Molecular and Evolutionary Characteristics of Chicken Parvovirus (ChPV) Genomes Detected in Chickens with Runting–Stunting Syndrome
Abstract
:1. Introduction
2. Materials and Methods
2.1. Clinical Samples and Viral Metagenomics
2.2. Sequence and Phylogenetic Analysis
2.3. Recombination Analysis
2.4. Selective Pressure Analysis
2.5. Protein Modeling of Viral Capsid and B and T Epitope Prediction
3. Results
3.1. Viral Metagenomics
3.2. Sequence and Phylogenetic Analysis
3.3. Recombination Analysis
3.4. Selective Pressure Analysis
3.5. Protein Modeling of Viral Capsid and T and B Epitope Prediction
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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Gene | Codon Position | FEL p-Value 2 | FUBAR Probability α < β Positive 2 | SLAC P-[dN/dS > 1] 2 |
---|---|---|---|---|
NS1 | 131 | — | 0.006 | |
331 | — | 0.042 | — | |
349 | — | 0.020 | — | |
534 | 0.0819 | 0.015 | — | |
615 | 0.0182 | 0.006 | 0.0879 | |
617 1 | 0.0940 | — | — | |
637 | 0.0098 | 0.000 | 0.0223 | |
640 | 0.0018 | 0.000 | 0.0061 | |
645 | 0.0044 | 0.000 | 0.0303 | |
647 | 0.0003 | 0.000 | 0.0018 | |
654 | 0.0133 | 0.006 | 0.0403 | |
NP1 | 2 | 0.0872 | 0.934 | — |
6 | 0.0855 | 0.946 | — | |
NP | 6 | 0.0133 | 0.972 | — |
15 | 0.0737 | 0.956 | — | |
16 | — | 0.948 | — | |
31 | — | 0.904 | — | |
35 | 0.0751 | — | — | |
45 | — | 0.917 | — | |
58 | 0.0835 | 0.916 | — | |
66 | — | 0.930 | — | |
67 | 0.0822 | — | — | |
68 | 0.0887 | — | — | |
69 | 0.0045 | 0.995 | 0.0427 | |
VP1 | 8 | 0.0360 | 0.918 | 0.0702 |
85 | 0.0777 | — | — | |
107 | 0.0342 | 0.904 | 0.0517 | |
134 | 0.0724 | 0.918 | — | |
187 | 0.0042 | 0.983 | — | |
188 | 0.0416 | 0.916 | 0.0677 | |
192 | 0.0261 | 0.940 | 0.0618 | |
210 | 0.0657 | — | — | |
215 | 0.0056 | 0.983 | 0.0214 |
VP1 Position 1 | Peptide | Chicken MHC-I Substitute Alleles 2 | |||
---|---|---|---|---|---|
ChPV | TuPV | HLA-B*40:06 | HLA-B*41:03 | HLA-B*41:04 | |
47 | ARKELTPQQKA | — | C | — | — |
48 | RKELTPQQKA | KKELTAQQKA | C + T | — | — |
49 | KELTPQQKA | KELTAQQKA | C + T | C + T | C |
84 | KEFFKNHQGA | KEFFKNHQGA | C + T | — | — |
128 | EEHPFNQEEL | EEAPFNEQEL | — | C + T | — |
135 | — | NEQELEEAM | — | T | — |
202 | RDMDQYKAI | RDFDKYQAI | T | C + T | C + T |
221 | SENQTQYF | AENETQYF | — | C + T | C + T |
221 | — | AENETQYFGF | — | T | T |
301 | QEGKYPRL | — | — | — | C |
301 | QEGKYPRLL | QEGRYPRIL | — | C + T | C + T |
353 | RESAFYCL | — | — | C | C |
372 | NEWETTFVF | NEWQTSYEF | C + T | C + T | C + T |
378 | — | YEFPDSTP | T | — | — |
446 | LENLANVAV | — | C | C | C |
469 | RPESDKDEYL | RPETDKDEYL | — | C + T | — |
581 | KESPGHIF | KESPGHVF | — | C + T | C + T |
581 | KESPGHIFV | KESPGHVFV | C + T | C + T | C + T |
