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 <i>Solanaceae</i> 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 re...
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| Format: | Article |
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MDPI AG
2024-03-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/16/3/460 |
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| author | Delaney Nash Isaac Ellmen Jennifer J. Knapp Ria Menon Alyssa K. Overton Jiujun Cheng Michael D. J. Lynch Jozef I. Nissimov Trevor C. Charles |
| author_facet | Delaney Nash Isaac Ellmen Jennifer J. Knapp Ria Menon Alyssa K. Overton Jiujun Cheng Michael D. J. Lynch Jozef I. Nissimov Trevor C. Charles |
| author_sort | Delaney Nash |
| collection | DOAJ |
| description | Tomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important <i>Solanaceae</i> 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. |
| first_indexed | 2024-04-24T17:45:29Z |
| format | Article |
| id | doaj.art-d3e9ecdaae984f71842a2c9ff574665f |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-04-24T17:45:29Z |
| publishDate | 2024-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-d3e9ecdaae984f71842a2c9ff574665f2024-03-27T14:07:57ZengMDPI AGViruses1999-49152024-03-0116346010.3390/v16030460A 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, CanadaDelaney Nash0Isaac Ellmen1Jennifer J. Knapp2Ria Menon3Alyssa K. Overton4Jiujun Cheng5Michael D. J. Lynch6Jozef I. Nissimov7Trevor C. Charles8Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, CanadaDepartment of Biology, University of Waterloo, Waterloo, ON N2L 3G1, CanadaDepartment of Biology, University of Waterloo, Waterloo, ON N2L 3G1, CanadaDepartment of Biology, University of Waterloo, Waterloo, ON N2L 3G1, CanadaDepartment of Biology, University of Waterloo, Waterloo, ON N2L 3G1, CanadaDepartment of Biology, University of Waterloo, Waterloo, ON N2L 3G1, CanadaDepartment of Biology, University of Waterloo, Waterloo, ON N2L 3G1, CanadaDepartment of Biology, University of Waterloo, Waterloo, ON N2L 3G1, CanadaDepartment of Biology, University of Waterloo, Waterloo, ON N2L 3G1, CanadaTomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important <i>Solanaceae</i> 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.https://www.mdpi.com/1999-4915/16/3/460Tomato Brown Rugose Fruit Virus (ToBRFV)ARTIC amplicon sequencinglineage abundance estimationwastewater |
| spellingShingle | Delaney Nash Isaac Ellmen Jennifer J. Knapp Ria Menon Alyssa K. Overton Jiujun Cheng Michael D. J. Lynch Jozef I. Nissimov Trevor C. Charles 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 Viruses Tomato Brown Rugose Fruit Virus (ToBRFV) ARTIC amplicon sequencing lineage abundance estimation wastewater |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | Tomato Brown Rugose Fruit Virus (ToBRFV) ARTIC amplicon sequencing lineage abundance estimation wastewater |
| url | https://www.mdpi.com/1999-4915/16/3/460 |
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