First Detection and Genetic Characterization of Swine Orthopneumovirus from Domestic Pig Farms in the Republic of Korea
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and RNA Extraction
2.2. Detection of SOV and other Pathogens
2.3. Genome Sequencing of SOV
2.4. Multiple Alignment and Phylogenetic Analysis
3. Results and Discussion
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Allan, G.M.; McNeilly, F.; Walker, I.W.; Young, J.A.; Fee, S.; Douglas, A.J.; Adair, B.M. Serological evidence for pneumovirus infections in pigs. Vet. Rec. 1998, 142, 8–12. [Google Scholar] [CrossRef] [PubMed]
- Hause, B.M.; Padmanabhan, A.; Pedersen, K.; Gidlewski, T. Feral swine virome is dominated by single-stranded DNA viruses and contains a novel Orthopneumovirus which circulates both in feral and domestic swine. J. Gen. Virol. 2016, 97, 2090–2095. [Google Scholar] [CrossRef] [PubMed]
- Renshaw, R.; Laverack, M.; Zylich, N.; Glaser, A.; Dubovi, E. Genomic analysis of a pneumovirus isolated from dogs with acute respiratory disease. Vet. Microbiol. 2011, 150, 88–95. [Google Scholar] [CrossRef] [PubMed]
- Martín-Valls, G.; Li, Y.; Díaz, I.; Cano, E.; Portugal, S.S.; Mateu, E. Diversity of respiratory viruses present in nasal swabs under influenza suspicion in respiratory disease cases of weaned pigs. Front. Vet. Sci. 2022, 9, 1014475. [Google Scholar] [CrossRef] [PubMed]
- Decaro, N.; Pinto, P.; Mari, V.; Elia, G.; Larocca, V.; Camero, M.; Terio, V.; Losurdo, M.; Martella, V.; Buonavoglia, C. Full-genome analysis of a canine pneumovirus causing acute respiratory disease in dogs, Italy. PLoS ONE 2014, 9, e85220. [Google Scholar] [CrossRef]
- Kim, H.R.; Park, J.; Kim, W.I.; Lyoo, Y.S.; Park, C.K. Prevalence and co-infection status of three pathogenic porcine circoviruses (PCV2, PCV3, and PCV4) by a newly established triplex real-time polymerase chain reaction assay. Korean J. Vet. Serv. 2022, 45, 87–99. [Google Scholar] [CrossRef]
- Kim, J.M.; Kim, H.R.; Jeon, G.T.; Baek, J.S.; Kwon, O.D.; Park, C.K. Molecular Detection of Porcine Parainfluenza Viruses 1 and 5 Using a Newly Developed Duplex Real-Time RT-PCR in South Korea. Animals 2023, 13, 598. [Google Scholar] [CrossRef] [PubMed]
- Katoh, K.; Standley, D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef] [PubMed]
- Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30, 1312–1313. [Google Scholar] [CrossRef] [PubMed]
