Unprecedented Genomic Diversity Of RNA Viruses In Arthropods Reveals The Ancestry Of Negative-sense RNA Viruses

Arthropods form the largest phylum in the animal kingdom and show a remarkable diversity. As they can actively interact with a wide range of other organisms including fungi, plants and vertebrates, they are considered as both a source and sink for viruses in an ecosystem. Although some arthropods, such as mosquitoes or ticks. are important vectors for well-studied viral diseases, the biodiversity of arthropod viruses, as well as the role that arthropods have played in the virus origin and evolution, remain unclear.Seventy species of arthropods from four classes (Insecta, Arachnida, Chilopoda, and Malacostraca) were collected in Beijing, Hubei, Xinjiang and Zhejiang of China. The arthropods included mosquitoes, flies, cockroaches, water striders, ticks, spiders, shrimps, crabs and millipedes. RNA was extracted from these thropods. Through RNA sequencing, de novo assembly, and similarity searches,94 novel negative sense RNA viruses were identified. Most notably, the newly identified arthropod viruses are distinct from both each other and previously described viruses, with the most divergent showing up to 86%amino acid sequence identity to its closest relatives. Overall, these data provide evidence for at least 16 potentially new families and genera of negative-sense RNA viruses, defined as whose RdRp sequences shared less than 25% amino acid identity with existing taxa.Phylogenetic analysis revealed that most of the newly described arthropod viruses were basal to the known major virus groups, indicating that arthropod viruses may beancestors of those causing disease in vertebrates and plants. Some new lineages filled in ’phylogenetic gaps’ etween existing viral genera or families. These data greatly expand the documented diversity of four viral families/orders, namely, the Arenaviridae, Bunyaviridae, Orthomyxoviridae, and Mononegavirales, as well as of three floating genera, namely, Tenuivirus, Emaravirus, and Varicosavirus. One important discovery was a large monophyletic group of viruses that fell between the major groups of segmented and unsegmented viruses, and we name this new virus family as the ’Chvviridae’.The diversity of genome structures in these viruses is also striking. The number of genome segments in negativesense RNA viruses varies from one to eight. Our phylogenetic analysis revealed no particular trend for this number to increase or decrease through evolutionary time. Hence, genome segmentation (i.e., genomes with>1 segment) has clearly evolved on multiple occasions within the negative-sense RNA viruses, such that it is a relatively flexible genetic trait. The new family Chuviridae included viruses with various genome organizations, ranging from unsegmented to bi-segmented and circular genomes.Our research suggests that arthropods are major reservoir hosts for many, if not all, of the negative-sense RNA viruses in vertebrates and plants, and hence have likely played a major role in their evolution. This is further supported by the high abundance of viral RNA in the arthropod transcriptome, as well as by the high frequencies of endogenous copies of these viruses in the arthropod genome. In particular, the unparalleled numbers and diversity of the arthropods combined with the wealth of lifestyles that arthropod species display imply that these animals are uniquely placed as hosts and carriers of viruses to act as a hotspot of viral evolution. Because arthropods interact with a wide range of organisms including vertebrate animals and plants, they can be seen as the direct or indirect source of many clinically or economically important viruses. The viral genetic and phenotypic diversity documented in arthropods here therefore provides a new perspective on fundamental questions of virus origins, diversity, host range, genome evolution, and disease emergence.