Next Article in Journal
Bacteriophages as Agents for Plant Disease Control: Where Are We After a Century?
Previous Article in Journal
Pathology, Tissue Distribution, and Phylogenetic Characterization of Largemouth Bass Virus Isolated from a Wild Smallmouth Bass (Micropterus dolomieu)
Previous Article in Special Issue
Distinguishing Lytic and Temperate Infection Dynamics in the Environment
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Viruses
Volume 17
Issue 8
10.3390/v17081032
viruses-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Afrina barna-like Virus, a Novel Virus Associated with Afrina sporoboliae, the Drop Seed Gall-Forming Nematode

by
Edison Reyes-Proaño
1,
Anna M. Griffin
1,
Aida Duarte
2,3,
Hongyan Sheng
4,
Brenda K. Schroeder
1,
Timothy D. Murray
4 and
Alexander V. Karasev
1,*
1
Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844, USA
2
Plant Pathogen Confirmatory Diagnostics Laboratory, USDA-APHIS-PPQ, Laurel, MD 20708, USA
3
Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27607, USA
4
Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
*
Author to whom correspondence should be addressed.
Viruses 2025, 17(8), 1032; https://doi.org/10.3390/v17081032
Submission received: 18 June 2025 / Revised: 17 July 2025 / Accepted: 22 July 2025 / Published: 23 July 2025
(This article belongs to the Special Issue Diversity and Evolution of Viruses in Ecosystem 2025)
Browse Figures
Versions Notes

Abstract

A novel barna-like virus was found to be associated with field-collected Afrina sporoboliae plant-parasitic nematodes. The positive-sense, single-stranded RNA genome of this virus, named Afrina barna-like virus (AfBLV), comprises 4020 nucleotides encoding four open reading frames (ORFs). ORF 1 encodes a protein product spanning a transmembrane, a peptidase, and VPg domains, whereas an overlapping ORF 2 encodes an RNA-dependent RNA polymerase (RdRP). ORF2 may be expressed via a −1 translational frameshift. In phylogenetic reconstructions, the RdRP of AfBLV was placed inside a separate clade of barna and barna-like viruses related to but distinct from the genera in the Solemoviridae and Alvernaviridae families, within the overall lineage of Sobelivirales. ORF 3 of AfBLV encodes a protein product of 206 amino acids (aa) long with homology to a putative protein encoded by a similarly positioned gene of an uncharacterized virus sequence identified previously as Barnaviridae sp. ORF 4 encodes a 161 aa protein with no significant similarities to sequences in the GenBank databases. AfBLV is the first barnavirus found in a nematode. Sequence comparisons of the AfBLV genome and genomes of other barna-like viruses suggested that a recombination event was involved in the evolution of AfBLV. Analyses of the phylogeny of RdRPs and genome organizations of barna-like and solemo-like viruses support the re-classification of Barnavirus and Dinornavirus genera as members of the Solemoviridae family.

1. Introduction

The formally accepted virus family Barnaviridae includes a single genus, Barnavirus [1], which contains only one species approved by the International Committee of Taxonomy of Viruses (ICTV)—mushroom bacilliform virus (MBV) [1]. The particles of MBV represent bacilliform-shaped, non-enveloped 19 × 50 nm virions that encapsidate a 4.0 kb positive-sense, single-stranded RNA genome coding for four major and three minor open reading frames (ORFs) [2]. ORF 1 codes for a protein of 22 kDa while ORFs 2, 3 and 4 encode for a serine protease, RNA-dependent RNA-Polymerase (RdRP), and a putative capsid protein (CP) of 73, 47 and 22-kDa, respectively [2]. Although the only approved member of the genus Barnavirus, MBV, has been associated with a fungal host, recent reports indicated that barna-like viruses may also be associated with other hosts, such as plants [3,4] and, possibly, mammals [5]. Barnaviridae, thus, represents a relatively poorly studied family of viruses, possibly in need of more research and phylogenetic refinement.
Afrina sporoboliae is a seed gall forming nematode able to induce seed galls in Sporobolus cryptandrus, a species of grass native to North America [6]. The life cycle of seed gall nematodes, such as A. sporoboliae, consists of the egg, four juvenile developmental stages, and the adult. The first two stages (J1 and J2) develop within the egg, and J2 hatch from the eggs inside seed galls, serving as the infective stage. During summer and fall, galls produced during the current season fall to the ground, and the nematodes enter the anhydrobiotic stage, where they can survive for many years. Galls rehydrate, releasing the nematodes onto the soil surface. The J2s migrate to nearby plants, where they penetrate tissue and induce the formation of new galls. Within galls, juvenile nematodes develop through two more stages (J3 and J4) into adults, which females produce several hundred eggs per gall [7]. A. sporoboliae is found in association with an undescribed Rathayibacter spp. and it is assumed that the nematode serves as the vector to deliver the bacterium to the plant inflorescence where it infects and produces seed galls [6,8]. This bacterium is related to the Select Agent Rathayibacter toxicus, a bacterium parasitic to grass hosts, which is a concern to the U.S. agriculture because it produces a tunicamycin toxin on ryegrass, causing Annual Ryegrass Toxicity when consumed by grazing livestock and is often fatal [9]. A. sporoboliae was initially found in Idaho in 2018 [6] and is the third Afrina species reported in North America. A. sporoboliae is currently the only Afrina species found on native plant species with no known disease management strategies. One of the possible biocontrol options for plant-parasitic nematode management is the use of viral pathogens; this option is considered in management of cyst nematodes affecting soybean and potato [10,11,12]. Multiple viruses from the families Flaviviridae, Picornaviridae, and Rhabdoviridae were found in populations of soybean cyst nematode [10] and potato cyst nematode [11,12,13].
To look for potential viruses circulating in A. sporoboliae populations, we subjected the nematode samples collected in Idaho to the RNAseq analysis using the total, ribodepleted RNA extracted from seed gall nematodes. In this study, we present the whole genome of Afrina barna-like virus (AfBLV), a new member of the Barnaviridae family that is associated with a population of drop seed gall-forming nematodes in Idaho.

