Genetic and Antigenic Characterization and Retrospective Surveillance of Bovine Influenza D Viruses Identified in Hokkaido, Japan from 2018 to 2020
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples, RNA Extraction, Diagnostic Test, and Ethics Statement
2.2. Cell Culture, Virus Isolation, and Velification
2.3. Sequence and Phylogenetic Analyses
2.4. Comparison of Antigenicity between Two BIDV Isolates Using A Neutralization Assay
2.5. Retrospective Surveillance
3. Results
3.1. Diagnosis of Cattle from Three BRD Outbreaks
3.2. Sequence and Phylogenetic Analyses
3.3. Comparison of Antigenicity between Two BIDV Isolates Using Neutralization Assay
3.4. Retrospective Surveillance
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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BRD Outbreaks | Age [Days] | RT-PCR | qRT-PCR | Virus Isolation | Bacteria Isolation | |||||
---|---|---|---|---|---|---|---|---|---|---|
BVDV | BRSV | BCoV | BIDV | Mycoplasma bovis | Pasteurella multocida | Mannheimia haemolytica | ||||
1 | 1 | 70 | − | − | − | − | − | − | + | − |
2 | 70 | − | − | − | − | BPIV3 | + | + | − | |
3 | 73 | − | + | + | − | BCoV | − | + | − | |
4 | 74 | − | − | − | + | − | − | + | − | |
5 | 82 | − | − | + | + | BIDV (HKD1) | − | + | − | |
2 | 1 | 90 | − | − | − | + | BIDV (HKD2) | − | − | − |
2 | 100 | − | + | − | + | BIDV | − | − | − | |
3 | 131 | − | + | − | + | − | − | − | + | |
4 | 123 | − | − | − | + | BIDV | − | − | − | |
5 | 114 | − | − | − | + | − | − | − | − | |
3 | 1 | 99 | − | − | − | − | − | + | − | − |
2 | 42 | − | − | + | − | BCoV | + | − | − | |
3 | 63 | − | + | + | + | − | + | − | + | |
4 | 35 | − | + | + | − | − | − | − | − | |
5 | 55 | − | + | + | + | BIDV (HKD3) | − | − | + | |
6 | 61 | − | − | + | − | − | + | + | − |
PB1 | PB2 | P3 | HEF | NP | M | NS | |
---|---|---|---|---|---|---|---|
Within three BIDVs | 95.9–97.4 | 96.7–98.8 | 97.7–98.7 | 92.5–98.5 | 97.4–98.3 | 96.8–98.6 | 97.3–98.6 |
vs. other BIDVs detected in Japan | 96.4–99.1 | 96.8–98.9 | 97.7–99.4 | 93.6–98.2 | 97.7–99.3 | 96.8–99.5 | 97.1–99.5 |
vs. other IDVs detected in other countries | 94.6–96.3 | 94.2–95.9 | 95.0–96.4 | 93.0–95.1 | 94.1–96.3 | 94.9–97.9 | 95.2–97.1 |
Strains | Genes | PB2 | PB1 | P3 | HEF | NP | M | NS |
---|---|---|---|---|---|---|---|---|
Cut-off Value (%) | 97.5 | 97.2 | 97.6 | 97.4 | 98.1 | 97.8 | 98.1 | |
Total Number of Genotypes | 5 | 4 | 5 | 6 | 7 | 4 | 5 | |
D/bovine/Hokkaido/HKD1/2018 | genotype 4 | genotype 3 | genotype 4 | genotype 5 | genotype 6 | genotype 4 | genotype 4 | |
D/bovine/Hokkaido/HKD2/2019 | genotype 5 | genotype 3 | genotype 5 | genotype 6 | genotype 7 | genotype 4 | genotype 5 | |
D/bovine/Hokkaido/HKD3/2020 | genotype 5 | genotype 4 | genotype 5 | genotype 6 | genotype 7 | genotype 4 | genotype 5 | |
D/bovine/Ibaraki/7768/2016 | genotype 4 | genotype 3 | genotype 4 | genotype 5 | genotype 6 | genotype 4 | genotype 4 | |
D/swine/Oklahoma/1334/2011 | genotype 1 | genotype 1 | genotype 1 | genotype 1 | genotype 1 | genotype 1 | genotype 1 | |
D/bovine/Oklahoma/660/2013 | genotype 2 | genotype 1 | genotype 1 | genotype 3 | genotype 2 | genotype 2 | genotype 1 | |
D/bovine/France/2986/2012 | genotype 3 | genotype 1 | genotype 3 | genotype 2 | genotype 3 | genotype 1 | genotype 2 | |
