Occurrence, Genetic Variability of Tomato Yellow Ring Orthotospovirus Population and the Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Its Rapid Detection
Abstract
1. Introduction
2. Materials and Methods
2.1. Virus Source
2.2. Viruses Infecting Tomatoes in Poland
2.3. Analysis of the TYRV Polish Population
2.4. Phylogenetic-Trait Association
2.5. RT-LAMP
3. Results
3.1. Viruses Infecting Tomato in Poland
3.2. Analysis of TYRV Population
3.3. Host Driven Structure of the TYRV Population
3.4. Optimisation of the RT-LAMP Conditions
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Virus Name | Primer Name | Primer Sequence 5′-3′ | Annealing Temp. | Reference | |
---|---|---|---|---|---|
cucumber mosaic virus | CMV | CMVCPf | GCTTCTCCGCGAG | 50 °C | [43] |
CMVCPr | GCCGTAAGCTGGATGGAC | ||||
cucumber mosaic virus | CMVsat-fwd | AAGGATCCGGGTCCTGBDDDGGAATG | 55 °C | [44] | |
satRNA | CMVsat-rev | AAGGATCCGTTTTGTTTGWTRGAGAAT TGCGYRGAG | |||
pepino mosaic virus | PepMV | TGB3F | GGTGGACAATATCAAGACGG | 51 °C | [41] |
TGB3R | CTGTATTGGGATTTGAGAAGTC | ||||
potato virus Y | PVY | PVYc3F | CAACGCAAAAACACTCAyAAAmGC | 57 °C | [45] |
PVYfR | TAAGTGrACAGACCCTCTyTTCTC | ||||
PVY3F | TGTAACGAAAGGGACTAGTGCAAAG | ||||
PVY3R | CCGCTATGAGTAAGTCCTGCACA | ||||
PVYCP2F | CCAGTCAAACCCGAACAAAGG | ||||
PVYCP1R | GGCATAGCGTGCTAAACCCA | ||||
tomato black ring virus | TBRV | TBRVR1-P1-KRF | GGTAAAAGTTCTGGGTGCT | 53 °C | [46] |
TBRVR1-P1-KRR | GCAAATCCACCTCCTTATCC | ||||
tomato black ring virus | CH_SAT_F1 | TAATTTTGAAAGTCTCTGA | 47 °C | [46] | |
satRNA | CH_SAT_R2 | GGACAGCTCGTTGGTTCTTAGA | |||
tomato brown rugose | ToBRFV | CaTa28 Fw | GGTGGTGTCAGTGTCTGTTT | 60 °C | [47] |
fruit virus | CaTa28 Rv | GCGTCCTTGGTAGTGATGTT | |||
CaTa28 Pr | 6FAM-AGAGAATGGAGAGAGCGGACGAGG-BHQ’1 | ||||
CSP1325 Fw | CATTTGAAAGTGCATCCGGTT T | ||||
CSP1325 Rv | GTACCACGTGTGTTTGCAGACA | ||||
CSP1325 Pr | VIC-ATGGTCCTCTGCACCTGCATCTTGAGA-BHQ’1 | ||||
tomato chlorosis virus | ToCV | ToCVCPF | ATGGAGAACAGTGCCGTTGC | 58 °C | [48] |
ToCVCPR | TTAGCAACCAGTTATCGATGC | ||||
tomato mosaic virus | ToMV | ToMV F | CGAGAGGGGCAACAAACAT | 66 °C | [49] |
ToMV R | ACCTGTCTCCATCTCTTTGG | ||||
tomato torrado virus | ToTV | 2TT5 | GATGAGAAAGGAAAGAAGCAG | 55 °C | [50] |
2TT6 | CATATCACCCAAATGCTTCTC | ||||
tobacco mosaic virus | TMV | TMV F | CGACATCAGCCGATGCAGC | 66 °C | [49] |
TMV R | ACCGTTTTCGAACCGAGACT | ||||
tomato spotted wilt | TSWV | TS1-F | GCCTATGGATTACCTCTTG | 45 °C | [51] |
orthotospovirus | TS1-R | GTTTCACTGTAATGTTCCA | |||
tomato yellow ring | TYRV | TY2-F | CTAACAAAGCCATGAAGA | 45 °C | [51] |
orthotospovirus | TY2-R | GAAGACCCAGCACCA |
Primers Name | Primer Sequence 5′-3′ |
---|---|
TYRV FIP | CACAGTAGAGCTAGGAACAACAATA-AAAATGGTTAAAGCAGGGC |
TYRV BIP | GGTCAAGATGATTGGACATTCCGA-TGCATTTTCCACAGCAATG |
TYRV F3 | GAGAAACAGAGCAGGGATT |
TYRV B3 | TCATACATTTTCTGTTTCTCAGT |
Year | No. of Collected Samples | No. of Infected Samples | Single Infection | Mixed Infection | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PepMV | TYRV | TSWV | CMV | PVY | ToMV | TBRV | TMV | ToTV | ToBRV * | ToCV * | TSWV+ TYRV | CMV+ PepMV | TSWV+ PepMV | CMV+ TYRV | |||