2. Materials and Methods

2.1. Sample Origin, RNA Extraction, High-Throughput Sequencing, and Sequence Analysis

Seed galls containing A. sporoboliae nematodes were collected in 2022 from S. cryptandrus plants in Idaho County, Idaho, and stored at room temperature. The seed galls were wrapped in one layer of cheesecloth, soaked in 50 mL of sterile distilled water in a 250 mL beaker overnight to induce nematode hatching. The nematodes fell to the bottom of the beaker and were harvested through centrifugation (3000 rpm for 4 min), washed twice with 5 mL sterile distilled water; the J2 nematodes were surface sterilized with 5 mL of 0.5% sodium hypochlorite (3 min) followed by two washes with 5 mL sterile water for sodium hypochlorite removal (3000 rpm for 4 min) and stored at −80 °C (Ref. [6] and Duarte et al., unpublished). Total RNA was extracted separately from nine nematode samples (from A1 to I9), which consisted of approximately 20,000 juvenile J2′s nematodes, following the protocol described by Kud et al. [14], the RLT lysis buffer was supplemented with 2.5% polyvinylpyrrolidone (PVP) and 1.5% β-mercaptoethanol prior tissue disruption. Samples were subjected to DNase treatment using a DNase kit (QIAGEN, Germantown, MD, USA) and submitted for high-throughput sequencing (HTS) at GENEWIZ facilities (Azenta, South Plainfield, NJ, USA). After quality control, samples with an RNA Integrity Number (RIN) exceeding 6 were subjected to ribodepletion using the FastSelect rRNA Worm Kit (Qiagen, Hilden, Germany) prior to the complementary DNA (cDNA) library construction. The cDNA library was generated using NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). The sequencing was accomplished using the NovaSeq X Plus platform in a 150 nt paired-ends format. The reads obtained through HTS were processed using a custom pipeline involving trimming, filtering, mapping and BLASTx analyses. Raw reads were trimmed and quality-filtered using Trimmomatic v0.39. Paired reads were mapped to the 30–1019090437_Afrina_sporoboliae_ERCC reference genome (Duarte et al., unpublished) and de novo assembled using SPAdes v3.15.3. Contigs were analyzed using BLASTn and BLASTx tools against a custom viral database retrieved from National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/ (accessed on 4 April 2024)). Pair-wise comparisons of nucleotide and amino acid sequences were conducted using BLASTn and BLASTx programs provided by NCBI. Genome conceptual translation and ORF predictions were performed using Geneious Prime 2023.1.1. Identification of conserved protein domains was performed using the CDD program provided by the NCBI (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi (accessed on 23 March 2025)) and HHPred [15]. Additionally, the conserved domain analysis was supplemented with a prediction for transmembrane domains using TMHMM (https://services.healthtech.dtu.dk/services/TMHMM-2.0/ (accessed on 23 March 2025)).

2.2. RT-PCR Validation, Sanger Sequencing of the Genome, and Phylogenetic Analysis

To validate the sequences found in the HTS data, two sets of specific primers (AfBLV-4F/4R and AfBLV-6F/6R) were designed (Supplementary Table S1). First strand cDNA and polymerase chain reaction (PCR) were synthesized from total RNA using SuperScript™ III Reverse Transcriptase (Thermo Fisher Scientific, Waltham, MA, USA) and GreenTaq DNA Polymerase (GenScript, Piscataway, NJ, USA), following the protocol described by Reyes-Proaño et al. [16]. Following the visualization of amplicons on 1.2% agarose gels, PCR products were treated using ExoSAP-It (Applied Biosystems, Waltham, MA, USA) as described by Green et al. [17] and submitted for Sanger sequencing to Elim Biopharmaceuticals (Hayward, CA, USA). The full-length genome of AfBLV was re-sequenced using overlapping PCR products amplified with specific primers (Supplementary Table S1). The cDNA of the 5′- and 3′-terminal regions were acquired using primers AfBLV_5-1 and AfBLV_3-3, respectively, using the 5′/3′ rapid amplification of cDNA ends (RACE) Kit (Roche, Indianapolis, IN, USA) following manufacturer’s instructions. The complete genome of AfBLV was assembled with Geneious Prime 2023.1.1. (Biomatters, Inc., Boston, MA, USA). Phylogenetic inferences were conducted using amino acid sequences from the RdRP coding sequence of virus species accepted by the ICTV as members of the order Sobelivirales. Sequences corresponding to RdRP were aligned using ClustalOmega3 and the best amino acid substitution model was determined using MEGAX. Phylogenetic tree was obtained using MEGAX using the LG+G+I+F as the best fit protein model with 1000 bootstrap replicates [18].

