Molecular Biotechnology

, Volume 61, Issue 12, pp 945–957 | Cite as

Structural Characterization of Open Reading Frame-Encoded Functional Genes from Tilapia Lake Virus (TiLV)

  • Varsha Acharya
  • Hirak Jyoti Chakraborty
  • Ajaya Kumar Rout
  • Sucharita Balabantaray
  • Bijay Kumar Behera
  • Basanta Kumar DasEmail author
Original paper


In recent years, large-scale mortalities are observed in tilapia due to infection with a novel orthomyxo-like virus named, tilapia lake virus (TiLV) which is marked to be a severe threat to universal tilapia industry. Currently, there are knowledge gaps relating to the antiviral peptide as well as there are no affordable vaccines or drugs available against TiLV yet. To understand the spreading of infection of TiLV in different organs of Oreochromis niloticus, RT-PCR analysis has been carried out. The gene segments of TiLV were retrieved from the NCBI database for computational biology analysis. The 14 functional genes were predicted from the 10 gene segments of TiLV. Phylogenetic analysis was employed to find out a better understanding for the evolution of tilapia lake virus genes. Out of 14 proteins, only six proteins show transmembrane helix region. Moreover, molecular modeling and molecular dynamics simulations of the predicted proteins revealed structural stability of the protein stabilized after 10-ns simulation. Overall, our study provided a basic bioinformatics on functional proteome of TiLV. Further, this study could be useful for development of novel peptide-based therapeutics to control TiLV infection.


TiLV ORF finder Phylogenetic analysis Molecular dynamics simulation Tissue tropism 



The authors thank the Director, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India, for providing institutional facility. The authors also thank Mr. Asim Kumar Jana (Senior Technical Assistant) and Mr. Prasenjit Paria, Research Scholar of the ICAR-CIFRI for providing simultaneous encourage and support for this work.

Compliance with Ethical Standards

Conflicts of interest

The authors have declared that they have no competing interests.

Supplementary material

12033_2019_217_MOESM1_ESM.doc (8.8 mb)
Supplementary material 1 (DOC 8985 kb)


