Genetic Characterization and Evolution of Porcine Deltacoronavirus Isolated in the Republic of Korea in 2022
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and RNA Extraction
2.2. Detection of Enteric Pathogens
2.3. Isolation and Genome Sequencing of PDCoV
2.4. Phylogenetic and Molecular Evolutionary Analyses
3. Results
3.1. Detection and Isolation of KPDCoV-2201
3.2. Full-Length Genomic Characterization of KPDCoV-2201
3.3. Phylogenetic and Molecular Evolutionary Analyses
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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Sample | Age | Results of Real-Time Reverse Transcription PCR (qRT-PCR) | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
PEDV | PEAV | TGEV | PToV | PDCoV | SADS | PSV | GARV | GBRV | GCRV | ||
Feces | 4 days | N/A | N/A | N/A | N/A | 24.75 | N/A | N/A | N/A | N/A | N/A |
Feces | 4 days | N/A | N/A | N/A | N/A | 21.08 | N/A | N/A | N/A | N/A | N/A |
Feces | 4 days | N/A | N/A | N/A | N/A | 19.04 | N/A | N/A | N/A | N/A | N/A |
Feces | 4 days | N/A | N/A | N/A | N/A | 19.87 | N/A | N/A | N/A | N/A | N/A |
Feces | 4 days | N/A | N/A | N/A | N/A | 21.84 | N/A | N/A | N/A | N/A | N/A |
Feces | 4 days | N/A | N/A | N/A | N/A | 21.96 | N/A | N/A | N/A | N/A | N/A |
Feces | Sow | N/A | N/A | N/A | N/A | 30.32 | N/A | N/A | N/A | N/A | N/A |
Feces | Sow | N/A | N/A | N/A | N/A | 32.29 | N/A | N/A | N/A | N/A | N/A |
Intestine | 4 days | N/A | N/A | N/A | N/A | 14.45 | N/A | N/A | N/A | N/A | N/A |
Strain/Year | Genbank Accession Number | Country | Full-Length * | 5′-UTR | ORF1a | ORF1b | S | E | M | NS6 | N | NS7 | 3′-UTR |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
% Identity to KPDCoV-2201 | |||||||||||||
KNU14-04/2014 | KM820765 | Korea | 99.2 | 99.3 | 99.2 | 99.3 | 98.8 | 98.8 | 99.7 | 98.9 | 98.8 | 98.8 | 98.0 |
KNU16-07/2016 | KY364365 | Korea | 99.2 | 99.3 | 99.2 | 99.3 | 98.7 | 98.8 | 99.7 | 98.9 | 98.5 | 98.3 | 98.2 |
KNU16-11/2016 | KY926512 | Korea | 98.7 | 98.5 | 98.9 | 98.9 | 97.9 | 98.4 | 99.8 | 98.6 | 97.9 | 97.5 | 97.4 |
DH1/2016 | KY354363 | Korea | 99.1 | 99.1 | 99.2 | 99.2 | 98.6 | 98.8 | 99.7 | 99.6 | 98.8 | 98.7 | 98.2 |
DH2/2016 | KY354364 | Korea | 99.1 | 99.1 | 99.2 | 99.2 | 98.6 | 98.8 | 99.7 | 99.6 | 98.8 | 98.7 | 98.2 |
AH2004/2004 | KP757890 | China | 98.4 | 99.1 | 98.4 | 98.8 | 97.4 | 97.6 | 98.9 | 98.9 | 97.7 | 97.8 | 97.5 |
HKU15-155/2010 | NC_039208 | China | 98.6 | 98.8 | 98.7 | 98.9 | 97.6 | 98.4 | 99.1 | 98.2 | 98.3 | 98.2 | 98.0 |
Sichuan/2019 | MK993519 | China | 97.7 | 98.3 | 97.5 | 98.2 | 97.4 | 98.4 | 98.5 | 98.6 | 97.9 | 98.0 | 94.9 |
IL2768/2014 | KJ584355 | United States | 99.2 | 99.3 | 99.3 | 99.3 | 98.8 | 98.8 | 99.8 | 99.3 | 98.6 | 98.3 | 98.2 |
YMG/2014 | LC260044 | Japan | 99.2 | † | 99.3 | 99.4 | 98.8 | 98.8 | 99.8 | 98.9 | 98.8 | 98.8 | 98.2 |
HaNoi6/2015 | KX834351 | Vietnam | 97.8 | 98.0 | 96.9 | 97.8 | 96.1 | 98.8 | 98.9 | 98.6 | 98.2 | 97.7 | 98.0 |
S5015L/2015 | KU051649 | Thailand | 96.9 | 98.5 | 96.7 | 97.5 | 95.8 | 98.4 | 98.3 | 98.2 | 96.5 | 96.7 | 95.9 |
P1_16_BTL_0115/2016 | KX118627 | Laos | 97.0 | 98.3 | 96.7 | 97.6 | 96.0 | 98.4 | 98.3 | 98.2 | 97.8 | 97.2 | 95.9 |
Peru_isolate_2019/2019 | MT227371 | Peru | 99.2 | † | 99.3 | 99.3 | 98.6 | 99.2 | 100 | 99.6 | 98.9 | 98.8 | † |
NTU_C253_21/2021 | OM777140 | Taiwan | 99.0 | † | 99.1 | 99.1 | 98.5 | 98.8 | 99.8 | 98.9 | 98.8 | 98.5 | 98.5 |
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Kim, H.-R.; Park, J.; Lee, K.-K.; Jeoung, H.-Y.; Lyoo, Y.S.; Park, S.-C.; Park, C.-K. Genetic Characterization and Evolution of Porcine Deltacoronavirus Isolated in the Republic of Korea in 2022. Pathogens 2023, 12, 686. https://doi.org/10.3390/pathogens12050686
Kim H-R, Park J, Lee K-K, Jeoung H-Y, Lyoo YS, Park S-C, Park C-K. Genetic Characterization and Evolution of Porcine Deltacoronavirus Isolated in the Republic of Korea in 2022. Pathogens. 2023; 12(5):686. https://doi.org/10.3390/pathogens12050686
Chicago/Turabian StyleKim, Hye-Ryung, Jonghyun Park, Kyoung-Ki Lee, Hye-Young Jeoung, Young S. Lyoo, Seung-Chun Park, and Choi-Kyu Park. 2023. "Genetic Characterization and Evolution of Porcine Deltacoronavirus Isolated in the Republic of Korea in 2022" Pathogens 12, no. 5: 686. https://doi.org/10.3390/pathogens12050686
APA StyleKim, H. -R., Park, J., Lee, K. -K., Jeoung, H. -Y., Lyoo, Y. S., Park, S. -C., & Park, C. -K. (2023). Genetic Characterization and Evolution of Porcine Deltacoronavirus Isolated in the Republic of Korea in 2022. Pathogens, 12(5), 686. https://doi.org/10.3390/pathogens12050686