Prediction of Nipah Virus Epitopes for T and B lymphocytes Restricted to Thai Population Using Immunoinformatics Approaches
Abstract
Nipah virus (NiV) causes a zoonotic disease by transmission from fruit bats as an important carrier to human. The infections lead to life-threatening encephalitis in humans and animals. Diagnosis is currently difficult, and there are no effective antiviral drugs and vaccines for NiV infection. Thailand is at risk of the outbreak because of a report of the detection of NiV specific antibodies in a strain similar to the infection in Malaysia. Viral RNA of NiV from urine sample of Pteropus lylei in Thailand are detected and viral strains resemble to Bangladesh and Malaysia strains. Therefore, vaccines for the prevention of infections are crucial necessary. During viral infection, the viral antigens are presented to T cells by the presentation of antigen-presenting cells (APCs) via HLA molecules, which are specific to HLA alleles. Therefore, the structural proteins are fusion glycoprotein F0 (F) and glycoprotein (G) proteins were subjected to target molecules for study. These proteins are antigenic molecules on the viral particle and involve in the infection process. To determine the immunogenic capacity of F and G protein by presenting of APCs, which can be linked to enhance adaptive immunity. The epitope position of proteins that can be presented to B cells and T cells via specific HLA class I and class II-restricted to Thai population were predicted. In this study, the most common HLA alleles found in Thai population can present F and G proteins to B cells and T cells with several epitopes. These epitopes from both proteins were also conserved in NiV strain from India, Bangladesh, and Malaysia. Suggest that the F and G protein of NiV can be used for design and developed as a vaccine to prevent NiV specific infection in Thai people. Furthermore, this will able to increase the health quality, social and environmental systems in Thailand and establish a system to support patients including surveillance, treatment, diagnosis, and prevention of disease outbreaks in a wide range. Keywords : immunoinformatics ; Nipah virus ; glycoprotein ; Fusion Glycoprotein F0References
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Broder, C. C., Xu, K., Nikolov, D. B., Zhu, Z., Dimitrov, D. S., Middleton, D., Pallister, J., Geisbert, T. W.,
Bossart, K. N., & Wang, L. F. (2015). A treatment for and vaccine against the deadly Hendra and Nipah viruses. Antiviral Research, 100(1), 8–13.
Bui, H-H., Sidney, J., Lim W., Fusseder, N., & Sette, A. (2007). Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics, 8, 361, doi:10.1186/1471-2105-8-361.
Chong, H. T., Kamarulzaman, A., Tan, C. T., Goh, K. J., Thayaparan, T., Kunjapan, S. R., Chew, N. K., Chua, K. B., & Lam, S. K. (2001). Treatment of acute Nipah encephalitis with ribavirin. Annals of Neurology, 49(6),
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Chua, K. B., Bellini, W. J., Rota, P. A., Harcourt, B. H., Tamin, A., Lam, S. K., Ksiazek, T. G., Rollin, P. E.,
Zaki, S. R., Shieh, W., Goldsmith, C. S., Gubler, D. J., Roehrig, J. T., Eaton, B., Gould, A. R., Olson, J.,
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a recently emergent deadly paramyxovirus. Science, 26, 288(5470), 1432-5.
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De Wit, E., & Munster, V. J. (2015). Animal models of disease shed light on Nipah virus pathogenesis and transmission. Journal of Pathology, 235(2), 196–205.
Dhanda, S. K., Mahajan, S., Paul, S., Yan, Z., Kim, H., Jespersen, M. C., Jurtz, V., Andreatta, M., Greenbaum, J A., Marcatili, P., Sette, A., Nielsen , M., & Peters, B. (2019). IEDB-AR: immune epitope database—analysis resource in 2019. Nucleic Acids Research, 47(W1), W502–W506.
Ding, J., Lu, Y., & Chen, Y-H. (2000). Candidate multi-epitope vaccines in aluminium adjuvant induce high levels of antibodies with prede¢ned multi-epitope speci¢city against HIV-1. EMS Immunology and Medical Microbiology, 29, 123-127.
Escalona, E., Sáez, D., & Oñate, A. (2017). Immunogenicity of a Multi-Epitope DNA Vaccine Encoding Epitopes from Cu-Zn Superoxide Dismutase and Open Reading Frames of Brucella abortus in Mice. Front Immunol, 8, 125, 1-10.
Fleri, W., Paul, S., Dhanda, S. K., Mahajan, S., Xu, X., Peters, B., & Sette, A. (2017). The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design. Frontiers in Immunology, 8(MAR), 1–16.
