Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates

Abstract

Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling toward vertebrates and land plants has limited our understanding of their diversity and evolution. Here, we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated viral genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.

Prevalence of a vertically transmitted single-stranded DNA virus in spinybacked orbweavers (Gasteracantha cancriformis) from Florida, USA

“…SpOrbCV-1 (GenBank accession number MH545519) and SpOrbCV-2 (GenBank accession number MH545515) were recently described as a part of a CRESS DNA viral discovery effort in terrestrial arthropods [2]. Since SpOrbCV-1 cannot be accommodated within established CRESS DNA viral families, we further evaluated the characteristics of this virus and other is marked by a conserved nonanucleotide motif at the apex of a predicted stem-loop structure [28].…”

“…Additionally, RCA products obtained from virus particles isolated from a collection of 106 spiders from various families (Supplemental Table S1) were tested to evaluate if SpOrbCVs could be detected in other spider species using the same PCR assay. This spider collection included specimens from areas where we identified spinybacked orbweavers positive for SpOrbCVs and specimens originally collected for CRESS DNA virus discovery purposes [2]. whereas products producing weak bands were confirmed through Sanger sequencing with the relevant PCR primers.…”

“…Given that many CRESS DNA viruses have only been identified through sequencing, little is known about the ecology of a large number of CRESS DNA viruses, including the host species for both classified (e.g., Genomoviridae and Smacoviridae) and unclassified viruses. Terrestrial arthropods have been recently identified as an untapped reservoir of CRESS DNA viral diversity, highlighting the need to further investigate viral prevalence and transmission in this dominant and undersampled group of animals [2].…”

“…Endogenous viral sequences within spider chromosomes indicate that these arachnids have been infected by both CRESS DNA viruses and double-stranded DNA polyomaviruses [19,20]. Studies within the past four years have also revealed a diversity of novel extant viruses in multiple spider species, including more than 20 CRESS DNA [2] and 100 RNA viruses [21][22][23][24] encompassing various viral families and unclassified species. Moreover, RNA viruses have been detected in multiple spider organs, including brain, venom glands and silk glands, indicating that viral infection may play a role in spider ecology [21].…”

“…The present study investigated two CRESS DNA viruses, namely spinybacked orbweaver circular virus (SpOrbCV) 1 and 2, that were reported from specimens of Gasteracantha cancriformis, commonly known as the spinybacked orbweaver [2]. Spinybacked orbwearvers are generally considered beneficial spiders since they trap and consume insects considered pests, such as whiteflies, and are typically found in wooded areas where there is abundant foliage and branches [25].…”