Ramu stunt virus genome reveals previously unreported segments and nucleocapsid domain duplication in Mechlorovirus

Authors: Abrahamian, Peter; Grinstead, Samuel; MOLLOV, DIMITRE - Animal And Plant Health Inspection Service (APHIS)

Submitted to: Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2026
Publication Date: 8/1/2026
Citation: Abrahamian, P., Grinstead, S.C., Mollov, D. 2026. Ramu stunt virus genome reveals previously unreported segments and nucleocapsid domain duplication in Mechlorovirus. Virus Evolution. https://doi.org/10.1016/j.virol.2026.111041.
DOI: https://doi.org/10.1016/j.virol.2026.111041

Interpretive Summary: Sugarcane is a globally important crop for food and bioenergy production. Ramu stunt virus (RmSV) is a serious sugarcane pathogen that has currently been reported only from Papua New Guinea. However, its spread could threaten other sugarcane producing countries, including the U.S. because the resistance status of domestic cultivars is unknown. For almost a decade, scientists believed the RmSV genome contained six genetic segments. This research shows that this virus is far more complex, containing nine segments and making it the largest known genome in its virus family. Also surprising was the finding that two of these segments are duplicates of a coat protein gene that helps the virus protect its genetic material. This redundancy may give the virus added flexibility to survive in harsh environments, such as sugarcane fields and in the insects that spread the virus. We also discovered that the virus produces a protein similar to one in another plant virus and that is responsible for severe symptoms, which correlates with the significant stunting observed in RmSV infected sugarcane plants. These findings are important because they revise our understand of the virus’s evolution and adaptability. This research helps improve diagnostic tests, guides breeding for resistant sugarcane cultivars, and strengthens biosecurity measures to protect domestic sugar production from emerging global threats.

Technical Abstract: Ramu stunt virus (RmSV), a member of the genus Mechlorovirus within the family Phenuiviridae, was previously described as a six-segmented RNA virus infecting sugarcane. In this study, we re-examined type material and additional isolates using high-throughput sequencing and RT-PCR validation, revealing that RmSV possesses a nine-segmented genome making it the largest reported in the Phenuiviridae. This expanded architecture includes duplicated RNA segments (RNA 2a and RNA 2b) encoding nucleocapsid-like proteins and two novel segments (RNA 7 and RNA 8). Comparative analysis showed that RNA 2a and 2b share about 84% amino acid identity, while RNA 5 encodes a third nucleocapsid homolog, indicating unprecedented domain redundancy. Structural modeling confirmed that all three nucleocapsid proteins maintain a conserved fold despite low sequence identity, with electrostatic mapping suggesting differential RNA-binding potential. Additionally, RNA 6 encodes a hypothetical protein structurally similar to the rice stripe virus disease-specific S-protein, implicating a role in symptom development. Transcript abundance analysis revealed RNA 6 as the most highly expressed segment across isolates. These findings revise the genomic composition of RmSV, highlight mechanisms of genome plasticity in plant-infecting bunyaviruses, and underscore practical implications for diagnostic assay design, resistance breeding, and biosecurity surveillance.