New Genomic Insights into the Hydrangea ringspot virus
Background: Hydrangea ringspot virus (HdRSV) is a member of the Potexvirus genus that affects ornamental Hydrangea species worldwide. Despite its early detection and known economic relevance, its genomic diversity and global distribution have remained poorly characterized, with limited genomic data available.  Methods: To elucidate the diversity and evolution of HdRSV, we generated the first American HdRSV genome from a symptomatic Hydrangea macrophylla plant collected in Colombia and complemented it with a large-scale screening of 214 publicly available Hydrangea RNA-seq datasets from the NCBI SRA. Following rigorous quality filtering, viral genome reconstruction, and reference mapping, 29 novel complete HdRSV genomes were recovered. Combined with 13 reference genomes from GenBank, these sequences were analyzed using maximum-likelihood phylogenetics, global distribution mapping, and viral expression quantification through TPM normalization.  Results: Our analyses identified two strongly supported evolutionary lineages, designated HdRSV-L1 and HdRSV-L2, revealing a previously unrecognized bipartite population structure within the species. Both lineages co-occur in China and Germany, indicating long-term coexistence and potential recombination opportunities. HdRSV was detected in 78% of analyzed transcriptomes, demonstrating widespread infection. Viral RNA was present in all tissue types, with roots exhibiting the highest viral loads, indicating pantropic infection with preferential root accumulation. HdRSV-L1 displayed significantly higher expression levels than HdRSV-L2, particularly in H. serrata, suggesting enhanced replication efficiency or host adaptation.  Conclusions: This study provides the most comprehensive genomic dataset to date for Hydrangea ringspot virus, including the first sequence from the Americas. The discovery of two divergent lineages and their differential tissue tropism refines our understanding of HdRSV evolution, epidemiology, and host adaptation. Our findings underscore the importance of integrating metatranscriptomic mining with traditional sampling to uncover hidden viral diversity in ornamental plant systems and highlight the need for broader genomic surveillance across underrepresented regions.
Background: Hydrangea ringspot virus (HdRSV) is a member of the Potexvirus genus that affects ornamental Hydrangea species worldwide. Despite its early detection and known economic relevance, its genomic diversity and global distribution have remained poorly characterized, with limited genomic data available.  Methods: To elucidate the diversity and evolution of HdRSV, we generated the first American HdRSV genome from a symptomatic Hydrangea macrophylla plant collected in Colombia and complemented it with a large-scale screening of 214 publicly available Hydrangea RNA-seq datasets from the NCBI SRA. Following rigorous quality filtering, viral genome reconstruction, and reference mapping, 29 novel complete HdRSV genomes were recovered. Combined with 13 reference genomes from GenBank, these sequences were analyzed using maximum-likelihood phylogenetics, global distribution mapping, and viral expression quantification through TPM normalization.  Results: Our analyses identified two strongly supported evolutionary lineages, designated HdRSV-L1 and HdRSV-L2, revealing a previously unrecognized bipartite population structure within the species. Both lineages co-occur in China and Germany, indicating long-term coexistence and potential recombination opportunities. HdRSV was detected in 78% of analyzed transcriptomes, demonstrating widespread infection. Viral RNA was present in all tissue types, with roots exhibiting the highest viral loads, indicating pantropic infection with preferential root accumulation. HdRSV-L1 displayed significantly higher expression levels than HdRSV-L2, particularly in H. serrata, suggesting enhanced replication efficiency or host adaptation.  Conclusions: This study provides the most comprehensive genomic dataset to date for Hydrangea ringspot virus, including the first sequence from the Americas. The discovery of two divergent lineages and their differential tissue tropism refines our understanding of HdRSV evolution, epidemiology, and host adaptation. Our findings underscore the importance of integrating metatranscriptomic mining with traditional sampling to uncover hidden viral diversity in ornamental plant systems and highlight the need for broader genomic surveillance across underrepresented regions.
Centro Nacional de Secuenciacion Genomica