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


Autoři: Simon Käfer aff001;  Sofia Paraskevopoulou aff001;  Florian Zirkel aff003;  Nicolas Wieseke aff004;  Alexander Donath aff002;  Malte Petersen aff005;  Terry C. Jones aff001;  Shanlin Liu aff007;  Xin Zhou aff008;  Martin Middendorf aff004;  Sandra Junglen aff001;  Bernhard Misof aff002;  Christian Drosten aff001
Působiště autorů: Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany aff001;  Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany aff002;  Institute of Virology, University of Bonn Medical Centre, Bonn, Germany aff003;  Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, Germany aff004;  Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany aff005;  Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom aff006;  BGI-Shenzhen, China Beishan Industrial Zone, Shenzhen, Guangdong Province, China aff007;  College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China aff008;  Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China aff009;  German Center for Infection Research (DZIF), associated partner site Charité, Berlin, Germany aff010
Vyšlo v časopise: Re-assessing the diversity of negative strand RNA viruses in insects. PLoS Pathog 15(12): e1008224. doi:10.1371/journal.ppat.1008224
Kategorie: Research Article
doi: 10.1371/journal.ppat.1008224

Souhrn

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.

Klíčová slova:

Animal phylogenetics – Insects – Invertebrate genomics – Phylogenetic analysis – Phylogenetics – Taxonomy – Viral genomics – Viral taxonomy


Zdroje

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Hygiena a epidemiologie Infekční lékařství Laboratoř

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