Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease
Abstract
:1. Introduction
2. Materials and Methods
2.1. Viral Metagenomics
2.2. PCR and Sequencing
2.3. Quantitative Real-Time PCR (qPCR)
2.4. Case Control Study
3. Results
3.1. Viral Metagenomics
3.1.1. Orthomyxoviridae
3.1.2. Coronaviridae
3.1.3. Tobaniviridae
3.1.4. Flaviviridae
3.1.5. Picornaviridae
3.1.6. Parvoviridae
- Bocoparvovirus
- Erythroparvovirus
- Copiparvovirus
3.1.7. Polyomaviridae
3.1.8. Papillomaviridae
3.2. Case–Control Study of Virus Detection: BRD Cases versus Control Animals
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Target Pathogen | Name | Primer/Probe Sequence 5′-3′ 1 |
---|---|---|
Bovine nidovirus | BNV_Fwd | GTCAACTGGAGTAGGTCGAAAG |
BNV_Rev | TCAGCCTCATTCCTAACATCAC | |
BNV_Probe | TEX615-AGGTACCATTACTATACTGAGCTGGCAGC-BHQ-2 | |
Bovine rhinitis A virus | BRAV_Fwd | AGGTACCCGGAGGTAACAA |
BRAV_Rev | GGTGCCTGATGAGACATAGAAG | |
BRAV_Probe | 6FAM-CCCAGGTCAGATCCAGAGTGTCAC-BHQ-1 | |
Bovine rhinitis B virus | BRBV_Fwd | GCGATTGTGTCCTAGGGTTT |
BRBV_Rev | GCCACTGAGGTTAGCTTCTC | |
BRBV_Probe | Cy5-CTGTCCTTTGCACGGCGTGG-BHQ-2 2 | |
Influenza D virus | IDV_Fwd | GAGGAATGCTGATGGGAATGT |
IDV_Reverse | CTTTGTAGCCCAGTCCAGTAAC | |
IDV_Probe | HEX-ATTACAGGGAGGAAGCATTGGCCA-BHQ-1 | |
Ungulate bocaparvovirus 6 | UBPV6_Fwd | GGGAAGAGTGGCTTCAGTTTAG |
UBPV6_Rev | GGCTCTTCTCCTTGTTCTTCTG | |
UBPV6_Probe | HEX-TCCAGATACAATCAGAAGAAGCGCCA-ZEN/IABkFQ |
IDV Sequence Data (Current Study) | IDV Reference | |||||||
---|---|---|---|---|---|---|---|---|
Segment | Protein | Length (nt) | Coverage (%) | Nucleotide Identity (%) | Amino Acid Similarity (%) | GenBank | Length (nt) | Reference Accession |
1 | polymerase PB2 | 1054 | 44.6% | 98.0 | 99.2 | OQ348274 | 2364 | LC270265.1 |
2 | polymerase PB1 | 929 | 39.9% | 98.5 | 99.7 | OQ348275 | 2330 | LC270266.1 |
3 | polymerase 3 P3 | 918 | 41.0% | 98.4 | 98.7 | OQ348276 | 2195 | LC270267.1 |
4 | haemagglutinin-esterase HE | 248 | 12.1% | 94.8 | 92.7 | OQ348277 | 2049 | LC270268.1 |
5 | nucleoprotein | NT 1 | 1775 | LC270269.1 | ||||
6 | P42 | NT 1 | 1219 | LC270270.1 | ||||
7 | non-structural protein 2 | NT 1 | 868 | LC270271.1 |
Open Reading Frame | BCoV-Aus Bases | BCoV-ENT Bases; Identity (%) | BuCoV B1-28F Bases; Identity (%) |
---|---|---|---|
Complete genome | 30,999 | 31,028; 98.9 | 30,985; 98.5 |
orf 1ab polyprotein | 21,278 | 21,284; 99.1 | 21,284; 98.4 |
32 kDa nonstructural protein | 837 | 837; 98.7 | 837; 98.1 |
haemaglutinin esterase (HE) | 1275 | 1275; 99.1 | 1275; 97.7 |
spike structural protein (S) | 4092 | 4092; 98.3 | 4092; 98.8 |
4.9 kDa nonstructural protein | 89 | 90; 92.2 | 78; 100 |
4.8 kDa nonstructural protein | 142 | 138; 85.6 | 135; 90.2 |
12.7 kDa nonstructural protein | 330 | 330; 98.5 | 330; 99.4 |
small membrane protein (E) | 255 | 255; 100 | 255; 99.6 |
matrix protein (M) | 693 | 693; 98.7 | 693; 100 |