D/bovine /Shandong/Y125/2014 | genotype 3 | genotype 2 | genotype 1 | genotype 1 | genotype 4 | genotype 3 | genotype 3 |
Viral Neutralizing Antibody Titers for Serum Samples from Farm A | Viral Neutralizing Antibody Titers for Serum Samples from Farm B | ||||||||
---|---|---|---|---|---|---|---|---|---|
Sample Number | HKD1 Isolate | HKD2 Isolate | Sample Number | HKD1 Isolate | HKD2 Isolate | ||||
Pre | Post | Pre | Post | Pre | Post | Pre | Post | ||
1 | 64 | 512 | 128 | 128 | 1 | <2 | 4 | <2 | 64 |
2 | 8 | 256 | 8 | 16 | 2 | <2 | 4 | <2 | 64 |
3 | 8 | 128 | 16 | 32 | 3 | 2 | 2 | 32 | 128 |
4 | 32 | 4096 | 32 | 512 | 4 | <2 | 8 | <2 | 128 |
5 | 32 | 256 | 64 | 64 | 5 | 2 | 4 | 8 | 128 |
6 | 64 | 512 | 64 | 64 | |||||
7 | <2 | 32 | <2 | 4 | |||||
8 | 8 | 64 | 16 | 16 |
Collection Year | Viral Neutralizing Antibody Titers Against HKD1 | Total Number of Positive Samples | Ratio of Positive Samples (%) | Total Number of Samples | |||||
<10 (Negative) | 10 | 20 | 40 | 80 | ≥160 | ||||
2009 | 53 | 2 | 6 | 6 | 9 | 20 | 43 | 45 | 96 |
2010 | 37 | 1 | 4 | 13 | 14 | 27 | 59 | 61 | 96 |
2011 | 31 | 3 | 6 | 11 | 13 | 32 | 65 | 68 | 96 |
2012 | 40 | 0 | 6 | 9 | 13 | 28 | 56 | 58 | 96 |
2013 | 39 | 3 | 1 | 9 | 11 | 33 | 57 | 59 | 96 |
2014 | 37 | 4 | 6 | 11 | 7 | 31 | 59 | 61 | 96 |
2015 | 51 | 3 | 1 | 9 | 7 | 25 | 45 | 47 | 96 |
2016 | 52 | 0 | 3 | 9 | 7 | 25 | 44 | 46 | 96 |
2017 | 50 | 3 | 1 | 3 | 11 | 38 | 46 | 48 | 96 |
2018 | 39 | 1 | 1 | 1 | 11 | 43 | 57 | 59 | 96 |
Total | 429 | 20 | 35 | 81 | 103 | 292 | 531 | 55 | 960 |
Collection Year | Viral Neutralizing Antibody Titers Against HKD2 | Total Number of Positive Samples | Ratio of Positive Samples | Total Number of Samples | |||||
<10 (Negative) | 10 | 20 | 40 | 80 | ≥160 | ||||
2009 | 53 | 6 | 9 | 9 | 10 | 9 | 43 | 45 | 96 |
2010 | 33 | 0 | 1 | 16 | 17 | 29 | 63 | 66 | 96 |
2011 | 28 | 2 | 9 | 8 | 18 | 31 | 68 | 71 | 96 |
2012 | 39 | 0 | 3 | 10 | 20 | 24 | 57 | 59 | 96 |
2013 | 38 | 4 | 1 | 10 | 8 | 35 | 58 | 60 | 96 |
2014 | 36 | 3 | 6 | 7 | 11 | 33 | 60 | 63 | 96 |
2015 | 52 | 1 | 6 | 10 | 8 | 19 | 44 | 46 | 96 |
2016 | 50 | 1 | 5 | 5 | 9 | 26 | 46 | 48 | 96 |
2017 | 47 | 5 | 3 | 2 | 8 | 31 | 49 | 51 | 96 |
2018 | 37 | 2 | 4 | 5 | 6 | 42 | 59 | 61 | 96 |
Total | 413 | 24 | 47 | 82 | 115 | 279 | 547 | 57 | 960 |
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Hayakawa, J.; Masuko, T.; Takehana, T.; Suzuki, T. Genetic and Antigenic Characterization and Retrospective Surveillance of Bovine Influenza D Viruses Identified in Hokkaido, Japan from 2018 to 2020. Viruses 2020, 12, 877. https://doi.org/10.3390/v12080877
Hayakawa J, Masuko T, Takehana T, Suzuki T. Genetic and Antigenic Characterization and Retrospective Surveillance of Bovine Influenza D Viruses Identified in Hokkaido, Japan from 2018 to 2020. Viruses. 2020; 12(8):877. https://doi.org/10.3390/v12080877
Chicago/Turabian StyleHayakawa, Jun, Tomomi Masuko, Tae Takehana, and Tohru Suzuki. 2020. "Genetic and Antigenic Characterization and Retrospective Surveillance of Bovine Influenza D Viruses Identified in Hokkaido, Japan from 2018 to 2020" Viruses 12, no. 8: 877. https://doi.org/10.3390/v12080877