3. Results

3.1. High-Throughput Sequencing Analysis of the Nematode Samples

High-throughput sequencing of each of the nine field samples of A. sporoboliae produced between 50 and 84 million paired-end raw reads, and, after removal of reads mapped to the nematode genome (between 78.39 and 89.76%), allowed to assemble de novo between 22,846 and 30,048 contigs over 500 nt in length (Table 1). Initial bioinformatics analysis revealed the presence of a single, ca. 4.0 kb virus-related contig in sample A1 encoding four open reading frames (ORFs) (Figure 1A). Given the number of ORFs, their organization, and presence of characteristic conserved domains with visible similarity to barna- and barna-like sequences (see below), it was assumed that the identified contig represented complete or nearly complete genome of a new barna-like virus from A. sporoboliae and it was named Afrina barna-like virus (AfBLV). To exclude the possibility of AfBLV originating from S. cryptandrus or contaminating fungal organisms, the reads were mapped against fungal and plant databases retrieved from the NCBI. The number of reads mapped against fungal genomes varied between 0.0015% and 0.0060%, depending on an individual sample, significantly lower than the number of reads mapped to the AfBLV genome (Table 1), excluding the fungal origin of AfBLV. The number of reads mapped against a Sporobolus maritimus plant genome (GCA_965119375.1) varied between 0.0395% and 0.0921%, depending on an individual sample, and was significantly lower than the number of reads mapped to the AfBLV genome (Table 1), excluding the plant origin of AfBLV.

3.2. Sanger Sequencing of the Afrina barna-like Virus Genome

The presence of the AfBLV in all nine samples of A. sporoboliae was confirmed using RT-PCR with subsequent Sanger sequencing of the PCR products (Table 1). The entire genome of AfBLV was Sanger sequenced from the A1 sample, and this Sanger-derived sequence was found to be 99.1% identical to the sequence obtained via HTS. The 5′ and 3′-termini of the AfBLV genome were amplified using the RACE approach, as described in the Materials and Methods Section, and the complete genome of AfBLV was found to be 4020 nt long (Figure 1A) with the 5′-untranslated region (UTR) being 28 nt, and the 3′-UTR being 39 nt. The complete genome of AfBLV was assembled from the Sanger-derived sequence reads and deposited in the GenBank database under the accession number PV941960. In pair-wise comparisons, a central ca. 2.3 kb section of the AfBLV genome exhibited 75% nucleotide sequence identity to the uncharacterized Barnaviridae sp. isolate XZS182276 (‘BarV’, MW826417), while the 5′-terminal 1.2 kb and 3′-terminal 0.5 kb of AfBLV did not show significant nucleotide sequence similarity to either the ‘BarV’ sequence or to any other sequences in GenBank (see Figure 1B). This nucleotide sequence identity level translated into relatively high amino acid similarity levels for protein products encoded by ORFs 1–3 of AfBLV and ‘BarV’ sequence and to lesser extent for other barna-like virus protein products (Table 2). AfBLV, thus, represents the first barna-like virus found in a nematode host.
ORF 1 coded for a protein of 611 amino acids (aa) with a molecular weight of 66.1 kDa, containing a conserved V8-like Glu-specific endopeptidase domain (eMpr) identified by the CD-search program. This 66 kDa protein exhibited similarities with several peptidase-like proteins of barna and solemovirids, in particular, with one barna-related virus sequence obtained from metagenomic studies of rat feces [Barnaviridae sp. isolate XZS182276 (‘BarV’); MW826417.1] identified as the closest match in BLASTx searches (64.9% identity, 90% coverage). A transmembrane domain (TM) flanked by phenylalanine in position 4 and valine in position 29 was also identified in the protein product encoded by ORF1 (Figure 1A). Additionally, a HHPred search of this 66 kDa protein detected a region of 88 amino acids resembling the viral-protein-genome-linked protein (VPg) of sobemoviruses. The arrangement of these domains in the genome of AfBLV (Figure 1) resembled those found in the ORF 1-encoded proteins of poinsettia latent virus (AJ867490, Polemovirus), potato leafroll virus (D13954, Polerovirus) pea enation mosaic virus (L04573, Enamovirus) and in the ORF 2a-encoded protein of southern bean mosaic virus (DQ875594, Sobemovirus) [19].
ORF 2 of AfBLV coded for a 554 aa protein of 61.8 kDa with an easily identifiable RdRP domain, matching the RdRP-encoding protein of the same ‘BarV’ sequence (MW826417.1) with 81.9% identity at the aa level and 62% coverage. The presence of a putative heptameric slippery signal 1231UUUAAAC1237, right before ORF 2, suggested a −1 ribosomal frameshift as an expression strategy for ORF 2. ORF 3 coded for a putative protein of 212-aa and 23.6 kDa molecular weight; this protein shared the 73.3% aa sequence identity with the protein encoded by the ORF 3 of the same ‘BarV’ sequence (MW826417.1) with 83% coverage. In contrast, the downstream ORF 4 encoded a 162-aa protein of 17.8 kDa that produced no matches in the GenBank database when either BLASTx or BLASTp were used for analyses.

3.3. Afrina barna-like Virus Is a New Species in the Genus Barnavirus

The genome of AfBLV had a genomic organization similar to ‘BarV’ (MW826417.1) and to ApBLV-1 (MN386956.1) (Figure 1). Given the low similarities at the nucleotide and protein sequence levels and genetic relationships to species in the genus Barnavirus, we propose AfBLV to be a new member of this genus associated with A. sporoboliae, the drop seed gall forming nematodes. Although no formal threshold for species demarcation exists in the family Barnaviridae [1], the 75% nucleotide sequence identity lies at the very border of the species demarcation in other virus families, such as Potyviridae [20]. However, since this relatively distant similarity level corresponds to less than 60% of the AfBLV genome (Figure 1B), we feel confident that AfBLV represents a new virus species within the family Barnaviridae.
Since BLASTx searches identified barna-like virus sequences as the closest matches to AfBLV, phylogenetic relationship was inferred with RdRPs of all known barna and barna-like sequences available in the GenBank database, along with select sequences from the families Solemoviridae and Alvernaviridae; additional unclassified solemo-like virus sequences found recently in arthropods [21,22,23] were also included in the analysis (Figure 2). The resulting phylogenetic tree placed AfBLV in a well-supported clade containing a sole approved member of the family Barnaviridae, MBV, plus apple barna-like virus 1 (ApBLV-1) from apple leaf samples (QIC52820), and multiple viral sequences obtained from soil sediment metagenomic studies (see Figure 2). It is conceivable to propose that AfBLV, ApBLV-1, and related sequences from soil sediment metagenomics data be included into the genus Barnavirus along with the approved species, MBV. This same phylogenetic analysis placed the barna and barna-like virus clade close to viruses from the families Solemoviridae and Alvernaviridae within the order Solemovirales, and close to a separate clade of unclassified solemo-like viruses found in insects [21,23] and in ticks [22] (see Figure 2).

