Skip to main content

Advertisement

SpringerLink
Log in

The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015

  • Published:
Virus Genes Aims and scope Submit manuscript

Abstract

Porcine deltacoronavirus (PDCoV) was identified in intestinal samples collected from piglets with diarrhea in Thailand in 2015. Two Thai PDCoV isolates, P23_15_TT_1115 and P24_15_NT1_1215, were isolated and identified. The full-length genome sequences of the P23_15_TT_1115 and P24_15_NT1_1215 isolates were 25,404 and 25,407 nucleotides in length, respectively, which were relatively shorter than that of US and China PDCoV. The phylogenetic analysis based on the full-length genome demonstrated that Thai PDCoV isolates form a new cluster separated from US and China PDCoV but relatively were more closely related to China PDCoV than US isolates. The genetic analyses demonstrated that Thai PDCoVs have 97.0–97.8 and 92.2–94.0% similarities with China PDCoV at nucleotide and amino acid levels, respectively, but share 97.1–97.3 and 92.5–93.0 similarity with US PDCoV at the nucleotide and amino acid levels, respectively. Thai PDCoV possesses two discontinuous deletions of five amino acids in ORF1a/b region. One additional deletion of one amino acid was identified in P23_15_TT_1115. The variation analyses demonstrated that six regions (nt 1317–1436, 2997–3096, 19,737–19,836, 20,277–20,376, 21,177–21,276, and 22,371–22,416) in ORF1a/b and spike genes exhibit high sequence variation between Thai and other PDCoV. The analyses of amino acid changes suggested that they could potentially be from different lineages.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. P.C. Woo, S.K. Lau, C.S. Lam, C.C. Lau, A.K. Tsang, J.H. Lau, R. Bai, J.L. Teng, C.C. Tsang, M. Wang, B.J. Zheng, K.H. Chan, K.Y. Yuen, Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J. Virol. 86, 3995–4008 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. K. Jung, H. Hu, B. Eyerly, Z. Lu, J. Chepngeno, L.J. Saif, Pathogenicity of 2 porcine deltacoronavirus strains in gnotobiotic pigs. Emerg. Infect. Dis. 21, 650–654 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. P.C. Woo, Y. Huang, S.K. Lau, K.Y. Yuen, Coronavirus genomics and bioinformatics analysis. Viruses 2, 1804–1820 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. R. McBride, M. van Zyl, B.C. Fielding, The coronavirus nucleocapsid is a multifunctional protein. Viruses 6, 2991–3018 (2014)

    Article  PubMed  PubMed Central  Google Scholar 

  5. N. Homwong, M.C. Jarvis, H.C. Lam, A. Diaz, A. Rovira, M. Nelson, D. Marthaler, Characterization and evolution of porcine deltacoronavirus in the United States. Prev. Vet. Med. 123, 168–174 (2016)

    Article  PubMed  Google Scholar 

  6. D. Marthaler, Y. Jiang, J. Collins, K. Rossow, Complete genome sequence of strain SDCV/USA/Illinois121/2014, a porcine deltacoronavirus from the United States. Genome Announc. (2014). doi:10.1128/genomeA.00218-14

    PubMed  PubMed Central  Google Scholar 

  7. L. Wang, B. Byrum, Y. Zhang, Porcine coronavirus HKU15 detected in 9 US states, 2014. Emerg. Infect. Dis. 20, 1594–1595 (2014)

    Article  PubMed  PubMed Central  Google Scholar 

  8. A. Sinha, P. Gauger, J. Zhang, K.J. Yoon, K. Harmon, PCR-based retrospective evaluation of diagnostic samples for emergence of porcine deltacoronavirus in US swine. Vet. Microbiol. 179, 296–298 (2015)

    Article  CAS  PubMed  Google Scholar 

  9. S. Lee, C. Lee, Complete genome characterization of Korean porcine deltacoronavirus strain KOR/KNU14-04/2014. Genome Announc. (2014). doi:10.1128/genomeA.01191-14

    Google Scholar 

  10. D. Song, X. Zhou, Q. Peng, Y. Chen, F. Zhang, T. Huang, T. Zhang, A. Li, D. Huang, Q. Wu, H. He, Y. Tang, Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: identification, prevalence and full-length genome sequence analysis. Trans. Emerg. Dis. 62, 575–580 (2015)

    Article  CAS  Google Scholar 

  11. D. Goede, M.P. Murtaugh, J. Nerem, P. Yeske, K. Rossow, R. Morrison, Previous infection of sows with a “mild” strain of porcine epidemic diarrhea virus confers protection against infection with a “severe” strain. Vet. Microbiol. 176, 161–164 (2015)

    Article  PubMed  Google Scholar 

  12. J.D. Thompson, D.G. Higgins, T.J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. A.J. Drummond, A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007)

    Article  PubMed  PubMed Central  Google Scholar 

  14. A.J. Drummond, M.A. Suchard, D. Xie, A. Rambaut, Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. M. Sun, J. Ma, Y. Wang, M. Wang, W. Song, W. Zhang, C. Lu, H. Yao, Genomic and epidemiological characteristics provide new insights into the phylogeographical and spatiotemporal spread of porcine epidemic diarrhea virus in Asia. J. Clin. Microbiol. 53, 1484–1492 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. B.A. Jameson, H. Wolf, The antigenic index: a novel algorithm for predicting antigenic determinants. Comput. Appl. Biosci. 4, 181–186 (1988)

    CAS  PubMed  Google Scholar 

  17. J. Kyte, R.F. Doolittle, A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105–132 (1982)

    Article  CAS  PubMed  Google Scholar 

  18. L. Wang, B. Byrum, Y. Zhang, Detection and genetic characterization of deltacoronavirus in pigs, Ohio, USA, 2014. Emerg. Infect. Dis. 20, 1227–1230 (2014)

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Q. Chen, G. Li, J. Stasko, J.T. Thomas, W.R. Stensland, A.E. Pillatzki, P.C. Gauger, K.J. Schwartz, D. Madson, K.J. Yoon, G.W. Stevenson, E.R. Burrough, K.M. Harmon, R.G. Main, J. Zhang, Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States. J. Clin. Microbiol. 52, 234–243 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. D.A. Brian, R.S. Baric, Coronavirus genome structure and replication. Curr. Top. Microbiol. Immunol. 287, 1–30 (2005)

    CAS  PubMed  Google Scholar 

  21. D.Q. Liu, J.W. Ge, X.Y. Qiao, Y.P. Jiang, S.M. Liu, Y.J. Li, High-level mucosal and systemic immune responses induced by oral administration with Lactobacillus-expressed porcine epidemic diarrhea virus (PEDV) S1 region combined with Lactobacillus-expressed N protein. Appl. Microbiol. Biotechnol. 93, 2437–2446 (2012)

    Article  CAS  PubMed  Google Scholar 

  22. D.B. Sun, L. Feng, H.Y. Shi, J.F. Chen, S.W. Liu, H.Y. Chen, Y.F. Wang, Spike protein region (aa 636789) of porcine epidemic diarrhea virus is essential for induction of neutralizing antibodies. Acta Virol. 51, 149–156 (2007)

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Research Council of Thailand [Grant Number 5080001], and Agricultural research development agency (Public organization). The funding provided by Special Task Force for Activating Research (STAR), swine viral evolution and vaccine research (SVEVR), Chulalongkorn University.

Authors’ contribution

C.J.S. and D.N. conceived and designed the experiments; C.J.S., G.T. and T.T. performed the experiments; C.J.S. and K.S. analyzed the data; C.J.S., T.T. and A.T. contributed reagents/materials/analysis tools; C.J.S. and D.N. composed the manuscript.

Author information

Authors and Affiliations

  1. Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand

    Athip Lorsirigool, Kepalee Saeng-chuto, Adthakorn Madapong, Gun Temeeyasen, Thitima Tripipat & Dachrit Nilubol

  2. Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, 12120, Thailand

    Pavita Kaewprommal & Jittima Piriyapongsa

  3. Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand

    Angkana Tantituvanont

Authors
  1. Athip Lorsirigool
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kepalee Saeng-chuto
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Adthakorn Madapong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gun Temeeyasen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Thitima Tripipat
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Pavita Kaewprommal
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Angkana Tantituvanont
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jittima Piriyapongsa
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Dachrit Nilubol
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dachrit Nilubol.

Ethics declarations

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Additional information

Edited by Keizo Tomonaga.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lorsirigool, A., Saeng-chuto, K., Madapong, A. et al. The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015. Virus Genes 53, 240–248 (2017). https://doi.org/10.1007/s11262-016-1413-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11262-016-1413-z

Keywords

Search

Navigation