Easy, low cost, and precise Identification and interpretation of Newcastle virus and differentiation of its velogenic from lentogenic strains by using the nested RT-ARMS PCR

Document Type : Research Paper

Authors

1 DVM Graduated, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran

2 Professor, Department of Clinical Science, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran

3 Assistant Professor, Department of Genetics, Faculty of Basic Sciences, Shahrekord University, and Research Institute of Biotechnology, Shahrekord University, Shahrekord, Iran

Abstract

    Newcastle disease is a viral disease of poultry that is caused by type 1 paramyxovirus, from the Avulavirus genus and its fast and precise diagnosis is of high importance. Virulence of this virus depends on Fusion protein (F), one of six proteins of this virus, which can be used for detection of the virus virulence. So, this study aims to design new primers according to bioinformatics science progression and suggest a cheaper and easier method for the identification of Newcastle virus (NDV) as well as distinguish lentogenic from velogenic strains with higher sensitivity and specificity. First, all available strains of Newcastle viruses were collected from NCBI data bank using Blast tool and after multiple alignments, universal and specific primers were designed. In the next step, identification of NDV was set up using universal primers by PCR on cDNA of the control positive sample. Then differentiation of lentogenic from velogenic strains set up by ARMS (Amplification Refractory mutation system)-PCR (Polymerase chain reaction) using specific primers. Because the method was performed on cDNA obtained from reverse transcription reaction (RT), and because the PCR product of the first PCR reaction was used as a template for nested second PCR reaction it is called “nested RT-ARMS PCR”. Afterward, some samples from broiler farms were tested by this method and then compared by Real-Time PCR as a golden standard test. The results showed that sensitivity and specificity of identification of the virus and its strains were fully compatible in both methods. To sum up, this method which consumes a little bit more time but lower expenses, equipment and complexity in comparison with Real-Time PCR, can be suggested as a suitable substitution for the detection of NDV and distinguishing its velogenic from lentogenic strains.

Keywords

References

Alexander, D.J. (2003). Newcastle disease. In: Disease of poultry (1st ed). Iowashate university press. Iowa, Pp: 64-87.
Alexander, D.J., & Senne D.A. (2008). Newcastle disease,other Avain paramyxoviruses, and pneumovirus infection (12th ed., pp:75-115). Blackwell, Ames, Iowa.
Baratchi, S., Ghorashi, S.A., Hosseini, M., & Pourbakhsh S.A. (2003). Differentiation of virulent and non-virulent Newcastle disease virus isolates using RT-PCR. Iranian Journal of Biotechnology, 4(1), 61-63.
Fuller, C.M., Collins, M.S., Easton, A.J., & Alexander, D.J. (2007). Partial characterization of five cloned viruses differing in pathogenicity, obtained from a single isolate of pigeon paramyxovirus type1 (PPMV-1) following passage in fowls eggs. Archives of Virology, 152(8), 1575-82.
Pham, H.M., Konnai, S., Usui, T., Chang, K.S., Murata, S. Mase, M., Ohashi, K., & Onuma, M. (2005). Rapid detection and differentiation of Newcastle disease virus by Real-Time PCR with melting curve analysis. Archives of Virology, 150(12), 2429-2438.
Kant, A., Koch, G., Van Roozelaar, D.J., Balk F., & Ter Huurne, A. (1997). Differentiation of virulent and non‐virulent strains of Newcastle disease virus within 24 hours by polymerase chain reaction, Avian Pathology, 26(4), 837-849.
Kianizadeh, M., Aini, I., Omar, A.R., Yusoff, K., & Sahrabadi, M. (2002). Sequence and phylogenetic analysis of the fusion protein cleavage site of Newcastle disease virus field isolates from Iran, Acta virologica, 46(4), 247-51.
Kovics, S., & Horvath, J. (2000). Newcastle disease virus (NDV): brief history of its oncolytic strains, Journal of Clinical Virology, 16(1), 1-15.
Mase, M., Imai, K., Sanada, Y., Sanada, N., Yuasa, N., Imada, T., Tsukamoto, K., & Yamaguchi, S. (2002). Phylogenetic analysis of Newcastle Disease Virus Genotypes Isolated in Japan, Journal of Clinical Virology, 40(10), 3826–3830.
Wise, M.G., Suarez, D.L., Seal, B.S., Pedersen, J.C., Senne, D.A., King, D.J., Kapczynski, D.R., & Spackman, E. (2003). Development of a Real-Time Reverse Transcription PCR for Detection of Newcastle disease virus RNA in clinical Samples, Journal of Clinical Microbiology, 42(1), 329-38.
Naghavi, M. R., Gharehyazi, B., & Hosseini-Salcadeh, G.H. (2013). Molecular Markers (4th ed). Tehran University press. Iran, Pp:160.
Newton, C.R., Graham, A., Heptinstall, L.E., Powell, S.J., Summers, C., Kalsheker, N., Smith, J.C., & Markham, A.F. (1989). Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res, 17(7), 2503–2516.
Office International des Epizooties. (2001). Newcastle disease. Manual of standards for diagnostic tests and vaccines (4th ed), Paris: OLG.
Snoeck, C.J., Owoade, A.A., Hymann, E.C., Alkali, B.R., Okwen, M.P., Adeyanju, A.T.,  Komoyo, G.F., Nakouné, E., Le Faou, A., & Muller, C.P. (2013). High genetic diversity of Newcastle disease virus in poultry in west and central Africa: Cocirculation of genotype XIV and newly definded genotypes XVII and XVIII. Journal of Clinical Microbiology, 51(7), 2250-60.
Swayne, D.E., Glisson, J.R., & Jackwood, M.W. (1998). A laboratory manual for the isolation and identification of avian pathogens (4th ed). Pennsylvania, Pennsylvania University Press, US. Pp:1563-1630.
Vahidi, V., Zolfaghari, M., Ahmadi, A., shojapour, M., Moaddab, S.R., & Arjomandzadegan, M. (2014). Detecion of opioxacin resistance by rapid Molecular Method of Allele Specific PCR in Mycobacterium tuberculosis. Biological Journal of Microorganisms, 3(9), 21-34.
Veronique, J., & Jestin, A. (1990). Detection of Newcastle disease virus RNA in infected allantoic fluids by in vitro enzymatic amplification (PCR), Archives Virology, 118,151-161.

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