ToBRFV

ToBRFV provides real-time genomic tracking and visualization of Tomato brown rugose fruit virus (ToBRFV) outbreaks to support genomic epidemiology of infections in tomato and pepper crops.

Key Features:

• Nextstrain integration: Uses Nextstrain to construct phylogenetic visualizations and explore relationships among ToBRFV genomes.
• Illumina sequencing: Employs Illumina sequencing to confirm ToBRFV infections in sampled tomato material.
• Genome dataset: Analyzed a collection of 50 ToBRFV genomes obtained from outbreak sites.
• Epidemiological survey: Based on sampling from 68 Dutch tomato companies with infections confirmed at 17 companies.
• Phylogenetic clustering: Identified three main genomic clusters among the collected ToBRFV genomes, interpreted as three hypothesized sources.
• Genotype–epidemiology linkage: Visualizes potential connections between ToBRFV genotypes, company locations, and epidemiological traits.
• Temporal scope: Includes genomic data compiled up to November 2019.
• Biological scope: Focused on Tomato brown rugose fruit virus (a Tobamovirus) affecting tomato and pepper crops.

Scientific Applications:

• Outbreak tracking: Monitor spatial and temporal spread of ToBRFV using genome-based phylogenetics.
• Genomic epidemiology: Link viral genotypes to epidemiological metadata from horticultural companies for transmission inference.
• Source hypothesis generation: Support formulation of hypotheses about potential infection sources and cluster origins.

Methodology:

Illumina sequencing was used to generate ToBRFV genomes, and Nextstrain was used to visualize phylogenetic relationships and potential connections between genotypes, companies, and epidemiological traits.