Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination
Abstract
:1. Introduction
2. Materials and Methods
2.1. Virus Isolation
2.2. RNA Extraction and Complementary Deoxyribonucleic Acid (cDNA) Synthesis
2.3. Real-Time PCR and Sequencing
2.4. Genotyping and Comparison of S1 Gene Sequences
2.5. Characteristics of the Complete Genome
2.6. Recombination Analysis
2.7. GenBank Accession Numbers
3. Results
3.1. Phylogenetic Analysis and Sequence Comparison Based on the S1 Gene
3.2. Complete Genome Sequences
3.3. Recombination Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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IBV Isolate | Type of Sample | Commodity | Age | Size of the Flock | Main Complaint |
---|---|---|---|---|---|
IBV/Ck/Can/17-035614 | Cecal tonsils | Layers | 6 weeks | 100,000 | Uneven flock |
IBV/Ck/Can/17-036989 | Kidneys | Layers | 22 weeks | NA | Drop in egg production |
IBV/Ck/Can/18-048192T | Trachea | Broilers | NA | NA | NA |
IBV/Ck/Can/18-048430 | Tracheal swab | Broilers | 34 days | 9408 | Routine sampling |
IBV/Ck/Can/18-049707 | Cecal tonsils | Broiler breeders | 41 weeks | 20,358 | Increased mortality |
Nucleotide Identity (%) | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18-048192T | 18-049707 | 18-048430 | 17-036989 | 17-035614 | DMV/1639 | PA/Wolg/98 | Qu-mv | Conn | Mass | 4/91 | CAL1737 | CU_82792 | DE/072 | ||
Amino Acid Identity (%) | 18-048192T | 99.5 | 99.8 | 99.4 | 99.7 | 96.5 | 90.1 | 78.8 | 77.2 | 77.2 | 76.0 | 76.5 | 56.4 | 55.8 | |
18-049707 | 99.3 | 99.6 | 99.9 | 99.7 | 96.5 | 90.1 | 78.6 | 77.2 | 77.2 | 75.8 | 76.2 | 56.3 | 55.6 | ||
18-048430 | 99.6 | 99.3 | 99.5 | 99.8 | 96.4 | 89.9 | 78.7 | 77.2 | 77.2 | 75.3 | 76.4 | 56.4 | 55.8 | ||
17-036989 | 99.1 | 99.8 | 99.1 | 99.6 | 96.4 | 90.0 | 78.5 | 77.2 | 77.2 | 75.7 | 75.5 | 55.3 | 55.6 | ||
17-035614 | 99.4 | 99.4 | 99.6 | 99.3 | 96.7 | 89.9 | 78.6 | 77.3 | 77.3 | 75.8 | 76.1 | 56.3 | 55.6 | ||
DMV/1639 | 94.8 | 95.2 | 95.0 | 95.0 | 95.3 | 91.1 | 79.7 | 78.4 | 78.4 | 76.2 | 75.1 | 56.0 | 55.3 | ||
PA/Wolg/98 | 87.5 | 87.3 | 87.1 | 87.1 | 87.1 | 87.5 | 79.6 | 78.6 | 78.6 | 76.3 | 76.1 | 56.5 | 56.0 | ||
Qu-mv | 76.3 | 76.1 | 76.1 | 75.9 | 75.9 | 75.9 | 76.1 | 78.6 | 79.3 | 77.0 | 75.9 | 57.2 | 56.8 | ||
Conn 46 | 75.5 | 76.9 | 75.6 | 75.5 | 75.6 | 75.3 | 75.7 | 74.3 | 95.1 | 77.6 | 80.3 | 58.7 | 57.9 | ||
M41 | 73.0 | 73.3 | 73.2 | 73.2 | 73.3 | 73.4 | 73.9 | 74.2 | 90.3 | 78.3 | 80.6 | 58.6 | 57.9 | ||
4/91 | 75.5 | 75.5 | 75.3 | 75.3 | 75.3 | 74.7 | 74.4 | 75.1 | 73.9 | 73.8 | 77.2 | 56.2 | 55.8 | ||
CAL1737 | 72.8 | 72.8 | 72.7 | 72.7 | 72.8 | 71.2 | 71.6 | 72.3 | 77.6 | 78.3 | 74.4 | 57.6 | 57.2 | ||
CU_82792 | 45.2 | 45.5 | 45.4 | 45.5 | 45.4 | 44.6 | 46.1 | 48..0 | 48.4 | 49.3 | 45.3 | 47.1 | 96.3 | ||
DE/072 | 45.7 | 45.9 | 45.9 | 45.9 | 45.9 | 45.0 | 46.6 | 47.8 | 48.8 | 49.5 | 45.5 | 48.0 | 93.6 |
IBV/Ck/Can/17-035614 | IBV/Ck/Can/17-036989 | IBV/Ck/Can/18-048192T | IBV/Ck/Can/18-048430 | IBV/Ck/Can/18-049707 | |
---|---|---|---|---|---|