2014 | 54 | 25 | 7 | 8 | 6 | - | - | - | - | - | - | x | x | 4 | - | - | - |
2015 | 41 | 11 | 11 | - | - | - | - | - | - | - | - | x | x | - | - | - | - |
2016 | 37 | 11 | 10 | - | - | 1 | - | - | - | - | - | x | x | - | - | - | - |
2017 | 22 | 6 | 5 | 1 | - | - | - | - | - | - | - | x | x | - | - | - | - |
2018 | 24 | 6 | 6 | - | - | - | - | - | - | - | - | x | x | - | - | - | - |
2019 | 20 | 5 | 3 | - | - | 2 | - | - | - | - | - | x | - | - | - | - | |
2020 | 18 | 11 | 7 | - | - | - | 2 | - | - | - | - | - | - | - | 2 | - | - |
2021 | 18 | 14 | 7 | 1 | 1 | 1 | - | 1 | 1 | - | - | - | - | - | - | 1 | 1 |
Total | 234 | 89 | 56 | 10 | 7 | 4 | 2 | 1 | 1 | 0 | 0 | 0 | 0 | 4 | 2 | 1 | 1 |
Isolate Origin (Host Plant) | Observed Value | Null Value | p-Value | ||||
---|---|---|---|---|---|---|---|
Mean | Lower HPD | Upper HPD | Mean | Lower HPD | Upper HPD | ||
95% CI | 95% Cl | 95% CI | 95% CI | ||||
AI | 2.96 | 2.45 | 3.47 | 4.00 | 3.49 | 4.59 | 0.00 |
PS | 18.21 | 17.00 | 19.00 | 24.93 | 22.74 | 26.82 | 0.00 |
MC (SL) | 15.00 | 15.00 | 15.00 | 2.70 | 2.00 | 3.66 | 0.01 |
MC (AL) | 1.00 | 1.00 | 1.00 | 1.01 | 1.00 | 1.09 | 1.00 |
MC (CH) | 1.00 | 1.00 | 1.00 | 1.01 | 1.00 | 1.06 | 1.00 |
MC (GL) | 1.00 | 1.00 | 1.00 | 1.01 | 1.00 | 1.07 | 1.00 |
MC (ST) | 3.11 | 2.00 | 5.00 | 1.89 | 1.28 | 2.52 | 0.04 |
MC (AR) | 1.08 | 1.00 | 2.00 | 1.21 | 1.00 | 2.00 | 1.00 |
MC (CA) | 1.00 | 1.00 | 1.00 | 1.02 | 1.00 | 1.04 | 1.00 |
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Zarzyńska-Nowak, A.; Budzyńska, D.; Taberska, A.; Jędrzejczak, N.; Minicka, J.; Borodynko-Filas, N.; Hasiów-Jaroszewska, B. Occurrence, Genetic Variability of Tomato Yellow Ring Orthotospovirus Population and the Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Its Rapid Detection. Viruses 2022, 14, 1405. https://doi.org/10.3390/v14071405
Zarzyńska-Nowak A, Budzyńska D, Taberska A, Jędrzejczak N, Minicka J, Borodynko-Filas N, Hasiów-Jaroszewska B. Occurrence, Genetic Variability of Tomato Yellow Ring Orthotospovirus Population and the Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Its Rapid Detection. Viruses. 2022; 14(7):1405. https://doi.org/10.3390/v14071405
Chicago/Turabian StyleZarzyńska-Nowak, Aleksandra, Daria Budzyńska, Agnieszka Taberska, Norbert Jędrzejczak, Julia Minicka, Natasza Borodynko-Filas, and Beata Hasiów-Jaroszewska. 2022. "Occurrence, Genetic Variability of Tomato Yellow Ring Orthotospovirus Population and the Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Its Rapid Detection" Viruses 14, no. 7: 1405. https://doi.org/10.3390/v14071405
APA StyleZarzyńska-Nowak, A., Budzyńska, D., Taberska, A., Jędrzejczak, N., Minicka, J., Borodynko-Filas, N., & Hasiów-Jaroszewska, B. (2022). Occurrence, Genetic Variability of Tomato Yellow Ring Orthotospovirus Population and the Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Its Rapid Detection. Viruses, 14(7), 1405. https://doi.org/10.3390/v14071405