Emergence and Full Genome Analysis of Tomato Torrado Virus in South Africa
Abstract
:1. Introduction
2. Materials and Methods
2.1. RNA Extraction
2.2. Reverse Transcription–Polymerase Chain Reaction (RT-PCR)
2.3. Cloning and Sequencing
2.4. Genome Analysis
3. Results
3.1. Survey Analysis
3.2. Virus Detection
3.3. Sequence Analysis
3.4. RNA-1
3.5. RNA-2
3.6. Phylogeny
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Torradovirus Isolate (RNA 1) | 5′UTR | Polyprotein | ORF 1 Polyprotein | 3′UTR | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Protease co. | Helicase | Protease | RdRP | |||||||||
nt (%) | nt (%) | aa (%) | nt (%) | aa (%) | nt (%) | aa (%) | nt (%) | aa (%) | nt (%) | aa (%) | nt (%) | |
ToT-186 (MH587229) South Africa | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
ToTV T795 (KX132808) Italy | 99.06 | 99.05 | 99.72 | 99.71 | 100 | 98.97 | 100 | 99.33 | 100 | 98.94 | 100 | 97.82 |
ToTV Ros (KM091449) Poland | 98.13 | 99.07 | 99.30 | 99.42 | 99.56 | 99.31 | 100 | 100 | 100 | 99.07 | 100 | 97.36 |
ToTV Wal03 (EU563948) Poland | 100 | 98.96 | 99.53 | 99.71 | 100 | 98.97 | 100 | 99.66 | 100 | 98.94 | 99.60 | 99.50 |
ToTV Kra (KJ940975) Poland | 100 | 99.10 | 99.49 | 99.57 | 100 | 98.97 | 100 | 99 | 100 | 99.07 | 100 | 99.67 |
ToTV (DQ388879) Spain | 98.13 | 98.98 | 99.58 | 99.71 | 100 | 98.63 | 100 | 99.66 | 100 | 99.80 | 100 | 98.76 |
ToChV-G01 (FJ560489) Guatemala | 72.89 | 38.20 | 30.56 | N/A | N/A | 24.82 | 14.43 | N/A | N/A | 72.02 | 87.95 | 61.19 |
ToChSV (GQ305131) Guatemala | 71.02 | 38.01 | 31.86 | N/A | N/A | 30.30 | 21.21 | 30.34 | 14.92 | 24.20 | 13.09 | 62.05 |
ToMarV PRI (EF681764) Mexico | 63.55 | 26.34 | 13.38 | N/A | N/A | 79.59 | 98.96 | N/A | N/A | 26.23 | 13.25 | N/A |
ToMarV pJL89 (KT756876) Mexico | 66.35 | 26.53 | 13.42 | N/A | N/A | 79.59 | 98.96 | N/A | N/A | 25.97 | 13.25 | 61.24 |
ToMarV M (KT756874) Mexico | 66.35 | 26.56 | 13.42 | N/A | N/A | 79.59 | 98.96 | N/A | N/A | 26.10 | 13.25 | 61.40 |
ToNDV R (KC999058) USA | 66.35 | 48.56 | 49.83 | N/A | N/A | 78.91 | 97.93 | N/A | N/A | N/A | N/A | 62.24 |
Torradovirus Isolate (RNA-2) | ORF-2 | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
5′UTR | ORF 1 | MP | VP 35 | VP 26 | VP 23 | 3′UTR | ||||||
nt (%) | nt (%) | aa (%) | nt (%) | aa (%) | nt (%) | aa (%) | nt (%) | aa (%) | nt (%) | aa (%) | nt (%) | |
ToT-186 (MH587230) South Africa | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
ToTV T795 (KX132809) Italy | 97.34 | 99.47 | 98.94 | 99.08 | 100 | 98.78 | 100 | 99.43 | 100 | 99.38 | 99.53 | 99.53 |
ToTV Ros (KM114266) Poland | 97.87 | 98.95 | 98.94 | 98.93 | 100 | 98.64 | 99.18 | 99.01 | 99.57 | 99.53 | 99.53 | 99.53 |
ToTV Wal03 (EU563947) Poland | 97.87 | 99.3 | 99.47 | 98.48 | 100 | 99.05 | 100 | 99.29 | 100 | 99.07 | 100 | 99.59 |
ToTV Kra (KJ940974) Poland | 97.34 | 99.47 | 99.47 | 98.63 | 99.08 | 98.5 | 99.59 | 99.15 | 100 | 99.53 | 99.53 | 99.53 |
ToTV (DQ388880) Spain | 97.34 | 98.6 | 98.94 | 98.93 | 100 | 98.91 | 100 | 99.01 | 100 | 98.92 | 99.53 | 99.46 |
ToChV-G01 (FJ560490) Guatemala | 46.27 | 57.41 | 70 | 70.06 | 80.36 | 63.27 | 73.87 | 73.55 | 87.28 | 65.74 | 81.94 | 31.43 |
ToChV-G02 (GU071087) Guatemala | 46.27 | 60.73 | 71.05 | 71.27 | 80.36 | 63.55 | 73.87 | 73.69 | 86.86 | 65.59 | 80.55 | 31.43 |
ToChSV (GQ305132) Guatemala | 40.42 | 63.52 | 73.68 | 70.36 | 80.82 | 64.9 | 74.69 | 74.68 | 91.52 | 64.36 | 81.94 | 49.23 |
PRI-TMarV0601 (EF681765) Mexico | 36.7 | 60.73 | 72.1 | 70.36 | 80.82 | 64.22 | 76.32 | 73.41 | 89.83 | 65.74 | 79.62 | 45.88 |
ToMarV pJL89 (KT756877) Mexico | 36.17 | 60.38 | 73.68 | 70.06 | 81.27 | 66.66 | 75.51 | 73.41 | 89.4 | 66.05 | 80.55 | 46.62 |
ToMarV M (KT756875) Mexico | 36.17 | 60.55 | 73.68 | 69.9 | 81.27 | 66.53 | 75.51 | 73.55 | 89.4 | 65.89 | 80.55 | 46.62 |
ToNDV R (KC999059) USA | 35.63 | 61.6 | 70.52 | 70.06 | 81.27 | 64.9 | 74.28 | 72.15 | 91.1 | 66.35 | 80.55 | 46.48 |
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Moodley, V.; Gubba, A.; Mafongoya, P.L. Emergence and Full Genome Analysis of Tomato Torrado Virus in South Africa. Viruses 2020, 12, 1167. https://doi.org/10.3390/v12101167
Moodley V, Gubba A, Mafongoya PL. Emergence and Full Genome Analysis of Tomato Torrado Virus in South Africa. Viruses. 2020; 12(10):1167. https://doi.org/10.3390/v12101167
Chicago/Turabian StyleMoodley, Vaneson, Augustine Gubba, and Paramu L. Mafongoya. 2020. "Emergence and Full Genome Analysis of Tomato Torrado Virus in South Africa" Viruses 12, no. 10: 1167. https://doi.org/10.3390/v12101167