Comparative Analysis of Novel Strains of Porcine Astrovirus Type 3 in the USA
Abstract
:1. Introduction
2. Materials and Methods
2.1. Diagnostic Samples
2.2. RT-qPCR and Sanger Sequencing
2.3. Phylogenic and Sequence Analysis
2.4. UTRs and Frameshift Signal Analysis
2.5. Identification of Putative Genome-Linked Virus Protein (VPg)
2.6. Linear Antigen Epitope Prediction
3. Results
3.1. Diagnostic Samples
3.2. RT-qPCR and Sanger Sequencing
3.3. Phylogenic and Sequence Analysis
3.4. UTR Analysis
3.4.1. 5′UTR Analysis
3.4.2. Frameshift Analysis
3.4.3. 3′UTR Analysis
3.5. Identification of Putative VPg and RNA-Protein Binding Regions
3.6. Linear Antigen Epitope Prediction
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Primer ID | Sequence Target | Region Target | |
---|---|---|---|
POAstV3 US-MO123—JX556691 (5′-3′) | PoAstV3 USA/IA/7023/2017—KY940545 (5′-3′) | ||
F1_T7 | ATGGTACCTAATACGACTCACTATAGCCAAATAGAGCTGCCCGTTGGTCC | ORF1 | |
R1008 | CAGAGTAGCGTACATCGGGCATG | CGGAGTAACGCACATCGGGCATG | ORF1a |
F392 | TCTCCCAAGAGCTCTCCCAA | NA | ORF1a |
R1345 | CCTGTTCCTGAGCCATCCTG | NA | ORF1a |
F485 | GCCGGTTAGGGTTCATCACA | ORF1a | |
R1591 | GCAACTGACAGAGCACCTGA | ORF1a | |
F845 | CATATTCAAAGGCCCAAGTTCTGGCCCTTG | CATACTCAAAGCCCAGGTTCTAGCTCTTG | ORF1a |
R1662 | CAGGTGAACCACTCATACCATTCCGA | CAGGTGAGCCACTCATACCATTCCGG | ORF1a |
F1465 | GTCCATCGTGTGCCGGATAAGGACATAG | GTCCACCGTGTGCCAGATAAGGACATAG | ORF1a |
R2217 | GTGTCTTGAGGCTCTTCCTTAACAGGC | GTGTCCTGAGGCTCTTCCTTAACAGGC | ORF1a |
F2001 | CCGTGCTGTCTGGTCAGAAGAAGAGTAC | CCGTGCTGTCTGGTCAGAAGAGGAATAC | ORF1a |
R3203 | CCACATTGGCCAGAGCGTGTC | ORF1a | |
F2462 | GGGAGAAAGGCTTGGTTCCT | ORF1a | |
R3920 | CAGGGAGGTTATGGCCAAGG | ORF2 | |
F3127 | GTTCTGACCCTATATTTGCACGTATAGGATGTCAC | GTTCTGACCCTATATTTGCACGTATAGGTTGTCAC | ORF1a |
R4855 | GTCACACGATCTAGTGTTCCAAGGGC | GTCACACGATCCAGAGTTCCAAGGGC | ORF2 |
F4308 | CTTCTCAGTGCGAGTCTCGG | ORF2 | |
R5326 | AAAGTGGTGGCCGTAGATGG | ORF2 | |
F4672 | CCGCGACAGACGTGGTGG | ORF2 | |
R5924 | CGTCAGTCACATTATAGTTGCCAAGGG | CGTCAGCCACATTGTAGTTACCAAGGG | ORF2 |
F5486 | GAGCTGGTAAAGGCATGGGT | NA | ORF2 |
R6283 | TGGATAAGAGCGTCGGCATC | ORF2 | |
F6108 | CCGTCCGACCATGATTGACA | ORF2 | |
R6352 | CGAGGGTACAGGGGCTTAGA | TCTAAGCCCCTGTACCCTCG | 3′ UTR |
F5598 | ACCTGGTATCGGCTGGACT | ORF2 | |
R6405_M13 | TGTAAAACGACGGCCAGTGCCTAAAGAAAAAAAAGAAAATCAATTTAA | 3′ UTR | |
F2804 | CCCTAATATAGCCGCCACGT | NA | ORF1a |
R3987 | GTGTCCTGATGTGCCTAGCA | NA | ORF2 |
F946 | ACCCACAGTGAAAGGACAGC | NA | ORF1 |
F5623 | CCTGGTATCGGCTGGACTGTT | NA | ORF2 |
Strain Origin | ORF1a | nsp1a | ORF1ab | nsp1ab | ORF2 | Capsid Protein |
---|---|---|---|---|---|---|
USA | 89.7–100% | 94.7–100% | 91.9–100% | 96.3–100% | 90.7–100% | 93.5–100% |
Japan | 89.1–100% | 95.2–99.9% | 89.4–99.9% | 95.3–99.9% | 65.1–99.9% | 65.6–99.9% |
Spain | 92.9% | 96.3% | 93.2% | 96.6% | 92.7% | 95.6% |
Hungary | 99.6–99.7% | 99.4–99.6% | 99.6–99.6% | 99.6–99.7% | 99.1–99.4% | 98.8–99.2% |
Prediction Tool: SVMTriP Online Prediction Tool | |||||
---|---|---|---|---|---|
Recommended epitopes | Score | ORF 2 region | ORF 2 position | VaxiJen v2.0 result (score) | |
USA | AKHMSTAYEKLPLNALTVGE | 1 | Conserved | 355–374 | Probable antigen (0.5478) |
YKHEKWGDNLKFSSWLVRFT | 0.92 | Variable | 593–612 | Probable antigen (0.8778) | |
Hungary | AKHMSTAYEKLPLNALTVGE | 1 | Conserved | 292–311 | Probable antigen (0.5478) |
TNCADVLAYKHEKWGDNLKF | 0.953 | Variable | 522–541 | Probable antigen (0.8269) | |