4. Discussion

The family Solemoviridae currently comprises four approved genera, Sobemovirus, Polemovirus, Polerovirus, Enamovirus, and Hubsclerovirus. These are viruses with positive-sense, single-strand RNA genome of 4–6 kb that are encapsidated with CP into icosahedral virions (20–34 nm in diameter); the great majority of solemovirids infect plants [19], with the exception of the genus Hubsclerovirus comprising fungal solemovirids [24]. There are two families, Barnaviridae, described in the introduction, and Alvernaviridae that are closely related to Solemoviridae.
The ICTV-approved family Alvernaviridae includes a single genus, Dinornavirus [25], which contains only one species approved by the ICTV, Heterocapsa circularisquama RNA virus 01 (HcRNAV01) [25]. The particles of HcRNAV01 are polyhedral, approximately 30 nm in diameter and encapsidate a 4.4 kb positive-sense, single-stranded RNA genome coding for two ORFs [26]. ORF1 codes for a protein with serine protease and RdRP domains, and ORF2 encodes the CP [26]. The only approved member of the genus Dinornavirus, HcRNAV01, has been associated with a dinoflagellate (Heterocapsa circularisquama) as a host. This phylogenetic analysis indicates that at least two other virus sequences, Bactericera cockerelli solemo-like virus 1 (BcSLV-1) [21] from an insect host, and Gingko biloba sobemo-like virus 1 (GbSLV) [27] from a plant host, are closely related to dinornavirids (Figure 2), and may be placed in the same genus Dinornavirus. Similarly to the family Barnaviridae, the family Alvernaviridae appears to be a relatively poorly studied family of viruses, and in need of phylogenetic refinement.
Careful inspection of the phylogeny of virus RdRP sequences from ICTV-approved families Barnaviridae, Alvernaviridae, and Solemoviridae (Figure 2) prompted us to propose some taxonomic changes within the family Solemoviridae to improve and simplify classification of these related viruses. Specifically, two ICTV-approved genera, Barnavirus and Dinornavirus seem to represent distinct clades inside the family Solemoviridae (Figure 2) and could be considered for inclusion in the family Solemoviridae. The two old family names, Barnaviridae and Alvernaviridae could be retired and abolished due to re-location of the single genus in each of the two families into Solemoviridae. The arrangement of the conserved motifs in replication-associated proteins, the −1 ribosomal frame-shifting strategy for the expression of the RdRP protein, and the monophyletic lineage in the RdRP-based phylogeny, all support the expansion of the family Solemoviridae to include the genera Barnavirus and Dinornavirus. These suggestions to rearrange the family Solemoviridae are summarized in Figure 2.
Recombination is one of the main forces driving evolution of positive-strand RNA viruses [28,29,30]. Here, we present the first evidence of recombination involved in the evolution of barnaviruses. The genome of the newly found AfBLV is apparently built from three segments, with a central 2.3 kb section of the genome exhibiting 75% nucleotide sequence identity to the genome of an uncharacterized Barnaviridae sp. isolate XZS182276 (‘BarV’, MW826417); and the 1.2 kb 5′-terminal section and the 0.5 kb 3′-terminal sections of the genome coming from a barnavirus only distantly related to AfBLV (no significant nt similarity) (Figure 1B). This central section of the genome includes the entire ORFs 2 and 3 of AfBLV, encoding RdRP and an unknown protein (Figure 1A,B). It is tempting to speculate that ORFs 2 and 3 of barna-like viruses may be responsible for more conserved virus functions, e.g., virus replication, while ORFs 1 and 4 could represent virus functions specific for different host species supporting barnavirus replication. It is difficult to speculate about the host specificity of BarV though, since limited information in the GenBank annotation file specifies rat feces as the origin of the virus sample and no publication is available, but a nematode could be one possible source.
Recently, several reports based on metagenomics analyses, indicated that barna-like viruses may be associated not only with fungi, but also with other hosts, such as plants [3,4] and, possibly, mammals [5]. The discovery of AfBLV isolated from A. sporoboliae expands the host range of barnaviruses even further and now includes at least one phylum of invertebrate animals. Different viruses were found in populations of free-living [31,32,33] and parasitic [23,34], including plant-parasitic, nematodes [10,11,12,13,35,36,37,38]; however, to the best of our knowledge, AfBLV is the first barna-like virus found in a nematode species. The impact of this virus on the nematode is unknown and further work is needed to assess the effect of the virus on the nematode’s life cycle; nevertheless, the discovery of AfBLV could potentially expand the biocontrol strategies to manage the Afrina sporoboliae nematodes.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/v17081032/s1, Table S1: Primers used for genome resequencing, detection and 5′/3′ acquisition of AfBLV.

