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 Vol. 16; no. 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:	Journal Article
Language:	English
Published:	Switzerland MDPI AG 01-03-2024 MDPI
Subjects:	ARTIC amplicon sequencing Biochemical assays Contamination Crop diseases Crop yield Crops Diseases and pests Distribution DNA sequencing Ebola virus Epidemics Flowers & plants Fruit Genetic aspects Genomes Humans Identification and classification Infections lineage abundance estimation Methods Municipal wastewater Mutation Nucleotide sequencing Ontario Pathogens Phylogenetics Plant viruses Proteins RNA polymerase Severe acute respiratory syndrome coronavirus 2 Solanum lycopersicum Tobamovirus - genetics Tomato Brown Rugose Fruit Virus (ToBRFV) Tomatoes Virus diseases of plants Viruses Wastewater Wastewater treatment Water Purification Water treatment Ontario Canada Ontario Canada lineage abundance estimation wastewater ARTIC amplicon sequencing Tomato Brown Rugose Fruit Virus (ToBRFV)
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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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1999-4915 1999-4915
DOI:	10.3390/v16030460