nucleocapsid protein (N) | 1347 | 1347; 98.7 | 1347; 99.5 |
internal protein (I) | 624 | 624; 98.7 | 624; 99.5 |
Characteristic | BNV-Aus | BNV TCH5 | Nucleotide Identity (%) | Amino Acid Similarity (%) |
---|---|---|---|---|
complete genome | 20,262 | 20,261 | 85.9 | |
replicase polyprotein (pp1a/b) | 15,323 | 15,332 | 87.2 | 90.5 |
glycoprotein S (S) | 1686 | 1689 | 81.9 | 83.5 |
membrane protein 1 (M1) | 696 | 696 | 87.2 | 91.8 |
nucleocapsid (N) | 534 | 537 | 85.8 | 86.5 |
glycoprotein G2 (G2) | 1371 | 1368 | 75.6 | 64.1 |
hypothetical protein | 267 | 267 | 94.8 | 92.0 |
Risk Factor | qPCR Result | Cases (%) | Controls (%) | OR | 95%CI | p Value |
---|---|---|---|---|---|---|
Infected with one or more virus | Positive | 61 (43.3) | 35 (23.8) | 2.4 | 1.5–4.0 | 0.0005 |
Negative | 80 (56.7) | 112 (76.2) | ||||
Bovine herpesvirus 1 | Positive | 19 (13.5) | 0 (0) | 47 | 2.8–785.8 | 0.0074 |
Negative | 122 (86.5) | 147 (100) | ||||
Bovine coronavirus | Positive | 2 (1.4) | 3 (2.0) | 0.7 | 0.1–4.2 | 0.7 |
Negative | 139 (98.6) | 144 (98.0) | ||||
Bovine respiratory syncytial virus | Positive | 6 (4.3) | 2 (1.4) | 3.2 | 0.6–16.2 | 0.2 |
Negative | 135 (95.7) | 147 (98.6) | ||||
Bovine parainfluenza virus | Positive | 1 (0.7) | 0 (0) | 3.1 | 0.1–78 | 0.5 |
Negative | 140 (99.3) | 147 (100) | ||||
Bovine viral diarrhoea virus 1 | Positive | 3 (2.1) | 0 (0) | 7.5 | 0.4–145.6 | 0.2 |
Negative | 138 (97.9) | 147 (100) | ||||
Influenza D virus | Positive | 16 (11.3) | 10 (6.8) | 1.8 | 0.8–4.0 | 0.2 |
Negative | 125 (88.7) | 137 (93.2) | ||||
Bovine rhinitis A virus | Positive | 3 (2.1) | 9 (6.1) | 0.3 | 0.1–1.3 | 0.1 |
Negative | 138 (97.9) | 138 (93.9) | ||||
Bovine rhinitis B virus | Positive | 0 (0) | 0 (0) | Not carried out | - | - |
Negative | 141 (100) | 147(100) | ||||
Bovine nidovirus | Positive | 15 (10.6) | 14 (9.5) | 1.1 | 0.5–2.4 | 0.8 |
Negative | 126 (89.4) | 133 (90.5) | ||||
Ungulate bocaparvovirus 6 | Positive | 8 (5.7) | 2 (1.4) | 4.4 | 0.9–20.9 | 0.07 |
Negative | 133 (94.3) | 145 (98.6) |
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Ambrose, R.K.; Blakebrough-Hall, C.; Gravel, J.L.; Gonzalez, L.A.; Mahony, T.J. Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease. Viruses 2023, 15, 455. https://doi.org/10.3390/v15020455
Ambrose RK, Blakebrough-Hall C, Gravel JL, Gonzalez LA, Mahony TJ. Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease. Viruses. 2023; 15(2):455. https://doi.org/10.3390/v15020455
Chicago/Turabian StyleAmbrose, Rebecca K., Claudia Blakebrough-Hall, Jennifer L. Gravel, Luciano A. Gonzalez, and Timothy J. Mahony. 2023. "Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease" Viruses 15, no. 2: 455. https://doi.org/10.3390/v15020455
APA StyleAmbrose, R. K., Blakebrough-Hall, C., Gravel, J. L., Gonzalez, L. A., & Mahony, T. J. (2023). Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease. Viruses, 15(2), 455. https://doi.org/10.3390/v15020455