Gu, Y., Sun, X., Li, B., Huang, J., Zhan, B., & Zhu, X. (2017). Vaccination with a Paramyosin-Based Multi-Epitope Vaccine Elicits Significant Protective Immunity against Trichinella spiralis Infection in Mice. Front Microbiol, 3, 8,1475.
Hajissa, H., Zakaria, R., Suppian, R., & Mohamed, Z. (2019). Epitope-based vaccine as a universal vaccination strategy against Toxoplasma gondii infection: A mini-review. Journal of Advanced Veterinary and Animal Research, 6(2), 174–182.
Jespersen, M. C., Peters, B., Nielsen, M. & Marcatili, P. (2017). BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Research, 45(W1), W24–W29.
Lei, Y., Zhao,F., Shao, J., Li, Y., Li, S., Chang, H., & Zhang, Y. (2019), Application of built-in adjuvants for epitope-based vaccines. PeerJ, 1-48.
Mazzola, L. T., & Kelly-Cirino, C. (2019). Diagnostics for Nipah virus: a zoonotic pathogen endemic to Southeast Asia. BMJ Global Health, 4(Suppl 2), e001118, 1-10.
Ministry of Public Health. (2015). Guidelines for reporting communicable diseases and communicable disease surveillance Disease Act 2558. Retrieved November 1, 2019, from http://odpc8.ddc.moph.go.th/upload_epi_article/dWoQeKhEGHvLqR1IfCYF.pdf. (in Thai)
Ojha, R., Pareek, A., Pandey, R. K., Prusty, D., & Prajapati, V. K. (2019). Strategic Development of a Next-Generation Multi-Epitope Vaccine To Prevent Nipah Virus Zoonotic Infection. ACS Omega, 4(8), 13069–13079.
Palucka, K., & Banchereau, J. (2013). Dendritic cell-based cancer therapeutic vaccines Karolina. Immunity, 39(1), 38–48.
Parvege, M, M., Rahman, M., Nibir, Y, M., & Hossain, M. S. (2016). Two highly similar LAEDDTNAQKT and LTDKIGTEI epitopes in G glycoprotein may be useful for effective epitope based vaccine design against pathogenic Henipavirus. Computational Biology and Chemistry, 61, 270-280.
Pickering, B. S., Hardham, J. M., Smith, G., Weingartl, E. T., Dominowski, P. J., Foss, D. L., Mwangi, D.,
Broder, C. C., Roth, J. A., & Weingartl, H. M. (2016). Protection against henipaviruses in swine requires both, cell-mediated and humoral immune response. Vaccine, 34(40), 4777–4786.
Prescott, J., de Wit, E., Feldmann, H., & Munster, V. J. (2012). The immune response to Nipah virus infection. Archives of Virology, 157(9), 1635–1641.
Sanchez-Trincado, J. L., Gomez-Perosanz, M., & Reche, P. A. (2017). Fundamentals and Methods for T- and
B-Cell Epitope Prediction. Journal of Immunology Research, 2017, 1-14.
Satterfield, B. A., Dawes, B. E., & Milligan, G. N. (2016). Status of vaccine research and development of vaccines for Nipah virus: Prepared for WHO PD-VAC July 30, 2015. Vaccine, 34(26), 2971–2975.
Schneidman-Duhovny, D., Khuri, N., Dong, G. Q., Winter, M. B., Shifrut, E., Friedman, N., Craik , C. S.,
Pratt , K. P., Paz , P., Aswad , F., & Sali, A. (2018). Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition. PLoS ONE, 13(11), 1–22.
Thakur, N., & Bailey, D. (2019). Advances in diagnostics, vaccines and therapeutics for Nipah virus. Microbes and Infection, 1-9.
Wacharapluesadee, S., & Hemachudha, T. (2007). Duplex nested RT-PCR for detection of Nipah virus RNA from urine specimens of bats. Journal of Virological Methods, 141(1),97-101.
Wacharapluesadee, S., Lumlertdacha, B., Boongird, K., Wanghongsa, S., Chanhome, L., Rollin, P., Stockton, P., Rupprecht , C. E., Ksiazek , T. G., & Hemachudha, T. (2005). Bat Nipah virus, Thailand. Emerging Infectious Diseases, 11(12), 1949–1951.
Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303.
Wiwanitkit, V. (2017). Nipah Virus Infection in Thailand: Status. Journal of Neuroinfectious Diseases, 08(01), 7326.