Author Contributions

Conceptualization, B.K.S. and A.V.K.; methodology, E.R.-P. and A.M.G.; software, E.R.-P.; validation, E.R.-P., A.M.G. and A.V.K.; formal analysis, E.R.-P., A.D., H.S. and A.V.K.; investigation, E.R.-P. and A.M.G.; resources, B.K.S., T.D.M. and A.V.K.; data curation, A.D., H.S., E.R.-P. and A.V.K.; writing—original draft preparation, E.R.-P. and A.V.K.; writing—review and editing, B.K.S., T.D.M. and A.V.K.; visualization, E.R.-P. and A.V.K.; supervision, A.V.K.; project administration, A.V.K.; funding acquisition, B.K.S., T.D.M. and A.V.K. All authors have read and agreed to the published version of the manuscript.

Funding

Anna Griffin was a recipient of an Idaho INBRE undergraduate fellowship and a recipient of the University of Idaho President’s Research Transfer Ticket award. This work was funded in part by grants from USDA Animal and Plant Health Inspection Service PPA 7721 (grant AP22PPQS&T00C122), USDA-ARS (58–2072-2–046), USDA-NIFA (Hatch project IDA1712) and the Idaho Agricultural Experiment Station. The project was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant #P20GM103408.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The AfBLV genome sequence reported is available in GenBank under accession number PV941960.

Acknowledgments

The authors are grateful to Chloe Ramirez for help with nematode RNA extractions.