5′UTR | 1–530 (530 nt) | 1–528 (528 nt) | 1–528 (528 nt) | 1–528 (528 nt) | 1–528 (528 nt) |
1a | 531–12,419 (11889 nta-3962 aab) | 529–12,417 (11889 nt-3962 aa) | 529–12,360 (11832 nt-3943 aa) | 529–12,393 (11865 nt-3954 aa) | 529–12,417 (11889 nt-3962 aa) |
1ab | 531–20,452 (19922 nt-6639 aa) | 529–20,450 (19922 nt-6639 aa) | 529–20,393 (19865 nt-6620 aa) | 529–20,426 (19898 nt-6631 aa) | 529–20,450 (19922 nt-6639 aa) |
S | 20,403–23,903 (3501 nt-1166 aa) | 20,401–23,901 (3501 nt-1166 aa) | 20,344–23,844 (3501 nt-1166 aa) | 20,377–23,877 (3501 nt-1166 aa) | 20,401–23,901 (3501 nt-1166 aa) |
3a | 23,903–24,076 (174 nt-57 aa) | 23,901–24,074 (174 nt-57 aa) | 23,844–24,017 (174 nt-57 aa) | 23,877–24,050 (174 nt-57 aa) | 23,901–24,074 (174 nt-57 aa) |
3b | 24,076–24,270 (195 nt-64 aa) | 24,074–24,268 (195 nt-64 aa) | 24,017–24,211 (195 nt-64 aa) | 24,050–24,244 (195 nt-64 aa) | 24,074–24,268 (195 nt-64 aa) |
E | 24,251–24,580 (330 nt-109 aa) | 24,249–24,578 (330 nt-109 aa) | 24,192–24,521 (330 nt-109 aa) | 24,225–24,554 (330 nt-109 aa) | 24,249–24,578 (330 nt-109 aa) |
M | 24,552–25,229 (678 nt-225 aa) | 24,550–25,227 (678 nt-225 aa) | 24,493–25,170 (678 nt-225 aa) | 24,526–25,203 (678 nt-225 aa) | 24,550–25,227 (678 nt-225 aa) |
4b | 25,230–25,514 (285 nt-94 aa) | 25,228–25,512 (285 nt-94 aa) | 25,171–25,455 (285 nt-94 aa) | 25,204–25,488 (285 nt-94 aa) | 25,228–25,512 (285 nt-94 aa) |
4c | 25,435–25,605 (171 nt-56 aa) | 25,433–25,603 (171 nt-56 aa) | 25,376–25,546 (171 nt-56 aa) | 25,409–25,579 (171 nt-56 aa) | 25,433–25,603 (171 nt-56 aa) |
5a | 25,589–25,786 (198 nt-65 aa) | 25,587–25,784 (198 nt-65 aa) | 25,530–25,727 (198 nt-65 aa) | 25,563–25,760 (198 nt-65 aa) | 25,587–25,784 (198 nt-65 aa) |
5b | 25,783–26,031 (249 nt-82 aa) | 25,781–26,029 (249 nt-82 aa) | 25,724–25,972 (249 nt-82 aa) | 25,757–26,005 (249 nt-82 aa) | 25,781–26,029 (249 nt-82 aa) |
N | 25,974–27,203 (1230 nt-409 aa) | 25,972–27,201 (1230 nt-409 aa) | 25,915–27,144 (1230 nt-409 aa) | 25,948–27,177 (1230 nt-409 aa) | 25,972–27,201 (1230 nt-409 aa) |
6b | 27,212–27,436 (225 nt-74 aa) | 27,210–27,434 (225 nt-74 aa) | 27,153–27296 (144 nt-47 aa) | 27,186–27,410 (225 nt-74 aa) | 27210–27,434 (225 nt-74 aa) |
3′UTR | 27,437–27,710 (274 nt) | 27,435–27,708 (274 nt) | 27,297–27,638 (342 nt) | 27,411–27,684 (274 nt) | 27,435–27,708 (274 nt) |
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Hassan, M.S.H.; Ojkic, D.; Coffin, C.S.; Cork, S.C.; van der Meer, F.; Abdul-Careem, M.F. Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination. Viruses 2019, 11, 1054. https://doi.org/10.3390/v11111054
Hassan MSH, Ojkic D, Coffin CS, Cork SC, van der Meer F, Abdul-Careem MF. Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination. Viruses. 2019; 11(11):1054. https://doi.org/10.3390/v11111054
Chicago/Turabian StyleHassan, Mohamed S. H., Davor Ojkic, Carla S. Coffin, Susan C. Cork, Frank van der Meer, and Mohamed Faizal Abdul-Careem. 2019. "Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination" Viruses 11, no. 11: 1054. https://doi.org/10.3390/v11111054