World Health Organization. (2018). Nipah virus. Retrieved November 1, 2019, from https://www.who.int/news-room/fact-sheets/detail/nipah-virus.
Yadav, P. D., Shete, A. M., Kumar, G. A., Sarkale, P., Sahay, R. R., Radhakrishnan, C., Lakra, R., Pardeshi, P., Gupta, N., Gangakhedkar, R. R., Rajendran, V. R., Sadanandan, R., & Mourya, D. T. (2019). Nipah Virus Sequences from Humans and Bats during Nipah Outbreak, Kerala, India, 2018. Emerging infectious diseases, 25(5),
Yatim, K. M., & Lakkis, F. G. (2015). A brief journey through the immune system. Clinical Journal of the American S
Broder, C. C., Xu, K., Nikolov, D. B., Zhu, Z., Dimitrov, D. S., Middleton, D., Pallister, J., Geisbert, T. W.,
Bossart, K. N., & Wang, L. F. (2015). A treatment for and vaccine against the deadly Hendra and Nipah viruses. Antiviral Research, 100(1), 8–13.
Bui, H-H., Sidney, J., Lim W., Fusseder, N., & Sette, A. (2007). Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics, 8, 361, doi:10.1186/1471-2105-8-361.
Chong, H. T., Kamarulzaman, A., Tan, C. T., Goh, K. J., Thayaparan, T., Kunjapan, S. R., Chew, N. K., Chua, K. B., & Lam, S. K. (2001). Treatment of acute Nipah encephalitis with ribavirin. Annals of Neurology, 49(6),
810–813.
Chua, K. B., Bellini, W. J., Rota, P. A., Harcourt, B. H., Tamin, A., Lam, S. K., Ksiazek, T. G., Rollin, P. E.,
Zaki, S. R., Shieh, W., Goldsmith, C. S., Gubler, D. J., Roehrig, J. T., Eaton, B., Gould, A. R., Olson, J.,
Field, H., Daniels, P., Ling, A. E., Peters, C. J., Anderson, L. J., & Mahy, B. W. (2000). Nipah virus:
a recently emergent deadly paramyxovirus. Science, 26, 288(5470), 1432-5.
Department of Disease Control. (2018). Disease Control Department asked the public aware, but do not panic. Thailand has not found Nipah virus-infected patients. The infection can be prevented by avoiding close contact with fruit bats and secretions. Retrieved November 1, 2019, from https://www.riskcomthai.org/2017/detail.php?id=37522. (in Thai)
De Wit, E., & Munster, V. J. (2015). Animal models of disease shed light on Nipah virus pathogenesis and transmission. Journal of Pathology, 235(2), 196–205.
Dhanda, S. K., Mahajan, S., Paul, S., Yan, Z., Kim, H., Jespersen, M. C., Jurtz, V., Andreatta, M., Greenbaum, J A., Marcatili, P., Sette, A., Nielsen , M., & Peters, B. (2019). IEDB-AR: immune epitope database—analysis resource in 2019. Nucleic Acids Research, 47(W1), W502–W506.
Ding, J., Lu, Y., & Chen, Y-H. (2000). Candidate multi-epitope vaccines in aluminium adjuvant induce high levels of antibodies with prede¢ned multi-epitope speci¢city against HIV-1. EMS Immunology and Medical Microbiology, 29, 123-127.
Escalona, E., Sáez, D., & Oñate, A. (2017). Immunogenicity of a Multi-Epitope DNA Vaccine Encoding Epitopes from Cu-Zn Superoxide Dismutase and Open Reading Frames of Brucella abortus in Mice. Front Immunol, 8, 125, 1-10.
Fleri, W., Paul, S., Dhanda, S. K., Mahajan, S., Xu, X., Peters, B., & Sette, A. (2017). The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design. Frontiers in Immunology, 8(MAR), 1–16.
Gu, Y., Sun, X., Li, B., Huang, J., Zhan, B., & Zhu, X. (2017). Vaccination with a Paramyosin-Based Multi-Epitope Vaccine Elicits Significant Protective Immunity against Trichinella spiralis Infection in Mice. Front Microbiol, 3, 8,1475.
Hajissa, H., Zakaria, R., Suppian, R., & Mohamed, Z. (2019). Epitope-based vaccine as a universal vaccination strategy against Toxoplasma gondii infection: A mini-review. Journal of Advanced Veterinary and Animal Research, 6(2), 174–182.
Jespersen, M. C., Peters, B., Nielsen, M. & Marcatili, P. (2017). BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Research, 45(W1), W24–W29.
