found in metatranscriptomes along with trypanosomatids (detected previously in [14] or reported in a corresponding NCBI Sequence Read Archive record in the “Taxonomy Analysis” section)

Fig. 5

Genome variability of leishbuviruses from Leptomonas pyrrhocoris. A Schemes of genome organization of LeppyrLBVs and the reference species for the families Leishbuviridae and Phenuiviridae—Leishmania martiniquensis leishbuvirus 1 and Gouleako virus (Goukovirus gouleakoense), respectively. B Juxtaposition of schematic phylogeny and lengths of predicted nucleocapsid protein and glycoprotein demonstrating the gradual reduction of the latter in the evolution of Leishbuviridae

Fig. 6

Qin-like virus of Leptomonas pyrrhocoris. A ML phylogenetic tree of Qinviridae based on RDRP amino acid sequences. Numbers at the branches indicate Bayesian posterior probability (PP) and ML bootstrap supports (BS). Only supports PP ≥ 0.8 and BS ≥ 50 are shown, lower values are replaced with dashes. Circles correspond to maximal statistical support by both methods. The scale bar indicates the number of substitutions per site. Outgroup is shown in gray. Inversed font and background colors indicate the strains studied in this work. B genomic organization of LeppyrQLV1 and its closest available reference—Wilkie qin-like virus