  1. 1.
    Dinesh, R., George, M. R., John, K. R., & Abraham, S. (2017). TiLV-A worldwide menace to tilapiine aquaculture. Journal of Entomology and Zoology Studies, 5, 605–607.Google Scholar
  2. 2.
    FAO (Food and Agriculture Organization of the United Nations). Food and Agriculture Organization of the United Nations FishStatJ: A tool for fishery statistics analysis, version 1.0.1. Retrieved 2013, from
  3. 3.
    deGraaf, G., & Garibaldi, L. (2014). The value of African fisheries, FAO Fisheries and Aquaculture Circular. Rome: FAO.Google Scholar
  4. 4.
    Del-Pozo, J., Mishra, N., Kabuusu, R., Cheetham, S., Eldar, A., Bacharach, E., et al. (2017). Syncytial hepatitis of tilapia (Oreochromis niloticus L.) is associated with orthomyxovirus-like virions in hepatocytes. Veterinary Pathology. Scholar
  5. 5.
    FAO Cultured Aquatic Species Information Programme—Oreochromis niloticus (Linnaeus, 1758). 2005. Food and Agriculture Organization of the United Nations.Google Scholar
  6. 6.
    Eyngor, M., Zamostiano, R., Tsofack, J. E., Berkowitz, A., Bercovier, H., Tinman, S., et al. (2014). Identification of a novel RNA virus, lethal to Tilapia. Journal of Clinical Microbiology. Scholar
  7. 7.
    Ferguson, H. W., Kabuusu, R., Beltran, S., Reyes, E., Lince, J. A., & del-Pozo, J. (2014). Syncytial hepatitis of farmed tilapia, Oreochromis niloticus (L.): A case report. Journal of Fish Diseases. Scholar
  8. 8.
    Bacharach, E., Mishra, N., Briese, T., Zody, M. C., Tsofack, J. E., Zamostiano, R., et al. (2016). Characterization of a novel orthomyxo-like virus causing mass die-offs of tilapia. MBio, 7, e00431-16.CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Dong, H. T., Siriroob, S., Meemetta, W., Santimanawong, W., Gangnonngiw, W., Pirarat, N., et al. (2017). Emergence of tilapia lake virus in Thailand and an alternative semi-nested RT-PCR for detection. Aquaculture, 476, 111–118.CrossRefGoogle Scholar
  10. 10.
    Fathi, M., Dickson, C., Dickson, M., Leschen, W., Baily, J., Muir, F., et al. (2017). Identification of Tilapia Lake Virus in Egypt in Nile tilapia affected by ‘summer mortality’ syndrome. Aquaculture, 473, 430–432.CrossRefGoogle Scholar
  11. 11.
    Amal, M. N., Koh, C. B., Nurliyana, M., Suhaiba, M., Nor-Amalina, Z., Santha, S., et al. (2018). A case of natural co-infection of Tilapia Lake Virus and Aeromonasveronii in a Malaysian red hybrid tilapia (Oreochromis niloticus × O. mossambicus) farm experiencing high mortality. Aquaculture, 485, 12–16.CrossRefGoogle Scholar
  12. 12.
    FIS Tilapia Lake Virus Affects Seven Farms in Taoyuan [WWW Document] Fish Information and Services (2017) Accessed 2 Feb 2018.
  13. 13.
    Behera, B. K., Pradhan, P. K., Swaminathan, T. R., Sood, N., Paria, P., & Das, A. (2018). Emergence of tilapia lake virus associated with mortalities of farmed Nile tilapia Oreochromis niloticus (Linnaeus 1758) in India. Aquaculture, 484, 168–174.CrossRefGoogle Scholar
  14. 14.
    Tsofack, J. E., Zamostiano, R., Watted, S., Berkowitz, A., Rosenbluth, E., Mishra, N., et al. (2017). Detection of tilapia lake virus in clinical samples by culturing and nested reverse transcription-PCR. Journal of Clinical Microbiology, 55, 759–767.CrossRefGoogle Scholar
  15. 15.
    Thangaraj, R. S., Ravi, C., Kumar, R., Dharmaratnam, A., Saidmuhammed, B. V., Pradhan, P. K., et al. (2018). Derivation of two tilapia (Oreochromis niloticus) cell lines for efficient propagation of Tilapia Lake Virus (TiLV). Aquaculture, 492, 206–214.CrossRefGoogle Scholar
  16. 16.
    Tattiyapong, P., Dachavichitlead, W., & Surachetpong, W. (2017). Experimental infection of Tilapia Lake Virus (TiLV) in Nile tilapia (Oreochromis niloticus) and red tilapia (Oreochromis spp). Veterinary Microbiology, 207, 170–177.CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Jaemwimol, P., Rawiwan, P., Tattiyapong, P., Saengnual, P., Kamlangdee, A., & Surachetpong, W. (2018). Susceptibility of important warm water fish species to tilapia lake virus (TiLV) infection. Aquaculture, 497, 462–468.CrossRefGoogle Scholar
  18. 18.
