A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs

Over the last decade, viral metagenomics has been established as a non-targeted approach for identifying viruses in stock animals, including pigs. This has led to the identification of a vast diversity of small circular ssDNA viruses. The present study focuses on the investigation of eukaryotic circular Rep-encoding single-stranded (CRESS) DNA viral genomes present in serum of commercially reared pigs from southern Brazil. Several CRESS DNA viral genomes were detected, including representatives of the families Smacoviridae (n=5), Genomoviridae (n=3), Redondoviridae (n=1), Nenyaviridae (n=1) and other yet unclassified genomes (n=9), plus a circular DNA molecule, which probably belongs to the phylum Cressdnaviricota. A novel genus within the family Smacoviridae, tentatively named ‘Suismacovirus’, comprising 21 potential new species, is proposed. Although the reported genomes were recovered from pigs with clinical signs of respiratory disease, further studies should examine their potential role as pathogens. Nonetheless, these findings highlight the diversity of circular ssDNA viruses in serum of domestic pigs, expand the knowledge on CRESS DNA viruses’ genetic diversity and distribution and contribute to the global picture of the virome of commercially reared pigs.

The Effects of Packaged, but Misguided, Single-Stranded DNA Genomes Are Transmitted to the Outer Surface of the øX174 Capsid

Most icosahedral viruses condense their genomes into volumetrically constrained capsids. However, concurrent genome biosynthesis and packaging is specific to single-stranded (ss) DNA viruses. ssDNA genome packaging combines elements found in both double-stranded (ds) DNA and ssRNA systems. Similar to dsDNA viruses, the genome is packaged into a preformed capsid. Like ssRNA viruses, there are numerous capsid-genome associations. In ssDNA microviruses, the DNA binding protein J guides the genome between 60 icosahedrally ordered DNA binding pockets. It also partially neutralizes the DNA’s negative phosphate backbone. øX174-related microviruses, such as G4 and α3, have J proteins that differ in length and charge organization. This suggests that interchanging J proteins could alter the path used to guide DNA in the capsid. Previously, a øXG4J chimera, in which the øX174 J gene was replaced with the G4 gene, was characterized. It displayed lethal packaging defects, which resulted in procapsids being removed from productive assembly. Here, we report the characterization of another inviable chimera, øXα3J. Unlike øXG4J, øXα3J efficiently packaged DNA but produced non-infectious particles. These particles displayed a reduced ability to attach to host cells, suggesting internal DNA organization could distort the capsid’s outer surface. Mutations that restored viability altered J-coat protein contact sites. These results provide evidence that the organization of ssDNA can affect both packaging and post-packaging phenomena. Importance ssDNA viruses utilize icosahedrally ordered protein-nucleic acids interactions to guide and organize their genomes into preformed shells. As previously demonstrated, chaotic genome-capsid associations can inhibit øX174 packaging by destabilizing packaging complexes. However, the consequences of poorly organized genomes may extend beyond the packaging reaction. As demonstrated herein, it can lead to uninfectious packaged particles. Thus, ssDNA genomes should be considered an integral and structural virion component, affecting the properties of the entire particle, which includes the capsid’s outer surface.

A Mechanically Transmitted DNA Mycovirus Is Targeted by the Defence Machinery of Its Host, Botrytis cinerea

Eukaryotic circular single-stranded DNA (ssDNA) viruses were known only to infect plants and vertebrates until the discovery of the isolated DNA mycovirus from the fungus Sclerotinia sclerotiorum. Similar viral sequences were reported from several other sources and classified in ten genera within the Genomoviridae family. The current study reports two circular ssDNA mycoviruses isolated from the phytopathogen Botrytis cinerea, and their assignment to a newly created genus tentatively named Gemydayirivirus. The mycoviruses, tentatively named botrytis gemydayirivirus 1 (BGDaV1) and BGDaV2, are 1701 and 1693 nt long and encode three and two open reading frames (ORFs), respectively. Of the predicted ORFs, only ORF I, which codes for a replication initiation protein (Rep), shared identity with other proteins in GenBank. BGDaV1 is infective as cell-free purified particles and confers hypovirulence on its natural host. Investigation revealed that BGDaV1 is a target for RNA silencing and genomic DNA methylation, keeping the virus at very low titre. The discovery of BGDaV1 expands our knowledge of the diversity of genomoviruses and their interaction with fungal hosts.

