A Novel Tiled Amplicon Sequencing Assay Targeting the Tomato Brown Rugose Fruit Virus (ToBRFV) Genome Reveals Widespread Distribution in Municipal Wastewater Treatment Systems in the Province of Ontario, Canada

Tomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important crop species and can dramatically reduce tomato crop yields. The ToBRFV has rapidly spread around the globe due to its ability to escape detection by antiviral host genes which confer resistance to other tobamoviruse...

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Bibliographic Details
Published in:Viruses 2024-03, Vol.16 (3), p.460
Main Authors: Nash, Delaney, Ellmen, Isaac, Knapp, Jennifer J, Menon, Ria, Overton, Alyssa K, Cheng, Jiujun, Lynch, Michael D J, Nissimov, Jozef I, Charles, Trevor C
Format: Article
Language:English
Subjects:
ARTIC amplicon sequencing
Crop diseases
Crop yield
Crops
disease transmission
Ebola virus
Epidemics
evolution
excreta
Flowers & plants
Fruit
fruits
genome
Genomes
Humans
Infections
lineage abundance estimation
monitoring
Municipal wastewater
Mutation
Ontario
Pathogens
Phylogenetics
plant pathogens
Plant viruses
Proteins
RNA polymerase
Severe acute respiratory syndrome coronavirus 2
Solanaceae
Solanum lycopersicum
Tobamovirus
Tobamovirus - genetics
Tomato Brown Rugose Fruit Virus (ToBRFV)
tomatoes
Viruses
wastewater
Wastewater treatment
Water Purification
Water treatment
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Summary:Tomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important crop species and can dramatically reduce tomato crop yields. The ToBRFV has rapidly spread around the globe due to its ability to escape detection by antiviral host genes which confer resistance to other tobamoviruses in tomato plants. The development of robust and reproducible methods for detecting viruses in the environment aids in the tracking and reduction of pathogen transmission. We detected ToBRFV in municipal wastewater influent (WWI) samples, likely due to its presence in human waste, demonstrating a widespread distribution of ToBRFV in WWI throughout Ontario, Canada. To aid in global ToBRFV surveillance efforts, we developed a tiled amplicon approach to sequence and track the evolution of ToBRFV genomes in municipal WWI. Our assay recovers 95.7% of the 6393 bp ToBRFV RefSeq genome, omitting the terminal 5' and 3' ends. We demonstrate that our sequencing assay is a robust, sensitive, and highly specific method for recovering ToBRFV genomes. Our ToBRFV assay was developed using existing ARTIC Network resources, including primer design, sequencing library prep, and read analysis. Additionally, we adapted our lineage abundance estimation tool, Alcov, to estimate the abundance of ToBRFV clades in samples.
ISSN:1999-4915
1999-4915
DOI:10.3390/v16030460