Conflicts of Interest

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

References

  1. Revill, P.A. Family Barnaviridae. In Virus Taxonomy. Classification and Nomenclature of Viruses. Ninth Report of the International Committee on Taxonomy of Viruses; King, A.M.Q., Adams, M.J., Carstens, E.B., Lefkowitz, E.J., Eds.; Elsevier Academic Press: San Diego, CA, USA, 2012; pp. 961–964. [Google Scholar]
  2. Revill, P.A.; Davidson, A.D.; Wright, P.J. The Nucleotide Sequence and Genome Organization of Mushroom Bacilliform Virus: A Single-Stranded RNA Virus of Agaricus Bisporus (Lange) Imbach. Virology 1994, 202, 904–911. [Google Scholar] [CrossRef]
  3. Nibert, M.L.; Manny, A.R.; Debat, H.J.; Firth, A.E.; Bertini, L.; Caruso, C. A Barnavirus Sequence Mined from a Transcriptome of the Antarctic Pearlwort Colobanthus Quitensis. Arch. Virol. 2018, 163, 1921–1926. [Google Scholar] [CrossRef] [PubMed]
  4. Wright, A.A.; Cross, A.R.; Harper, S.J. A Bushel of Viruses: Identification of Seventeen Novel Putative Viruses by RNA-Seq in Six Apple Trees. PLoS ONE 2020, 15, e0227669. [Google Scholar] [CrossRef] [PubMed]
  5. Zhu, W.; Yang, J.; Lu, S.; Jin, D.; Pu, J.; Wu, S.; Luo, X.L.; Liu, L.; Li, Z.; Xu, J. RNA Virus Diversity in Birds and Small Mammals From Qinghai–Tibet Plateau of China. Front. Microbiol. 2022, 13, 780651. [Google Scholar] [CrossRef] [PubMed]
  6. Barrantes-Infante, B.L.; Schroeder, B.K.; Subbotin, S.A.; Murray, T.D. Afrina sporoboliae sp. n. (Nematoda: Anguinidae) Associated with Sporobolus cryptandrus from Idaho, United States: Phylogenetic Relationships and Population Structure. Phytopathology 2018, 108, 768–779. [Google Scholar] [CrossRef]
  7. Murray, T.D.; Duarte, A.; Luster, D.G.; McKirdy, S.J.; Rogers, E.E.; Schroeder, B.K.; Subbotin, S.A. Seed Gall Nematodes and Their Association with Toxigenic Bacteria. Annu. Rev. Phytopathol. 2025, 63. [Google Scholar] [CrossRef]
  8. Murray, T.D.; Schroeder, B.K.; Schneider, W.L.; Luster, D.G.; Sechler, A.; Rogers, E.E.; Subbotin, S.A. Rathayibacter toxicus, Other Rathayibacter Species Inducing Bacterial Head Blight of Grasses, and the Potential for Livestock Poisonings. Phytopathology 2017, 107, 804–815. [Google Scholar] [CrossRef]
  9. Davis, E.W.; Tabima, J.F.; Weisberg, A.J.; Lopes, L.D.; Wiseman, M.S.; Wiseman, M.S.; Pupko, T.; Belcher, M.S.; Sechler, A.J.; Tancos, M.A.; et al. Evolution of the U.S. Biological Select Agent Rathayibacter toxicus. mBio 2018, 9, e01280-18. [Google Scholar] [CrossRef]
  10. Bekal, S.; Domier, L.L.; Niblack, T.L.; Lambert, K.N. Discovery and Initial Analysis of Novel Viral Genomes in the Soybean Cyst Nematode. J. Gen. Virol. 2011, 92, 1870–1879. [Google Scholar] [CrossRef]
  11. Ruark, C.L.; Koenning, S.R.; Davis, E.L.; Opperman, C.H.; Lommel, S.A.; Mitchum, M.G.; Sit, T.L. Soybean Cyst Nematode Culture Collections and Field Populations from North Carolina and Missouri Reveal High Incidences of Infection by Viruses. PLoS ONE 2017, 12, e0171514. [Google Scholar] [CrossRef]
  12. Kud, J.; Dahan, J.; Orellana, G.E.; Dandurand, L.-M.; Karasev, A.V. A Novel Rhabdovirus Associated with the Idaho Population of Potato Cyst Nematode Globodera pallida. Viruses 2022, 14, 2718. [Google Scholar] [CrossRef] [PubMed]
  13. Ruark, C.L.; Gardner, M.; Mitchum, M.G.; Davis, E.L.; Sit, T.L. Novel RNA Viruses within Plant Parasitic Cyst Nematodes. PLoS ONE 2018, 13, e0193881. [Google Scholar] [CrossRef] [PubMed]
  14. Kud, J.; Pillai, S.S.; Raber, G.; Caplan, A.; Kuhl, J.C.; Xiao, F.; Dandurand, L.M. Belowground Chemical Interactions: An Insight Into Host-Specific Behavior of Globodera spp. Hatched in Root Exudates From Potato and Its Wild Relative, Solanum sisymbriifolium. Front. Plant Sci. 2022, 12, 802622. [Google Scholar] [CrossRef] [PubMed]
  15. Gabler, F.; Nam, S.; Till, S.; Mirdita, M.; Steinegger, M.; Söding, J.; Lupas, A.N.; Alva, V. Protein Sequence Analysis Using the MPI Bioinformatics Toolkit. Curr. Protoc. Bioinform. 2020, 72, e108. [Google Scholar] [CrossRef]
  16. Reyes-Proaño, E.; Knerr, A.J.; Karasev, A.V. Molecular Characterization of Birch Toti-like Virus, a Plant-Associated Member of the New Family Orthototiviridae. Arch. Virol. 2024, 169, 140. [Google Scholar] [CrossRef]
  17. Green, K.J.; Brown, C.J.; Gray, S.M.; Karasev, A.V. Phylogenetic Study of Recombinant Strains of Potato Virus Y. Virology 2017, 507, 40–52. [Google Scholar] [CrossRef]
  18. Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol. Biol. Evol. 2018, 35, 1547–1549. [Google Scholar] [CrossRef]
  19. Sõmera, M.; Fargette, D.; Hébrard, E.; Sarmiento, C. ICTV Virus Taxonomy Profile: Solemoviridae 2021. J. Gen. Virol. 2021, 102, 001707. [Google Scholar] [CrossRef]
  20. Inoue-Nagata, A.K.; Jordan, R.; Kreuze, J.; Li, F.; López-Moya, J.J.; Mäkinen, K.; Ohshima, K.; Wylie, S.J. ICTV Virus Taxonomy Profile: Potyviridae 2022. J. Gen. Virol. 2022, 103, 001738. [Google Scholar] [CrossRef]
  21. Dahan, J.; Orellana, G.E.; Wald, K.B.; Wenninger, E.J.; Cooper, W.R.; Karasev, A.V. Bactericera Cockerelli Picorna-like Virus and Three New Viruses Found Circulating in Populations of Potato/Tomato Psyllids (Bactericera cockerelli). Viruses 2024, 16, 415. [Google Scholar] [CrossRef]
  22. Pettersson, J.H.-O.; Shi, M.; Bohlin, J.; Eldholm, V.; Brynildsrud, O.B.; Paulsen, K.M.; Andreassen, Å.; Holmes, E.C. Characterizing the Virome of Ixodes Ricinus Ticks from Northern Europe. Sci. Rep. 2017, 7, 10870. [Google Scholar] [CrossRef]
  23. Shi, M.; Lin, X.-D.; Tian, J.-H.; Chen, L.-J.; Chen, X.; Li, C.-X.; Qin, X.-C.; Li, J.; Cao, J.-P.; Eden, J.-S.; et al. Redefining the Invertebrate RNA Virosphere. Nature 2016, 540, 539–543. [Google Scholar] [CrossRef]