Distribution of soil viruses across China and their potential role in phosphorous metabolism

Background: Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China.Results: More than 60% of viral genome fragments could not be classified, representing potential new viruses. Among the 27 viral families identified, 15 families belonged to dsDNA viruses and 12 families belonged to ssDNA viruses. Soil samples clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic as well as functional composition and were mainly driven by latitude. Phylogenetic analyses of the phoH gene showed a remarkable diversity and two new viral clades. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thy1, and RNR, were mainly identified in agricultural soils. Conclusions: The present work revealed that soil viral communities and their functions were distributed across China according to geographical location, with latitude as the dominant driving factor. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.

Primordial capsid and spooled ssDNA genome structures penetrate ancestral events of eukaryotic viruses

Marine algae viruses are important for controlling microorganism communities in the marine ecosystem, and played a fundamental role during the early events of viral evolution. Here, we have focused on one major group of marine algae viruses, the ssDNA viruses from the Bacilladnaviridae family. We present the capsid structure of the bacilladnavirus, Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II), determined at 2.3 Å resolution. Structural comparison to other viruses supports the previous theory where bacilladnaviruses were proposed to have acquired their capsid protein via horizontal gene transfer from a ssRNA virus. The capsid protein contains the widespread virus jelly-roll fold, but has additional unique features; a third β-sheet and a long C-terminal tail, which are located on the capsid surface and could be important for virus transmission. Further, low-resolution reconstructions of the CtenDNAV-II genome reveal a partially spooled structure, an arrangement previously only described for dsRNA and dsDNA viruses.

Insect Transmission of Plant Single-Stranded DNA Viruses

Of the approximately 1,200 plant virus species that have been described to date, nearly one-third are single-stranded DNA (ssDNA) viruses, and all are transmitted by insect vectors. However, most studies of vector transmission of plant viruses have focused on RNA viruses. All known plant ssDNA viruses belong to two economically important families, Geminiviridae and Nanoviridae, and in recent years, there have been increased efforts to understand whether they have evolved similar relationships with their respective insect vectors. This review describes the current understanding of ssDNA virus–vector interactions, including how these viruses cross insect vector cellular barriers, the responses of vectors to virus circulation, the possible existence of viral replication within insect vectors, and the three-way virus–vector–plant interactions. Despite recent breakthroughs in our understanding of these viruses, many aspects of plant ssDNA virus transmission remain elusive. More effort is needed to identify insect proteins that mediate the transmission of plant ssDNA viruses and to understand the complex virus–insect–plant three-way interactions in the field during natural infection.

Discovery and molecular characterisation of the first ambidensovirus in honey bees

Honey bees play a critical role in global food production as pollinators of numerous crops. Several stressors cause declines in populations of managed and wild bee species, such as habitat degradation, pesticide exposure and pathogens. Viruses act as key stressors and can infect a wide range of species. The majority of honey bee-infecting viruses are RNA viruses of the Picornavirales order. Although some ssDNA viruses are common in insects, such as densoviruses, they have not yet been found in honey bees. Densoviruses were however found in bumblebees and ants. Here, we show that densoviruses are indeed present in the transcriptome of the eastern honey bee (<em>Apis cerana</em>) from southern China. On the basis of non-structural and structural transcripts, we inferred the genome structure of the Apis densovirus. Phylogenetic analysis has shown that this novel Apis densovirus belongs to the <em>Scindoambidensovirus</em> genus in the Densovirinae subfamily. Apis densovirus possesses ambisense genome organisation and encodes three non-structural proteins and a split VP (capsid) protein. The availability of a nearly complete Apis densovirus genome may enable the analysis of its potential pathogenic impact on honey bees. Our findings can thus guide further research into the densoviruses in honey bees and bumblebees.