- Park, J.; Kim, H.R.; Kim, J.M.; Lee, K.K.; Kim, W.I.; Lyoo, Y.S.; Kwon, O.D.; Park, C.K.; Park, S.C. First report of Porcine respirovirus 1 in South Korea. Transbound. Emerg. Dis. 2022, 69, 4041–4047. [Google Scholar] [CrossRef] [PubMed]
- Palinski, R.M.; Chen, Z.; Henningson, J.N.; Lang, Y.; Rowland, R.R.; Fang, Y.; Prickett, J.; Gauger, P.C.; Hause, B.M. Widespread detection and characterization of porcine parainfluenza virus 1 in pigs in the USA. J. Gen. Virol. 2016, 97, 281–286. [Google Scholar] [CrossRef] [PubMed]
- Woźniak, A.; Cybulski, P.; Denes, L.; Balka, G.; Stadejek, T. Detection of porcine respirovirus 1 (PRV1) in Poland: Incidence of co-infections with influenza A virus (IAV) and porcine reproductive and respiratory syndrome virus (PRRSV) in herds with a respiratory disease. Viruses 2022, 14, 148. [Google Scholar] [CrossRef] [PubMed]
- Richard, C.A.; Hervet, C.; Ménard, D.; Gutsche, I.; Normand, V.; Renois, F.; Meurens, F.; Eléouët, J.F. First demonstration of the circulation of a pneumovirus in French pigs by detection of anti-swine orthopneumovirus nucleoprotein antibodies. Vet. Res. 2018, 49, 118. [Google Scholar] [CrossRef] [PubMed]
- Battles, M.B.; McLellan, J.S. Respiratory syncytial virus entry and how to block it. Nat. Rev. Microbiol. 2019, 17, 233–245. [Google Scholar] [CrossRef] [PubMed]
- Pangesti, K.N.; Abd El Ghany, M.; Walsh, M.G.; Kesson, A.M.; Hill-Cawthorne, G.A. Molecular epidemiology of respiratory syncytial virus. Rev. Med. Virol. 2018, 28, e1968. [Google Scholar] [CrossRef] [PubMed]
- Glineur, S.F.; Renshaw, R.W.; Percopo, C.M.; Dyer, K.D.; Dubovi, E.J.; Domachowske, J.B.; Rosenberg, H.F. Novel pneumoviruses (PnVs): Evolution and inflammatory pathology. Virology 2013, 443, 257–264. [Google Scholar] [CrossRef]
Province | Farm | Age | Sample Type | SOV Detection (Ct Value) | Strain | Detection of Other Respiratory Pathogens |
---|---|---|---|---|---|---|
Chungcheongnam-do | CN1 | 5 weeks | Oral fluid | 27.32 | - | PRRSV-1 |
8 weeks | Oral fluid | 37.73 | - | PRRSV-1, PRRSV-2 | ||
9 weeks | Oral fluid | 35.93 | - | - | ||
4 weeks | Blood | NA | - | - | ||
8 weeks | Blood | NA | - | PRRSV-1, PRRSV-2 | ||
6 weeks | Lung tissue | NA | - | PRRSV-1, PRRSV-2, PCV2 | ||
6 weeks | Lymphoid tissue | NA | - | PRRSV-1, PRRSV-2, PCV2 | ||
Jeollabuk-do | JB2 | 4 weeks | Oral fluid | 25.13 | KSOV-2203 | PRV-1 |
5 weeks | Oral fluid | 28.8 | - | PRV-1 | ||
6 weeks | Oral fluid | 35.78 | - | PRV-1 | ||
7 weeks | Oral fluid | 38.74 | - | PRV-1 | ||
9 weeks | Oral fluid | NA | - | PRV-1 | ||
4 weeks | Lung tissue | NA | - | - | ||