Lei, Y., Zhao,F., Shao, J., Li, Y., Li, S., Chang, H., & Zhang, Y. (2019), Application of built-in adjuvants for epitope-based vaccines. PeerJ, 1-48.
Mazzola, L. T., & Kelly-Cirino, C. (2019). Diagnostics for Nipah virus: a zoonotic pathogen endemic to Southeast Asia. BMJ Global Health, 4(Suppl 2), e001118, 1-10.
Ministry of Public Health. (2015). Guidelines for reporting communicable diseases and communicable disease surveillance Disease Act 2558. Retrieved November 1, 2019, from http://odpc8.ddc.moph.go.th/upload_epi_article/dWoQeKhEGHvLqR1IfCYF.pdf. (in Thai)
Ojha, R., Pareek, A., Pandey, R. K., Prusty, D., & Prajapati, V. K. (2019). Strategic Development of a Next-Generation Multi-Epitope Vaccine To Prevent Nipah Virus Zoonotic Infection. ACS Omega, 4(8), 13069–13079.
Palucka, K., & Banchereau, J. (2013). Dendritic cell-based cancer therapeutic vaccines Karolina. Immunity, 39(1), 38–48.
Parvege, M, M., Rahman, M., Nibir, Y, M., & Hossain, M. S. (2016). Two highly similar LAEDDTNAQKT and LTDKIGTEI epitopes in G glycoprotein may be useful for effective epitope based vaccine design against pathogenic Henipavirus. Computational Biology and Chemistry, 61, 270-280.
Pickering, B. S., Hardham, J. M., Smith, G., Weingartl, E. T., Dominowski, P. J., Foss, D. L., Mwangi, D.,
Broder, C. C., Roth, J. A., & Weingartl, H. M. (2016). Protection against henipaviruses in swine requires both, cell-mediated and humoral immune response. Vaccine, 34(40), 4777–4786.
Prescott, J., de Wit, E., Feldmann, H., & Munster, V. J. (2012). The immune response to Nipah virus infection. Archives of Virology, 157(9), 1635–1641.
Sanchez-Trincado, J. L., Gomez-Perosanz, M., & Reche, P. A. (2017). Fundamentals and Methods for T- and
B-Cell Epitope Prediction. Journal of Immunology Research, 2017, 1-14.
Satterfield, B. A., Dawes, B. E., & Milligan, G. N. (2016). Status of vaccine research and development of vaccines for Nipah virus: Prepared for WHO PD-VAC July 30, 2015. Vaccine, 34(26), 2971–2975.
Schneidman-Duhovny, D., Khuri, N., Dong, G. Q., Winter, M. B., Shifrut, E., Friedman, N., Craik , C. S.,
Pratt , K. P., Paz , P., Aswad , F., & Sali, A. (2018). Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition. PLoS ONE, 13(11), 1–22.
Thakur, N., & Bailey, D. (2019). Advances in diagnostics, vaccines and therapeutics for Nipah virus. Microbes and Infection, 1-9.
Wacharapluesadee, S., & Hemachudha, T. (2007). Duplex nested RT-PCR for detection of Nipah virus RNA from urine specimens of bats. Journal of Virological Methods, 141(1),97-101.
Wacharapluesadee, S., Lumlertdacha, B., Boongird, K., Wanghongsa, S., Chanhome, L., Rollin, P., Stockton, P., Rupprecht , C. E., Ksiazek , T. G., & Hemachudha, T. (2005). Bat Nipah virus, Thailand. Emerging Infectious Diseases, 11(12), 1949–1951.
Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303.
Wiwanitkit, V. (2017). Nipah Virus Infection in Thailand: Status. Journal of Neuroinfectious Diseases, 08(01), 7326.
World Health Organization. (2018). Nipah virus. Retrieved November 1, 2019, from https://www.who.int/news-room/fact-sheets/detail/nipah-virus.
Yadav, P. D., Shete, A. M., Kumar, G. A., Sarkale, P., Sahay, R. R., Radhakrishnan, C., Lakra, R., Pardeshi, P., Gupta, N., Gangakhedkar, R. R., Rajendran, V. R., Sadanandan, R., & Mourya, D. T. (2019). Nipah Virus Sequences from Humans and Bats during Nipah Outbreak, Kerala, India, 2018. Emerging infectious diseases, 25(5),
Yatim, K. M., & Lakkis, F. G. (2015). A brief journey through the immune system. Clinical Journal of the American S
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2020-09-01
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