  24. Simmonds, P.; Adriaenssens, E.M.; Lefkowitz, E.J.; Oksanen, H.M.; Siddell, S.G.; Zerbini, F.M.; Alfenas-Zerbini, P.; Aylward, F.O.; Dempsey, D.M.; Dutilh, B.E.; et al. Changes to Virus Taxonomy and the ICTV Statutes Ratified by the International Committee on Taxonomy of Viruses (2024). Arch. Virol. 2024, 169, 236. [Google Scholar] [CrossRef]
  25. Nagasaki, K.; Tomaru, Y. New SsRNA Virus Family Infecting Dinoflagellates: Alvernaviridae. Propos. Int. Comm. Taxon. Viruses 2009, 2009, 016a-iP. Available online: https://ictv.global/ictv/proposals/2009.016a-iP.A.v7.Alvernaviridae.pdf (accessed on 17 July 2025).
  26. Nagasaki, K.; Shirai, Y.; Takao, Y.; Mizumoto, H.; Nishida, K.; Tomaru, Y. Comparison of Genome Sequences of Single-Stranded RNA Viruses Infecting the Bivalve-Killing Dinoflagellate Heterocapsa circularisquama. Appl. Environ. Microbiol. 2005, 71, 8888–8894. [Google Scholar] [CrossRef]
  27. Yang, S.; Shan, T.; Wang, Y.; Yang, J.; Chen, X.; Xiao, Y.; You, Z.; He, Y.; Zhao, M.; Lu, J.; et al. Virome of Riverside Phytocommunity Ecosystem of an Ancient Canal. Res. Sq. 2020. [Google Scholar] [CrossRef]
  28. Roossinck, M.J. Plant RNA Virus Evolution. Curr. Opin. Microbiol. 2003, 6, 406–409. [Google Scholar] [CrossRef] [PubMed]
  29. Nagy, P.D. Recombination in Plant Viruses. In Plant Virus Evolution; Roossinck, M.J., Ed.; Springer: Berlin/Heidelberg, Germany, 2008; pp. 133–156. [Google Scholar]
  30. Gibbs, A.; Ohshima, K. Potyviruses and the Digital Revolution. Annu. Rev. Phytopathol. 2010, 48, 205–223. [Google Scholar] [CrossRef] [PubMed]
  31. Félix, M.-A.; Ashe, A.; Piffaretti, J.; Wu, G.; Nuez, I.; Bélicard, T.; Jiang, Y.; Zhao, G.; Franz, C.J.; Goldstein, L.D.; et al. Natural and Experimental Infection of Caenorhabditis Nematodes by Novel Viruses Related to Nodaviruses. PLoS Biol. 2011, 9, e1000586. [Google Scholar] [CrossRef] [PubMed]
  32. Franz, C.J.; Zhao, G.; Félix, M.-A.; Wang, D. Complete Genome Sequence of Le Blanc Virus, a Third Caenorhabditis Nematode-Infecting Virus. J. Virol. 2012, 86, 11940. [Google Scholar] [CrossRef]
  33. Frézal, L.; Jung, H.; Tahan, S.; Wang, D.; Félix, M.-A. Noda-Like RNA Viruses Infecting Caenorhabditis Nematodes: Sympatry, Diversity, and Reassortment. J. Virol. 2019, 93, 10–1128. [Google Scholar] [CrossRef]
  34. Williams, S.H.; Che, X.; Oleynik, A.; Garcia, J.A.; Muller, D.; Zabka, T.S.; Firth, C.; Corrigan, R.M.; Briese, T.; Jain, K.; et al. Discovery of Two Highly Divergent Negative-Sense RNA Viruses Associated with the Parasitic Nematode, Capillaria hepatica, in Wild Mus Musculus from New York City. J. Gen. Virol. 2019, 100, 1350–1362. [Google Scholar] [CrossRef]
  35. Bekal, S.; Domier, L.L.; Gonfa, B.; McCoppin, N.K.; Lambert, K.N.; Bhalerao, K. A Novel Flavivirus in the Soybean Cyst Nematode. J. Gen. Virol. 2014, 95, 1272–1280. [Google Scholar] [CrossRef]
  36. Lin, J.; Ye, R.; Thekke-Veetil, T.; Staton, M.E.; Arelli, P.R.; Bernard, E.C.; Hewezi, T.; Domier, L.L.; Hajimorad, M.R. A Novel Picornavirus-like Genome from Transcriptome Sequencing of Sugar Beet Cyst Nematode Represents a New Putative Genus. J. Gen. Virol. 2018, 99, 1418–1424. [Google Scholar] [CrossRef]
  37. Vieira, P.; Nemchinov, L.G. A Novel Species of RNA Virus Associated with Root Lesion Nematode Pratylenchus Penetrans. J. Gen. Virol. 2019, 100, 704–708. [Google Scholar] [CrossRef]
  38. Vieira, P.; Subbotin, S.A.; Alkharouf, N.; Eisenback, J.; Nemchinov, L.G. Expanding the RNA Virome of Nematodes and Other Soil-Inhabiting Organisms. Virus Evol. 2022, 8, veac019. [Google Scholar] [CrossRef]
Viruses 17 01032 g001
Figure 1. Schematic representation of the Afrina barna-like virus (AfBLV) genome (GenBank accession PV941960) side-by-side with Barnaviridae sp. virus (‘BarV’, MW826417). (A) AfBLV and BarV genomes encode four open reading frames (ORFs), with conserved protein domains designated as thick black lines; TM = transmembrane domain, eMpr = V8-like Glu-specific endopeptidase, VPg = viral protein genome-linked, RdRP = RNA dependent RNA polymerase. ORFs 3 for both viruses are shaded in light green as an indication of a significant amino acid sequence similarity. (B) Schematic diagram of a possible recombinant structure of AfBLV: BarV genome is arbitrarily set as a ‘parental’ genome (blue color), with ABLV genome containing a ca. 2.3 kb segment (light blue color) with 75% nucleotide sequence identity to the ‘parental’ BarV genome; the rest of the ABLV genome displays no significant similarity to BarV at the nucleotide sequence level (white color).
Figure 1. Schematic representation of the Afrina barna-like virus (AfBLV) genome (GenBank accession PV941960) side-by-side with Barnaviridae sp. virus (‘BarV’, MW826417). (A) AfBLV and BarV genomes encode four open reading frames (ORFs), with conserved protein domains designated as thick black lines; TM = transmembrane domain, eMpr = V8-like Glu-specific endopeptidase, VPg = viral protein genome-linked, RdRP = RNA dependent RNA polymerase. ORFs 3 for both viruses are shaded in light green as an indication of a significant amino acid sequence similarity. (B) Schematic diagram of a possible recombinant structure of AfBLV: BarV genome is arbitrarily set as a ‘parental’ genome (blue color), with ABLV genome containing a ca. 2.3 kb segment (light blue color) with 75% nucleotide sequence identity to the ‘parental’ BarV genome; the rest of the ABLV genome displays no significant similarity to BarV at the nucleotide sequence level (white color).
Viruses 17 01032 g001
Viruses 17 01032 g002