6 weeks | Lung tissue | NA | - | - | ||
Jeollanam-do | JN5 | 4 weeks | Oral fluid | NA | - | PRRSV-1, PRV-1 |
6 weeks | Oral fluid | 24.92 | KSOV-2201 | PRRSV-2, PRV-1 | ||
7 weeks | Oral fluid | 30.37 | - | PRRSV-1, PRRSV-2, PRV-1 | ||
8 weeks | Oral fluid | 32.18 | - | PRRSV-1, PRRSV-2, PRV-1 | ||
9 weeks | Oral fluid | 36.57 | - | PRRSV-1, PRV-1 | ||
10 weeks | Oral fluid | 38.23 | - | PRRSV-1, PRV-1 | ||
reserve sows | Oral fluid | NA | - | - | ||
farrowing sows | Oral fluid | NA | - | PRRSV-1, PRRSV-2 | ||
1 week | Blood | NA | - | - | ||
2 weeks | Blood | NA | - | - | ||
3 weeks | Blood | NA | - | PRRSV-2 | ||
4 weeks | Blood | NA | - | - | ||
5 weeks | Blood | NA | - | - | ||
6 weeks | Blood | NA | - | PRRSV-2 | ||
7 weeks | Blood | NA | - | PRRSV-2 | ||
8 weeks | Blood | NA | - | PRRSV-2 | ||
Gyeongsangbuk-do | GB8 | 3 weeks | Oral fluid | 23.55 | KSOV-2202 | PCV2, PRV-1, MP |
7 weeks | Oral fluid | 29.26 | - | PCV2, PRV-1, MP | ||
9 weeks | Oral fluid | NA | - | PCV2, PRV-1, MP | ||
13 weeks | Oral fluid | NA | - | PCV2, PRV-1, MP |
Host/ | Complete | NS1 | NS2 | N | P | M | SH | G | F | M2-1 | M2-2 | L | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Strain | % Identity to KSOV-2201/KSOV-2202 | ||||||||||||
Mice/ J3666 | nt | 92.5/92.3 | 93.3/92.4 | 89.0/89.6 | 94.2/94.1 | 93.2/93.7 | 95.2/94.2 | 93.2/90.3 | 89.3/89.5 | 94.0/93.6 | 94.0/94.4 | 93.6/93.6 | 93.8/93.6 |
aa | 92.1/91.2 | 93.6/91.7 | 98.0/98.2 | 93.6/94.9 | 99.2/98.1 | 73.0/71.3 | 85.9/85.9 | 96.1/95.5 | 96.6/96.6 | 94.9/96.0 | 97.0/96.9 | ||
Mice/ mice_15 | nt | 92.3/92.2 | 93.3/92.4 | 89.0/89.6 | 94.3/94.2 | 92.7/93.1 | 94.8/93.7 | 90.3/87.5 | 89.0/89.4 | 93.9/93.5 | 94.0/94.4 | 93.6/93.6 | 93.8/93.6 |
aa | 92.1/91.2 | 93.6/91.7 | 98.2/98.5 | 92.6/93.6 | 98.4/97.3 | 82.8/80.6 | 86.3/85.7 | 96.1/95.5 | 96.6/96.6 | 94.9/96.0 | 97.0/96.8 | ||
Pig/Swine_pneumovirus_57 | nt | 98.2/95.4 | 91.0/89.5 | 98.1/94.9 | 98.8/96.4 | 98.2/95.7 | 99.5/96.9 | 99.6/96.1 | 97.3/93.9 | 99.2/97.1 | 99.4/97.4 | 99.0/96.3 | 99.3/96.6 |
aa | 87.4/84.0 | 98.7/93.6 | 99.2/98.7 | 98.0/97.3 | 100/98.8 | 100/95.7 | 94.9/92.3 | 99.3/98.1 | 99.4/98.3 | 100/96.0 | 99.4/97.9 | ||
Dog/ SMU-2020-CB19 | nt | 97.4/93.9 | 98.8/95.6 | 99.2/94.7 | 99.5/95.9 | 99.0/95.0 | 99.6/97.0 | 98.9/95.3 | 98.6/93.4 | 99.8/97.1 | 98.5/96.4 | 99.3/96.0 | 99.3/96.3 |
aa | 98.2/91.2 | 99.4/93.0 | 100/98.5 | 98.6/97.0 | 99.2/98.1 | 100/95.7 | 98.1/91.1 | 100/98.5 | 98.9/97.2 | 100/96.0 | 99.8/98.2 | ||