    Abdullah, A., Ramly, R., Ridzwan, M. S., Sudirwan, F., Abas, A., Ahmad, K., et al. (2018). First detection of tilapia lake virus (TiLV) in wild river carp (Barbonymus schwanenfeldii) at TimahTasoh Lake, Malaysia. Journal of Fish Diseases, 41, 1459–1462.CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Nicholson, P., Fathi, M. A., Fischer, A., Mohan, C., Schieck, E., Mishra, N., et al. (2017). Detection of Tilapia Lake Virus in Egyptian fish farms experiencing high mortalities in 2015. Journal of Fish Diseases, 40, 1925–1928.CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Surachetpong, W., Janetanakit, T., Nonthabenjawan, N., Tattiyapong, P., Sirikanchana, K., & Amonsin, A. (2017). Outbreaks of tilapia lake virus infection, Thailand, 2015–2016. Emerging Infectious Diseases, 23, 1031–1033.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Bigarré, L., Cabon, J., Baud, M., Heimann, M., Body, A., Lieffrig, F., et al. (2009). Outbreak of betanodavirus infection in tilapia, Oreochromis niloticus (L.), in fresh water. Journal of Fish Diseases, 32(8), 667–673.CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Rombel, I. T., Sykes, K. F., Rayner, S., & Johnston, S. A. (2002). ORF-FINDER: A vector for high-throughput gene identification. Gene, 282(1–2), 33–41.CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    McGuffin, L. J., Bryson, K., & Jones, D. T. (2000). The PSIPRED protein structure prediction server. Bioinformatics, 16, 404–405.CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406–425.PubMedPubMedCentralGoogle Scholar
  25. 25.
    Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874.CrossRefGoogle Scholar
  26. 26.
    Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution. Scholar
  27. 27.
    Kmiecik, S., & Kolinski, A. (2011). Simulation of chaperonin effect on protein folding: a shift from nucleation–condensation to framework mechanism. Journal of the American Chemical Society, 133, 10283–10289.CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Schwarz, R., & Dayhoff, M. (1979). Matrices for detecting distant relationships. In M. Dayhoff (Ed.), Atlas of protein sequences (pp. 353–358). Silver Spring, MD: National Biomedical Research Foundation.Google Scholar
  29. 29.
    Wallner, B., & Elofsson, A. (2003). Can correct protein models be identified? Protein Science, 12, 1073–1086.CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Šali, A., & Blundell, T. L. (1993). Comparative protein modeling by satisfaction of spatial restraints. Journal of Molecular Biology, 234, 779–815.CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26, 283–291.CrossRefGoogle Scholar
  32. 32.
    Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35, W407–W410.CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Vendruscolo, M., Kussell, E., & Domany, E. (1997). Recovery of protein structure from contact maps. Folding and Design, 2, 295–306.CrossRefGoogle Scholar
  34. 34.
    Paria, P., Chakraborty, H. J., Behera, B. K., Mohapatra, P. K., & Das, B. K. (2019). Computational characterization and molecular dynamics simulation of the thermostable direct hemolysin-related hemolysin (TRH) amplified from Vibrio parahaemolyticus. Microbial Pathogenesis, 127, 172–182.CrossRefGoogle Scholar
  35. 35.
    Chakraborty, H. J., Rout, A. K., Behera, B. K., Parhi, J., Parida, P. K., & Das, B. K. (2018). Insights into the aquaporin 4 of zebrafish (Danio rerio) through evolutionary analysis, molecular modeling and structural dynamics. Gene Reports, 11, 101–109.CrossRefGoogle Scholar
  36. 36.
    Chakraborty, H. J., Gangopadhyay, A., & Datta, A. (2019). Prediction and characterisation of lantibiotic structures with molecular modelling and molecular dynamics simulations. Scientific Reports, 9, 7169.CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Jamroz, M., Kolinski, A., & Kmiecik, S. (2013). CABS-flex: Server for fast simulation of protein structure fluctuations. Nucleic Acids Research, 41(W1), W427–W431.CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Kurcinski, M., Oleniecki, T., Ciemny, M. P., Kuriata, A., Kolinski, A., & Kmiecik, S. (2018). CABS-flex standalone: A simulation environment for fast modeling of protein flexibility. Bioinformatics, 35(4), 694–695.CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Gront, D., Kmiecik, S., Blaszczyk, M., Ekonomiuk, D., & Koliński, A. (2012). Optimization of protein models. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2, 479–493.Google Scholar
  40. 40.
    Koliński, A. (2004). Protein modeling and structure prediction with a reduced representation. Acta Biochimica Polonica, 51, 349–371.PubMedPubMedCentralGoogle Scholar
  41. 41.
    Jansen, M. D., Mohan, C. V. (2017). Tilapia lake virus (TiLV): Literature review. WorldFish.Google Scholar
  42. 42.
    Senapin, S., Shyam, K. U., Meemetta, W., Rattanarojpong, T., & Dong, H. T. (2018). In apparent infection cases of tilapia lake virus (TiLV) in farmed tilapia. Aquaculture, 487, 51–55.CrossRefGoogle Scholar
  43. 43.
    Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B. C., & Herrmann, R. (1996). Complete sequence analysis of the genome of the bacterium Mycoplasma pneumonia. Nucleic Acids Research, 24, 4420–4449.CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Frishman, D., & Mewes, H. W. (1997). Protein structural classes in five complete genomes. Nature Structural Biology, 4, 626–628.CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Wallin, E., & Heijne, G. V. (1998). Genome-wide analysis of integral membrane proteins from eubacterial, Archaean, and eukaryotic organisms. Protein Science, 7, 1029–1038.CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Sonnhammer, E. L., Von Heijne G., & Krogh, A. (1998). A hidden Markov model for predicting transmembrane helices in protein sequences (pp. 175–182).Google Scholar
  47. 47.
    Ginalski, K. (2006). Comparative modeling for protein structure prediction. Current Opinion in Structural Biology, 16, 172–177.CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Rout, A. K., Dehury, B., Maharana, J., Nayak, C., Baisvar, V. S., Behera, B. K., et al. (2018). Deep insights into the mode of ATP-binding mechanism in Zebrafish cyclin-dependent protein kinase-like 1 (zCDKL1): A molecular dynamics approach. Journal of Molecular Graphics and Modelling, 81, 175–183.CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Das, B. K., Roy, P., Rout, A. K., Sahoo, D. R., Panda, S. P., Pattanaik, S., et al. (2019). Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I: C induction. Scientific Reports, 9(1), 3956.CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Dikhit, M. R., Kumar, A., Das, S., Dehury, B., Rout, A. K., Jamal, F., et al. (2017). Identification of potential MHC Class-II-restricted epitopes derived from Leishmania donovani antigens by reverse vaccinology and evaluation of their CD4 + T-cell responsiveness against visceral leishmaniasis. Frontiers in Immunology, 8, 1763.CrossRefPubMedPubMedCentralGoogle Scholar
  51. 51.
    Dikhit, M. R., Das, S., Mahantesh, V., Kumar, A., Singh, A. K., Dehury, B., et al. (2018). The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8 + T lymphocyte response. Scientific Reports. Scholar
  52. 52.
    Dehury, B., Behera, S. K., & Mahapatra, N. (2017). Structural dynamics of casein kinase I (CKI) from malarial parasite Plasmodium falciparum (Isolate 3D7): insights from theoretical modelling and molecular simulations. Journal of Molecular Graphics and Modelling, 71, 154–166.CrossRefPubMedPubMedCentralGoogle Scholar
  53. 53.
    Girdhar, K., Dehury, B., Kumar, S. M., Daniel, V. P., Choubey, A., Dogra, S., et al. (2018). Novel insights into the dynamics behavior of glucagon-like peptide-1 receptor with its small molecule agonists. Journal of Biomolecular Structure & Dynamics. Scholar
  54. 54.
    Rout, A. K., Mishra, J., Dehury, B., Maharana, J., Acharya, V., Karna, S. K., et al. (2019). Structural bioinformatics insights into ATP binding mechanism in zebrafish (Danio rerio) cyclin-dependent kinase-like 5 (zCDKL5) protein. Journal of Cellular Biochemistry, 6, 9437–9447.CrossRefGoogle Scholar
  55. 55.
    Rout, A. K., Udgata, S. R., Dehury, B., Pradhan, S. P., Swain, H. S., Behera, B. K., et al. (2019). Structural bioinformatics insights into the CARD-CARD interaction mediated by the mitochondrial antiviral-signaling protein of black carp. Journal of Cellular Biochemistry. Scholar
  56. 56.
    Ode, H., Nakashima, M., Kitamura, S., Sugiura, W., & Sato, H. (2012). Molecular dynamics simulation in virus research. Frontiers in Microbiology, 3, 258–312.CrossRefPubMedPubMedCentralGoogle Scholar
  57. 57.
    Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural & Molecular Biology, 9, 646.CrossRefGoogle Scholar
  58. 58.
    Karplus, M., & Kuriyan, J. (2005). Molecular dynamics and protein function. Proceedings of the National academy of Sciences of the United States of America, 102, 6679–6685.CrossRefPubMedPubMedCentralGoogle Scholar
  59. 59.
    Mauksch, L. B., Dugdale, D. C., Dodson, S., & Epstein, R. (2008). Relationship, communication, and efficiency in the medical encounter: Creating a clinical model from a literature review. Archives of Internal Medicine, 168, 1387–1395.CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Kolinski, A., & Gront, D. (2007). Comparative modeling without implicit sequence alignments. Bioinformatics, 23, 2522–2527.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Varsha Acharya
    • 1
  • Hirak Jyoti Chakraborty
    • 1
  • Ajaya Kumar Rout
    • 1
  • Sucharita Balabantaray
    • 2
  • Bijay Kumar Behera
    • 1
  • Basanta Kumar Das
    • 1
    Email author
  1. 1.Biotechnology LaboratoryICAR-Central Inland Fisheries Research InstituteKolkataIndia
  2. 2.Department of BioinformaticsOdisha University of Agriculture and TechnologyBhubaneswarIndia

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