Figure 2. Maximum likelihood phylogenetic consensus tree based on the predicted amino acid sequence of the RdRP depicting the genetic association of AfBLV (PV941960) to other species in the order Sobelivirales. ICTV accepted families are highlighted in colored boxes as follows. Green: virus species belonging to the approved families Solemoviridae, Barnaviridae, and Alvernaviridae. Yellow: outgroup sequences of anemone nepovirus A (QED42866.1) and grapevine fanleaf virus (BAA00761.1) from the family Secoviridae were used for phylogenetic tree construction. Bootstrap values are represented at each node. Two panels to the right of the tree present the positions of the analyzed virus RdRP sequences in a current classification of genera from the Solemoviridae, Barnaviridae, and Alvernaviridae families, proposing amendments to this classification. Genera and families comprising virus species currently approved by ICTV are italicized; new genera Barnavirus (purple) and Dinornavirus (red) are highlighted in bold. Clades and lineages not classified in the current or proposed classifications are designated as “unclassified”.
Figure 2. Maximum likelihood phylogenetic consensus tree based on the predicted amino acid sequence of the RdRP depicting the genetic association of AfBLV (PV941960) to other species in the order Sobelivirales. ICTV accepted families are highlighted in colored boxes as follows. Green: virus species belonging to the approved families Solemoviridae, Barnaviridae, and Alvernaviridae. Yellow: outgroup sequences of anemone nepovirus A (QED42866.1) and grapevine fanleaf virus (BAA00761.1) from the family Secoviridae were used for phylogenetic tree construction. Bootstrap values are represented at each node. Two panels to the right of the tree present the positions of the analyzed virus RdRP sequences in a current classification of genera from the Solemoviridae, Barnaviridae, and Alvernaviridae families, proposing amendments to this classification. Genera and families comprising virus species currently approved by ICTV are italicized; new genera Barnavirus (purple) and Dinornavirus (red) are highlighted in bold. Clades and lineages not classified in the current or proposed classifications are designated as “unclassified”.
Viruses 17 01032 g002
Table 1. Summary of the high-throughput sequencing and Sanger-sequencing data generated for all nine Afrina sporoboliae samples.
Table 1. Summary of the high-throughput sequencing and Sanger-sequencing data generated for all nine Afrina sporoboliae samples.
SampleRaw ReadsPost-Trimming ReadsContigs
de novo Assembled		AfBLV 1# of Reads Assembled to the AfBLV Genome# of Reads (and %) Assembled to Fungi Genomes# of reads (and %) Mapped to A. sporoboliae# of Reads (and %) Mapped to S. maritimus
A153,376,24434,452,02628,061+157,5842074 (0.0060%)30,031,802 (87.17%)21,627 (0.0628%)
B262,948,37044,743,36630,048+191,9132037 (0.0046%)40,161,846 (89.76%)24,340 (0.0544%)
C358,966,45036,426,82428,292+140,7641491 (0.0041%)30,341,392 (83.29%)21,435 (0.0588%)
D450,944,37032,743,48628,154+187,6381973 (0.0060%)28,728,534 (87.74%)30,158 (0.0921%)
E556,670,03036,513,63227,370+152,6511601 (0.0044%)30,280,354 (82.93%)24,057 (0.0659%)
F650,546,93229,786,43822,846+79,619891 (0.0030%)23,349,988 (78.39%)14,400 (0.0483%)
G784,220,49249,407,81423,567+86,0062126 (0.0043%)38,836,542 (78.60%)24,243 (0.0491%)
H883,110,78249,872,07224,216+85,0551866 (0.0037%)39,912,720 (80.03%)23,123 (0.0464%)
I984,308,84650,441,59225,032+104,713777 (0.0015%)40,338,140 (79.97%)19,926 (0.0395%)
1 AfBLV = Afrina barna-like virus: + designates virus-positive status confirmed by RT-PCR and Sanger sequencing.
Table 2. Pair-wise comparisons between sequences of genomes, genes, and protein products of Afrina barna-like virus (AfBLV) and phylogenetically related barna-like virus sequences as percentages at the nucleotide (nt) and amino acid (aa) levels.
Table 2. Pair-wise comparisons between sequences of genomes, genes, and protein products of Afrina barna-like virus (AfBLV) and phylogenetically related barna-like virus sequences as percentages at the nucleotide (nt) and amino acid (aa) levels.
‘BarV’
MW826417		Barnaviridae sp.
MZ218180		Barnaviridae sp. MZ218210 1
ntaantaantaa
AfBLVORF 1 266.561.2NSNSNSNS
ORF 275.074.2NS35.351.349.9
ORF 364.269.8NSNS--
ORF 4NS 3NSNSNS--
Genome64.7-NS-NS-
1 Partial sequence; 2 ORF = open reading frame; 3 NS = not statistically significant.
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Reyes-Proaño, E.; Griffin, A.M.; Duarte, A.; Sheng, H.; Schroeder, B.K.; Murray, T.D.; Karasev, A.V. Afrina barna-like Virus, a Novel Virus Associated with Afrina sporoboliae, the Drop Seed Gall-Forming Nematode. Viruses 2025, 17, 1032. https://doi.org/10.3390/v17081032

AMA Style

Reyes-Proaño E, Griffin AM, Duarte A, Sheng H, Schroeder BK, Murray TD, Karasev AV. Afrina barna-like Virus, a Novel Virus Associated with Afrina sporoboliae, the Drop Seed Gall-Forming Nematode. Viruses. 2025; 17(8):1032. https://doi.org/10.3390/v17081032

Chicago/Turabian Style

Reyes-Proaño, Edison, Anna M. Griffin, Aida Duarte, Hongyan Sheng, Brenda K. Schroeder, Timothy D. Murray, and Alexander V. Karasev. 2025. "Afrina barna-like Virus, a Novel Virus Associated with Afrina sporoboliae, the Drop Seed Gall-Forming Nematode" Viruses 17, no. 8: 1032. https://doi.org/10.3390/v17081032

APA Style

Reyes-Proaño, E., Griffin, A. M., Duarte, A., Sheng, H., Schroeder, B. K., Murray, T. D., & Karasev, A. V. (2025). Afrina barna-like Virus, a Novel Virus Associated with Afrina sporoboliae, the Drop Seed Gall-Forming Nematode. Viruses, 17(8), 1032. https://doi.org/10.3390/v17081032

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Article metric data becomes available approximately 24 hours after publication online.
Back to TopTop