Dog/ Bari/100-12 | nt | 90.6/90.7 | 88.6/88.3 | 85.8/86.0 | 93.0/92.6 | 91.8/92.8 | 93.7/93.1 | 90.7/89.2 | 87.4/88.0 | 92.4/92.2 | 93.2/93.6 | 92.9/92.3 | 92.5/92.7 |
aa | 88.6/87.7 | 89.8/87.9 | 97.2/97.5 | 92.9/94.9 | 97.3/96.5 | 90.3/88.2 | 83.1/83.4 | 95.4/95.0 | 97.7/96.6 | 93.9/93.9 | 96.6/96.6 | ||
Dog/ CP_13_TH | nt | 90.7/90.8 | 88.6/88.3 | 87.3/87.5 | 92.9/92.5 | 92.0/92.6 | 93.7/93.0 | 91.8/91.0 | 86.9/87.4 | 92.4/92.1 | 93.2/93.2 | 93.3/91.9 | 92.4/92.6 |
aa | 87.7/86.8 | 90.4/88.5 | 98.2/98.5 | 92.9/94.6 | 97.7/96.9 | 91.4/89.2 | 82.2/82.9 | 95.2/94.8 | 97.7/96.6 | 93.9/93.9 | 96.8/96.7 | ||
Dog/ CP_82_TH | nt | 90.3/90.4 | 87.4/87.1 | 85.8/86.4 | 92.5/92.7 | 91.0/91.7 | 92.9/92.2 | 90.7/89.2 | 86.9/87.5 | 91.7/91.5 | 93.2/93.6 | 92.9/92.9 | 92.4/92.5 |
aa | 85.1/84.2 | 87.9/86.0 | 97.7/98.0 | 91.6/93.6 | 97.3/96.5 | 91.4/89.2 | 81.9/83.1 | 94.6/94.2 | 97.7/96.6 | 93.9/93.9 | 96.5/96.4 | ||
Dog/ SR1_TH | nt | 90.5/90.5 | 87.7/87.4 | 86.6/86.8 | 92.9/92.6 | 91.9/92.5 | 93.7/93.0 | 91.8/90.3 | 86.3/86.8 | 92.3/91.8 | 93.0/93.0 | 93.3/91.9 | 92.3/92.4 |
aa | 87.7/86.8 | 89.2/87.3 | 98.2/98.5 | 92.2/93.9 | 97.7/96.9 | 91.4/89.2 | 80.7/81.7 | 94.8//94.4 | 97.2/96.0 | 93.9/93.9 | 96.3/96.2 |
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Park, J.; Kim, H.-R.; Lee, E.-B.; Lee, S.-K.; Kim, W.-I.; Lyoo, Y.S.; Park, C.-K.; Ku, B.K.; Jeoung, H.-Y.; Lee, K.-K.; et al. First Detection and Genetic Characterization of Swine Orthopneumovirus from Domestic Pig Farms in the Republic of Korea. Viruses 2023, 15, 2371. https://doi.org/10.3390/v15122371
Park J, Kim H-R, Lee E-B, Lee S-K, Kim W-I, Lyoo YS, Park C-K, Ku BK, Jeoung H-Y, Lee K-K, et al. First Detection and Genetic Characterization of Swine Orthopneumovirus from Domestic Pig Farms in the Republic of Korea. Viruses. 2023; 15(12):2371. https://doi.org/10.3390/v15122371
Chicago/Turabian StylePark, Jonghyun, Hye-Ryung Kim, Eon-Bee Lee, Sang-Kwon Lee, Won-Il Kim, Young S. Lyoo, Choi-Kyu Park, Bok Kyung Ku, Hye-Young Jeoung, Kyoung-Ki Lee, and et al. 2023. "First Detection and Genetic Characterization of Swine Orthopneumovirus from Domestic Pig Farms in the Republic of Korea" Viruses 15, no. 12: 2371. https://doi.org/10.3390/v15122371
APA StylePark, J., Kim, H.-R., Lee, E.-B., Lee, S.-K., Kim, W.-I., Lyoo, Y. S., Park, C.-K., Ku, B. K., Jeoung, H.-Y., Lee, K.-K., & Park, S.-C. (2023). First Detection and Genetic Characterization of Swine Orthopneumovirus from Domestic Pig Farms in the Republic of Korea. Viruses, 15(12), 2371. https://doi.org/10.3390/v15122371