613 | VEIEWELEP | — | C | — | — |
615 | — | IEWELEHFT | T | — | — |
Total peptides | 16 | 22 | 17 |
VP1 Position 1 | Peptide | Chicken MHC-II Substitute Alleles 2 | ||||
---|---|---|---|---|---|---|
ChPV | TuPV | DRB1:1310 | DRB1:1366 | DRB1:1445 | DRB1:1482 | |
5 | APKGYVPSLPTTDEE | PPKGYVPSLPTTDEE | C + T | — | — | — |
6 | PKGYVPSLPTTDEEA | — | C | C | — | — |
58 | ERKRFFITQAQKNKK | DRKRFFITQAQKNKK | C + T | — | — | — |
59 | RKRFFITQAQKNKKP | RKRFFITQAQKNKKP | C + T | C + T | — | — |
293 | GTIQIFADQEGKYPR | GTIQIFADQEGRYPR | — | — | — | C + T |
295 | — | TIQIFADQEGRYPRI | — | — | — | T |
403 | LYDTWNVNGRGDDAK | — | C | C | — | — |
404 | YDTWNVNGRGDDAKR | — | C | C | — | — |
405 | DTWNVNGRGDDAKRG | — | C | C | — | — |
431 | — | GPYIYLSDTTAAGQQ | — | T | — | — |
494 | VRNSQIQVSTANKVQ | — | — | — | C | C |
495 | RNSQIQVSTANKVQV | — | — | — | C | C |
496 | NSQIQVSTANKVQVD | — | — | — | C | C |
497 | SQIQVSTANKVQVDT | — | — | — | C | C |
498 | QIQVSTANKVQVDTS | — | — | — | C | C |
585 | GHIFVKVTPKPTGAA | GHVFVKVTPKPTGAA | — | — | C + T | — |
586 | HIFVKVTPKPTGAAN | HVFVKVTPKPTGAAN | — | — | C + T | — |
648 | DENGQYQVNVNSGDI | DENGQYQINTTSADL | C + T | T | — | — |
649 | ENGQYQVNVNSGDIT | ENGQYQINTTSADLA | C + T | C + T | — | — |
650 | NGQYQVNVNSGDITR | NGQYQINTTSADLAR | C + T | C + T | — | — |
651 | — | GQYQINTTSADLARL | T | T | — | — |
661 | DITRLYMTKRAPRTN | — | — | — | C | — |
Total peptides | 17 | 13 | 10 | 8 |
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Chacón, R.D.; Sánchez-Llatas, C.J.; da Costa, A.C.; Valdeiglesias Ichillumpa, S.; Cea-Callejo, P.; Marín-Sánchez, O.; Astolfi-Ferreira, C.S.; Santander-Parra, S.; Nuñez, L.F.N.; Piantino Ferreira, A.J. Molecular and Evolutionary Characteristics of Chicken Parvovirus (ChPV) Genomes Detected in Chickens with Runting–Stunting Syndrome. Viruses 2024, 16, 1389. https://doi.org/10.3390/v16091389
Chacón RD, Sánchez-Llatas CJ, da Costa AC, Valdeiglesias Ichillumpa S, Cea-Callejo P, Marín-Sánchez O, Astolfi-Ferreira CS, Santander-Parra S, Nuñez LFN, Piantino Ferreira AJ. Molecular and Evolutionary Characteristics of Chicken Parvovirus (ChPV) Genomes Detected in Chickens with Runting–Stunting Syndrome. Viruses. 2024; 16(9):1389. https://doi.org/10.3390/v16091389
Chicago/Turabian StyleChacón, Ruy D., Christian J. Sánchez-Llatas, Antonio Charlys da Costa, Stefhany Valdeiglesias Ichillumpa, Pablo Cea-Callejo, Obert Marín-Sánchez, Claudete S. Astolfi-Ferreira, Silvana Santander-Parra, Luis F. N. Nuñez, and Antonio J. Piantino Ferreira. 2024. "Molecular and Evolutionary Characteristics of Chicken Parvovirus (ChPV) Genomes Detected in Chickens with Runting–Stunting Syndrome" Viruses 16, no. 9: 1389. https://doi.org/10.3390/v16091389