Re-assessing the diversity of negative strand RNA viruses in insects.

Simon Käfer,Malte Petersen,Christian Drosten,Shanlin Liu,Nicolas Wieseke,Terry C Jones,Bernhard Misof,Sofia Paraskevopoulou,Sandra Junglen,Alexander Donath,Xin Zhou,Martin Middendorf,Florian Zirkel

doi:10.1371/journal.ppat.1008224

Abstract

The spectrum of viruses in insects is important for subjects as diverse as public health, veterinary medicine, food production, and biodiversity conservation. The traditional interest in vector-borne diseases of humans and livestock has drawn the attention of virus studies to hematophagous insect species. However, these represent only a tiny fraction of the broad diversity of Hexapoda, the most speciose group of animals. Here, we systematically probed the diversity of negative strand RNA viruses in the largest and most representative collection of insect transcriptomes from samples representing all 34 extant orders of Hexapoda and 3 orders of Entognatha, as well as outgroups, altogether representing 1243 species. Based on profile hidden Markov models we detected 488 viral RNA-directed RNA polymerase (RdRp) sequences with similarity to negative strand RNA viruses. These were identified in members of 324 arthropod species. Selection for length, quality, and uniqueness left 234 sequences for analyses, showing similarity to genomes of viruses classified in Bunyavirales (n = 86), Articulavirales (n = 54), and several orders within Haploviricotina (n = 94). Coding-complete genomes or nearly-complete subgenomic assemblies were obtained in 61 cases. Based on phylogenetic topology and the availability of coding-complete genomes we estimate that at least 20 novel viral genera in seven families need to be defined, only two of them monospecific. Seven additional viral clades emerge when adding sequences from the present study to formerly monospecific lineages, potentially requiring up to seven additional genera. One long sequence may indicate a novel family. For segmented viruses, cophylogenies between genome segments were generally improved by the inclusion of viruses from the present study, suggesting that in silico misassembly of segmented genomes is rare or absent. Contrary to previous assessments, significant virus-host codivergence was identified in major phylogenetic lineages based on two different approaches of codivergence analysis in a hypotheses testing framework. In spite of these additions to the known spectrum of viruses in insects, we caution that basing taxonomic decisions on genome information alone is challenging due to technical uncertainties, such as the inability to prove integrity of complete genome assemblies of segmented viruses.

Highlights

Negative strand RNA viruses contain major groups of pathogenic viruses that cause rabies, hemorrhagic fevers, respiratory infections, measles, as well as a large range of important diseases and economically important conditions in livestock and plants [1,2,3,4]
In 1243 insect species of all orders, we found 488 independent viral sequences encoding an RNA-directed RNA polymerase, a signature gene for RNA viruses
We based our search on conserved sequence motifs within the RNA-directed RNA polymerase (RdRp) gene that is present in the genomes of all replicating RNA viruses without a DNA stage except deltaviruses, and is not present in the genome of the eukaryotic or prokaryotic cell

Summary

Introduction

Negative strand RNA viruses contain major groups of pathogenic viruses that cause rabies, hemorrhagic fevers, respiratory infections, measles, as well as a large range of important diseases and economically important conditions in livestock and plants [1,2,3,4]. Our current knowledge of negative strand RNA viruses is biased by the interest in medical disciplines and provides an incomplete image when it comes to more fundamental questions in viral evolution, such as the contribution of codivergence in the formation of major viral genetic lineages. These questions can only be addressed by systematic studies of larger taxonomic units of viral hosts, corresponding to whole orders or classes of animals, which is complicated by the difficulty to establish representative sample collections. The samples used in these studies only covered a limited range of insect species, contained many other groups of invertebrates such as spiders, worms, and molluscs, and were generated

Methods

Results

Discussion

Conclusion