LAKEVAKEVVKEEKRNQARS | 0.893 | Conserved | 15–34 | Probable non-antigen (0.1453) | |
Japan | IMTMTIPQRSNLARHMSTAY | 1 | Conserved | 347–368 | Probable non-antigen (0.0369) |
LAKEVAKEVVKEEKKVQARR | 0.964 | Conserved | 77–96 | Probable non-antigen (0.0094) | |
TNCADVLAYKHEKWGDNLKF | 0.892 | Variable | 591–610 | Probable antigen (0.8269) | |
Spain | AKHMSTAYEKLPLNALTVGE | 1 | Conserved | 355–374 | Probable antigen (0.5478) |
TNCADVLAYKHEKWGDDLKF | 0.879 | Variable | 585–604 | Probable antigen (0.8161) | |
ANQATSHSPVINNVFPVLGQ | 0.862 | Variable | 496–515 | Probable non-antigen (0.3368) | |
Germany | LAKEVAKEVVKEEKRFQARS | 1 | Conserved | 77–96 | Probable non-antigen (0.2543) |
PVFLGLNLGASSSTVDNIFL | 0.999 | Variable | 544–563 | Probable antigen (0.9103) | |
AKHMSTAYEKLPLNALTVGE | 0.911 | Conserved | 354–373 | Probable antigen (0.5478) | |
TNCADVLAYKHEKWGDNLKF | 0.869 | Variable | 584–603 | Probable antigen (0.8269) | |
Prediction tool: Immunomedicine predicted antigenic peptides web-based tool | |||||
Recommended epitopes | Score | ORF 2 region | ORF 2 position | VaxiJen v2.0 result (score) | |
USA | WVGDLFIVEVVG | >1.2 | Conserved | 298–309 | Probable non-antigen (0.0845) |
GNFYCLVSAPVISNVNQAPVTIVFNKVATPKLSTSSSLSHMRVSVSSVQPGTYGVIYT | >1.2 | Variable | 620–677 | Probable antigen (0.5617) | |
Hungary | WVGDLFIVEVVG | >1.2 | Conserved | 239–250 | Probable non-antigen (0.0845) |
GNYYCLVSAPVISAVNQAPVTIVFDKVATPKLSTSSS | >1.2 | Variable | 561–597 | Probable non-antigen (0.3268) | |
Japan | WVGDLFIVEVVG | >1.2 | Conserved | 308–319 | Probable non-antigen (0.0845) |
GNFYCLVSAPIISNVDQAPVTIVANKVATPKLSTSSSLSHMRVSVSSVQPGTYGVIYT | >1.2 | Variable | 626–683 | Probable antigen (0.5449) | |
Spain | GLWRLAGLKICCTPLVGPSAVTGSVYRLSLNL | >1.2 | Conserved | 195–226 | Probable non-antigen (0.1431) |
WVGDLFIVEVVG | >1.2 | Conserved | 302–313 | Probable non-antigen (0.0845) | |
GNFYCLVSAPVISNVDQAPVTIVFDKVATPKLSTSSSLSHMRVSVSSVQPGTYGVIYT | >1.2 | Variable | 624–681 | Probable antigen (0.5397) | |
Germany | GNFYCLVSAPVVSDVNQAPVTIVSNKVATPKLSTSSSLSHMRVSVSSVQPGMYGVIYTLGS | >1.2 | Variable | 619–679 | Probable antigen (0.5507) |
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Matias Ferreyra, F.; Harmon, K.; Bradner, L.; Burrough, E.; Derscheid, R.; Magstadt, D.R.; Michael, A.; de Almeida, M.N.; Schumacher, L.; Siepker, C.; et al. Comparative Analysis of Novel Strains of Porcine Astrovirus Type 3 in the USA. Viruses 2021, 13, 1859. https://doi.org/10.3390/v13091859
Matias Ferreyra F, Harmon K, Bradner L, Burrough E, Derscheid R, Magstadt DR, Michael A, de Almeida MN, Schumacher L, Siepker C, et al. Comparative Analysis of Novel Strains of Porcine Astrovirus Type 3 in the USA. Viruses. 2021; 13(9):1859. https://doi.org/10.3390/v13091859
Chicago/Turabian StyleMatias Ferreyra, Franco, Karen Harmon, Laura Bradner, Eric Burrough, Rachel Derscheid, Drew R. Magstadt, Alyona Michael, Marcelo Nunes de Almeida, Loni Schumacher, Chris Siepker, and et al. 2021. "Comparative Analysis of Novel Strains of Porcine Astrovirus Type 3 in the USA" Viruses 13, no. 9: 1859. https://doi.org/10.3390/v13091859
APA StyleMatias Ferreyra, F., Harmon, K., Bradner, L., Burrough, E., Derscheid, R., Magstadt, D. R., Michael, A., de Almeida, M. N., Schumacher, L., Siepker, C., Sitthicharoenchai, P., Stevenson, G., & Arruda, B. (2021). Comparative Analysis of Novel Strains of Porcine Astrovirus Type 3 in the USA. Viruses, 13(9), 1859. https://doi.org/10.3390/v13091859