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Updated: Jun 20, 2026
Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
Published on: July 27, 2018
Identification and molecular characterization of a marafivirus in Rubus spp
Sead Sabanadzovic1, Nina Abou Ghanem-Sabanadzovic
1Department of Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. ss501@msstate.edu
Abstract:
An undescribed virus with isometric particles and a diameter of ca. 30 nm was identified in diseased samples of wild and cultivated Rubus species and molecularly characterized. Its genome was 6,463 nt, excluding the 3'-terminal poly(A) tail, and contained a single open reading frame coding for a 2,035-amino-acid-long precursor polypeptide (p223). The amino terminal portion of p223, identified as a replication-associated polyprotein, contained conserved motifs of methyltransferase, endopeptidase/protease, helicase and RNA-dependent RNA polymerase. The carboxy terminus of the large polypeptide is involved in the formation of two viral coat protein subunits with deduced molecular masses of 23 and 21 kDa. Pairwise comparisons and phylogenetic analyses showed closest relationships of this virus with oat blue dwarf virus and citrus sudden death-associated virus, sharing levels of genome sequence conservation far below the species demarcation level established for tymovirids. Our data indicate that this virus, for which the name blackberry virus S (BlVS) is proposed, is a hitherto undescribed species of the genus Marafivirus, family Tymoviridae. A survey conducted in Mississippi, USA, has shown that BlVS is also present in cultivated Rubus germplasm. This work represents the first report of a marafivirus infecting small fruits.
Insights
A new virus, blackberry virus S (BlVS), has been identified in Rubus species. This marks the first marafivirus found infecting small fruits, impacting cultivation.
Area of Science:
- Plant Virology
- Molecular Biology
- Mycology
Background:
- Wild and cultivated Rubus species are susceptible to viral infections.
- The family Tymoviridae includes several plant-pathogenic viruses.
- Marafiviruses are known plant pathogens, but their diversity in small fruits is underexplored.
Purpose of the Study:
- To identify and characterize a novel virus found in diseased Rubus plants.
- To determine the phylogenetic relationships of the new virus within the Tymoviridae family.
- To report the first marafivirus identified in small fruit species.
Main Methods:
- Isolation and molecular characterization of the virus from infected Rubus samples.
- Genome sequencing and analysis of the viral RNA.
- Phylogenetic analysis to determine viral relationships.
Main Results:
- An undescribed virus, named blackberry virus S (BlVS), was identified with isometric particles (ca. 30 nm).
- The BlVS genome is 6,463 nt with a single open reading frame encoding a 2,035-amino-acid precursor polypeptide.
- Phylogenetic analysis places BlVS as a new species within the genus Marafivirus, family Tymoviridae, distinct from known tymovirids.
- BlVS was detected in cultivated Rubus germplasm in Mississippi, USA.
Conclusions:
- Blackberry virus S (BlVS) is a novel species within the genus Marafivirus, family Tymoviridae.
- This discovery represents the first report of a marafivirus infecting small fruits.
- The presence of BlVS in cultivated germplasm highlights potential risks to the berry industry.
