Main Article Content
Abstract
The aim of this study was to generate the bioinformatics analysis of the circulating NDVs in Southeast Asia, East Asia, and the vaccine virus strains through a database of isolates stored in GenBank® (National Center for Biotechnology Information, USA). The used isolates were AJ629062.1 (La Sota), AF309418.1 (B1), EF201805.1 (Mukteswar), KT445901.1 (Komarov), JX524203.1 (V4), AY935499.2 (I-2), KC987036.1 (F), KF767104.1 (Indonesia), KF767105.1 (Indonesia), KF767106.1 (Indonesia), HQ697255.1 (Indonesia), HQ697256.1 (Indonesia), HQ697261.1 (Indonesia), JX012096.2 (Malaysia), GU332646.1 (Vietnam), AF358786.1 (Taiwan), AF358788.1 (China), KT380032.1 (Republic of Korea), and KC503416.1 (Japan). As the results, this study have revealed the data of homology, pathotype, genetic distance, B cell epitope prediction, and molecular phylogenetic analysis of circulating NDVs in Southeast Asia and East Asia and vaccine virus strains. Thus, the results of this study can be used as a reference for vaccine design studies in the applications of poultry vaccine industry
Received: 28 August 2019; Accepted: 31 December 2019; Published: 11 January 2020.
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References
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- I. Cornax, P.J. Miller, C.L. Afonso, Characterization of live LaSota vaccine strain–induced protection in chickens upon early challenge with a virulent Newcastle disease virus of heterologous genotype, Avian diseases 56(3) (2012) 464-470.
- M. Mase, K. Imai, Y. Sanada, N. Sanada, N. Yuasa, T. Imada, K. Tsukamoto, S. Yamaguchi, Phylogenetic analysis of Newcastle disease virus genotypes isolated in Japan, Journal of Clinical Microbiology 40(10) (2002) 3826-3830.
- E. Serrão, J. Meers, R. Pym, R. Copland, D. Eagles, J. Henning, Prevalence and incidence of Newcastle disease and prevalence of Avian Influenza infection of scavenging village chickens in Timor-Lesté, Preventive veterinary medicine 104(3-4) (2012) 301-308.
- B. Nath, S. Kumar, Emerging variant of genotype XIII Newcastle disease virus from Northeast India, Acta tropica 172 (2017) 64-69.
- S.S. Ewies, A. Ali, S.M. Tamam, H.M. Madbouly, Molecular characterization of Newcastle disease virus (genotype VII) from broiler chickens in Egypt, Beni-Suef University journal of basic and applied sciences 6(3) (2017) 232-237.
- A. Wiseman, E.M. Berman, E. Klement, Risk factors for Newcastle disease in broiler farms in Israel, Preventive veterinary medicine 149 (2018) 92-97
- S. Xiao, A. Paldurai, B. Nayak, A. Samuel, E.E. Bharoto, T.Y. Prajitno, P.L. Collins, S.K. Samal, Complete genome sequences of Newcastle disease virus strains circulating in chicken populations of Indonesia, Am Soc Microbiol, 2012.
- D.D. Putri, E. Handharyani, R.D. Soejoedono, A. Setiyono, N.L.P.I. Mayasari, O.N. Poetri, Pathotypic characterization of Newcastle disease virus isolated from vaccinated chicken in West Java, