Data availability statement
The data that supports the findings of this study are available in the table 1 of this article
References .
Abascal, F., Zardoya, R., & Posada, D. (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics ,21 (9), 2104-2105.https://doi.org/10.1093/bioinformatics/bti263
Ajayi, T., Dara, R., Misener, M., Pasma, T., Moser, L., & Poljak, Z. (2018). Herd-level prevalence and incidence of porcine epidemic diarrhoea virus (PEDV) and porcine deltacoronavirus (PDCoV) in swine herds in Ontario, Canada. Transbound Emerg Dis , 65 (5), 1197-1207.https://doi.org/10.1111/tbed.12858
Balamurugan, V., Venkatesan, G., Sen, A., Annamalai, L., Bhanuprakash, V., & Singh, R. K. (2010). Recombinant protein-based viral disease diagnostics in veterinary medicine. Expert Rev Mol Diagn ,10 (6), 731-753.https://doi.org/10.1586/erm.10.61
Baudoux, P., Carrat, C., Besnardeau, L., Charley, B., & Laude, H. (1998). Coronavirus pseudoparticles formed with recombinant M and E proteins induce alpha interferon synthesis by leukocytes. J Virol , 72 (11), 8636-8643.https://doi.org/10.1128/JVI.72.11.8636-8643.1998
Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem , 72 , 248-254.https://doi.org/10.1006/abio.1976.9999
Cao, L., Qin, Z., Ge, X., Yin, X., Xia, C., Bu, R. E., Fang, Y., Liu, J., Gao, Y., & Ren, X. (2013). Generation of a monoclonal antibody to S1 protein of porcine epidemic diarrhea virus. Monoclon Antib Immunodiagn Immunother , 32 (5), 371-374.https://doi.org/10.1089/mab.2013.0045
Chen, Q., Gauger, P., Stafne, M., Thomas, J., Arruda, P., Burrough, E., Madson, D., Brodie, J., Magstadt, D., Derscheid, R., Welch, M., & Zhang, J. (2015). Pathogenicity and pathogenesis of a United States porcine deltacoronavirus cell culture isolate in 5-day-old neonatal piglets. Virology , 482 , 51-59.https://doi.org/10.1016/j.virol.2015.03.024
Clamp, M., Cuff, J., Searle, S. M., & Barton, G. J. (2004). The Jalview Java alignment editor. Bioinformatics , 20 (3), 426-427.https://doi.org/10.1093/bioinformatics/btg430
Cui, J., Li, F., & Shi, Z. L. (2019). Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol , 17 (3), 181-192.https://doi.org/10.1038/s41579-018-0118-9
de Haan, C. A., & Rottier, P. J. (2005). Molecular interactions in the assembly of coronaviruses. Adv Virus Res , 64 , 165-230.https://doi.org/10.1016/S0065-3527(05)64006-7
Emini, E. A., Hughes, J. V., Perlow, D. S., & Boger, J. (1985). Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol , 55 (3), 836-839.https://doi.org/10.1128/JVI.55.3.836-839.1985
Feng, Y., Xu, Z., & Zhu, L. (2020). Prevalence and phylogenetic analysis of porcine deltacoronavirus in Sichuan province, China.Arch Virol , 165 (12), 2883-2889.https://doi.org/10.1007/s00705-020-04796-z
He, W. T., Ji, X., He, W., Dellicour, S., Wang, S., Li, G., Zhang, L., Gilbert, M., Zhu, H., Xing, G., Veit, M., Huang, Z., Han, G. Z., Huang, Y., Suchard, M. A., Baele, G., Lemey, P., & Su, S. (2020). Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus. Mol Biol Evol , 37 (9), 2641-2654.https://doi.org/10.1093/molbev/msaa117
Hu, H., Jung, K., Vlasova, A. N., Chepngeno, J., Lu, Z., Wang, Q., & Saif, L. J. (2015). Isolation and characterization of porcine deltacoronavirus from pigs with diarrhea in the United States. J Clin Microbiol , 53 (5), 1537-1548.https://doi.org/10.1128/JCM.00031-15
Jung, K., Hu, H., & Saif, L. J. (2016). Porcine deltacoronavirus infection: Etiology, cell culture for virus isolation and propagation, molecular epidemiology and pathogenesis. Virus Res , 226 , 50-59.https://doi.org/10.1016/j.virusres.2016.04.009
Kapke, P. A., Tung, F. Y., Hogue, B. G., Brian, D. A., Woods, R. D., & Wesley, R. (1988). The amino-terminal signal peptide on the porcine transmissible gastroenteritis coronavirus matrix protein is not an absolute requirement for membrane translocation and glycosylation.Virology , 165 (2), 367-376.https://doi.org/10.1016/0042-6822(88)90581-8
Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol , 157 (1), 105-132.https://doi.org/10.1016/0022-2836(82)90515-0
Laude, H., Gelfi, J., Lavenant, L., & Charley, B. (1992). Single amino acid changes in the viral glycoprotein M affect induction of alpha interferon by the coronavirus transmissible gastroenteritis virus.J Virol , 66 (2), 743-749.https://doi.org/10.1128/JVI.66.2.743-749.1992
Le, V. P., Song, S., An, B. H., Park, G. N., Pham, N. T., Le, D. Q., Nguyen, V. T., Vu, T. T. H., Kim, K. S., Choe, S., & An, D. J. (2018). A novel strain of porcine deltacoronavirus in Vietnam. Arch Virol , 163 (1), 203-207.https://doi.org/10.1007/s00705-017-3594-8
Lednicky, J. A., Tagliamonte, M. S., White, S. K., Elbadry, M. A., Alam, M. M., Stephenson, C. J., Bonny, T. S., Loeb, J. C., Telisma, T., Chavannes, S., Ostrov, D. A., Mavian, C., Beau De Rochars, V. M., Salemi, M., & Morris, J. G., Jr. (2021). Independent infections of porcine deltacoronavirus among Haitian children. Nature ,600 (7887), 133-137.https://doi.org/10.1038/s41586-021-04111-z
Lee, J. H., Chung, H. C., Nguyen, V. G., Moon, H. J., Kim, H. K., Park, S. J., Lee, C. H., Lee, G. E., & Park, B. K. (2016). Detection and Phylogenetic Analysis of Porcine Deltacoronavirus in Korean Swine Farms, 2015. Transbound Emerg Dis , 63 (3), 248-252.https://doi.org/10.1111/tbed.12490
Li, C. K., Wu, H., Yan, H., Ma, S., Wang, L., Zhang, M., Tang, X., Temperton, N. J., Weiss, R. A., Brenchley, J. M., Douek, D. C., Mongkolsapaya, J., Tran, B. H., Lin, C. L., Screaton, G. R., Hou, J. L., McMichael, A. J., & Xu, X. N. (2008). T cell responses to whole SARS coronavirus in humans. J Immunol , 181 (8), 5490-5500.https://doi.org/10.4049/jimmunol.181.8.5490
Li, G., Chen, Q., Harmon, K. M., Yoon, K. J., Schwartz, K. J., Hoogland, M. J., Gauger, P. C., Main, R. G., & Zhang, J. (2014). Full-Length Genome Sequence of Porcine Deltacoronavirus Strain USA/IA/2014/8734.Genome Announc , 2 (2).https://doi.org/10.1128/genomeA.00278-14
Liu, C., Kokuho, T., Kubota, T., Watanabe, S., Inumaru, S., Yokomizo, Y., & Onodera, T. (2001). A serodiagnostic ELISA using recombinant antigen of swine transmissible gastroenteritis virus nucleoprotein.J Vet Med Sci , 63 (11), 1253-1256.https://doi.org/10.1292/jvms.63.1253
Liu, J., Sun, Y., Qi, J., Chu, F., Wu, H., Gao, F., Li, T., Yan, J., & Gao, G. F. (2010). The membrane protein of severe acute respiratory syndrome coronavirus acts as a dominant immunogen revealed by a clustering region of novel functionally and structurally defined cytotoxic T-lymphocyte epitopes. J Infect Dis , 202 (8), 1171-1180.https://doi.org/10.1086/656315
Lorsirigool, A., Saeng-Chuto, K., Madapong, A., Temeeyasen, G., Tripipat, T., Kaewprommal, P., Tantituvanont, A., Piriyapongsa, J., & Nilubol, D. (2017). The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015.Virus Genes , 53 (2), 240-248.https://doi.org/10.1007/s11262-016-1413-z
Lorsirigool, A., Saeng-Chuto, K., Temeeyasen, G., Madapong, A., Tripipat, T., Wegner, M., Tuntituvanont, A., Intrakamhaeng, M., & Nilubol, D. (2016). The first detection and full-length genome sequence of porcine deltacoronavirus isolated in Lao PDR. Arch Virol ,161 (10), 2909-2911.https://doi.org/10.1007/s00705-016-2983-8
Luo, S. X., Fan, J. H., Opriessnig, T., Di, J. M., Liu, B. J., & Zuo, Y. Z. (2017). Development and application of a recombinant M protein-based indirect ELISA for the detection of porcine deltacoronavirus IgG antibodies. J Virol Methods , 249 , 76-78.https://doi.org/10.1016/j.jviromet.2017.08.020
Ma, Y., Zhang, Y., Liang, X., Lou, F., Oglesbee, M., Krakowka, S., & Li, J. (2015). Origin, evolution, and virulence of porcine deltacoronaviruses in the United States. mBio , 6 (2), e00064.https://doi.org/10.1128/mBio.00064-15
Narayanan, K., Chen, C. J., Maeda, J., & Makino, S. (2003). Nucleocapsid-independent specific viral RNA packaging via viral envelope protein and viral RNA signal. J Virol , 77 (5), 2922-2927.https://doi.org/10.1128/jvi.77.5.2922-2927.2003
Neuman, B. W., Kiss, G., Kunding, A. H., Bhella, D., Baksh, M. F., Connelly, S., Droese, B., Klaus, J. P., Makino, S., Sawicki, S. G., Siddell, S. G., Stamou, D. G., Wilson, I. A., Kuhn, P., & Buchmeier, M. J. (2011). A structural analysis of M protein in coronavirus assembly and morphology. J Struct Biol , 174 (1), 11-22.https://doi.org/10.1016/j.jsb.2010.11.021
Nickle, D. C., Heath, L., Jensen, M. A., Gilbert, P. B., Mullins, J. I., & Kosakovsky Pond, S. L. (2007). HIV-specific probabilistic models of protein evolution. PLoS One , 2 (6), e503.https://doi.org/10.1371/journal.pone.0000503
Niederwerder, M. C., & Hesse, R. A. (2018). Swine enteric coronavirus disease: A review of 4 years with porcine epidemic diarrhoea virus and porcine deltacoronavirus in the United States and Canada.Transbound Emerg Dis , 65 (3), 660-675.https://doi.org/10.1111/tbed.12823
Pan, X., Kong, N., Shan, T., Zheng, H., Tong, W., Yang, S., Li, G., Zhou, E., & Tong, G. (2015). Monoclonal antibody to N protein of porcine epidemic diarrhea virus. Monoclon Antib Immunodiagn Immunother , 34 (1), 51-54.https://doi.org/10.1089/mab.2014.0062
Perez-Rivera, C., Ramirez-Mendoza, H., Mendoza-Elvira, S., Segura-Velazquez, R., & Sanchez-Betancourt, J. I. (2019). First report and phylogenetic analysis of porcine deltacoronavirus in Mexico.Transbound Emerg Dis , 66 (4), 1436-1441.https://doi.org/10.1111/tbed.13193
Plasterer, T. N. (2000). PROTEAN. Protein sequence analysis and prediction. Mol Biotechnol , 16 (2), 117-125.https://doi.org/10.1385/MB:16:2:117
Ren, X., Suo, S., & Jang, Y. S. (2011). Development of a porcine epidemic diarrhea virus M protein-based ELISA for virus detection.Biotechnol Lett , 33 (2), 215-220.https://doi.org/10.1007/s10529-010-0420-8
Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: a unified platform for automated protein structure and function prediction.Nat Protoc , 5 (4), 725-738.https://doi.org/10.1038/nprot.2010.5
Sanders, M. T., Brown, L. E., Deliyannis, G., & Pearse, M. J. (2005). ISCOM-based vaccines: the second decade. Immunol Cell Biol ,83 (2), 119-128.https://doi.org/10.1111/j.1440-1711.2005.01319.x
Shenyang, G., Enhui, Z., Baoxian, L., Xinyuan, Q., Lijie, T., Junwei, G., & Yijing, L. (2007). High-level prokaryotic expression of envelope exterior of membrane protein of porcine epidemic diarrhea virus.Vet Microbiol , 123 (1-3), 187-193.https://doi.org/10.1016/j.vetmic.2007.03.027
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Soding, J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol ,7 , 539.https://doi.org/10.1038/msb.2011.75
Song, D., Zhou, X., Peng, Q., Chen, Y., Zhang, F., Huang, T., Zhang, T., Li, A., Huang, D., Wu, Q., He, H., & Tang, Y. (2015). Newly Emerged Porcine Deltacoronavirus Associated With Diarrhoea in Swine in China: Identification, Prevalence and Full-Length Genome Sequence Analysis.Transbound Emerg Dis , 62 (6), 575-580.https://doi.org/10.1111/tbed.12399
Stadler, K., Masignani, V., Eickmann, M., Becker, S., Abrignani, S., Klenk, H. D., & Rappuoli, R. (2003). SARS–beginning to understand a new virus. Nat Rev Microbiol , 1 (3), 209-218.https://doi.org/10.1038/nrmicro775
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics ,30 (9), 1312-1313.https://doi.org/10.1093/bioinformatics/btu033
Stothard, P. (2000). The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences.Biotechniques , 28 (6), 1102, 1104.https://doi.org/10.2144/00286ir01
Su, M., Li, C., Guo, D., Wei, S., Wang, X., Geng, Y., Yao, S., Gao, J., Wang, E., Zhao, X., Wang, Z., Wang, J., Wu, R., Feng, L., & Sun, D. (2016). A recombinant nucleocapsid protein-based indirect enzyme-linked immunosorbent assay to detect antibodies against porcine deltacoronavirus. J Vet Med Sci , 78 (4), 601-606.https://doi.org/10.1292/jvms.15-0533
Sun, H. X., Xie, Y., & Ye, Y. P. (2009). ISCOMs and ISCOMATRIX.Vaccine , 27 (33), 4388-4401.https://doi.org/10.1016/j.vaccine.2009.05.032
Thachil, A., Gerber, P. F., Xiao, C. T., Huang, Y. W., & Opriessnig, T. (2015). Development and application of an ELISA for the detection of porcine deltacoronavirus IgG antibodies. PLoS One , 10 (4), e0124363.https://doi.org/10.1371/journal.pone.0124363
Wang, Q., Vlasova, A. N., Kenney, S. P., & Saif, L. J. (2019). Emerging and re-emerging coronaviruses in pigs. Curr Opin Virol ,34 , 39-49.https://doi.org/10.1016/j.coviro.2018.12.001
Wang, Y., Grunewald, M., & Perlman, S. (2020). Coronaviruses: An Updated Overview of Their Replication and Pathogenesis. Methods Mol Biol , 2203 , 1-29.https://doi.org/10.1007/978-1-0716-0900-2_1
Weiss, S. R., & Leibowitz, J. L. (2011). Coronavirus pathogenesis.Adv Virus Res , 81 , 85-164.https://doi.org/10.1016/B978-0-12-385885-6.00009-2
Woo, P. C., Lau, S. K., Lam, C. S., Lau, C. C., Tsang, A. K., Lau, J. H., Bai, R., Teng, J. L., Tsang, C. C., Wang, M., Zheng, B. J., Chan, K. H., & Yuen, K. Y. (2012). 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 (7), 3995-4008.https://doi.org/10.1128/JVI.06540-11
Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: protein structure and function prediction. Nat Methods , 12 (1), 7-8.https://doi.org/10.1038/nmeth.3213
Zhang, J. (2016). Porcine deltacoronavirus: Overview of infection dynamics, diagnostic methods, prevalence and genetic evolution.Virus Res , 226 , 71-84.https://doi.org/10.1016/j.virusres.2016.05.028
Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction.BMC Bioinformatics , 9 , 40.https://doi.org/10.1186/1471-2105-9-40
Zhang, Y., & Skolnick, J. (2004). Scoring function for automated assessment of protein structure template quality. Proteins ,57 (4), 702-710.https://doi.org/10.1002/prot.20264
Zhang, Y., & Skolnick, J. (2005). TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res ,33 (7), 2302-2309.https://doi.org/10.1093/nar/gki524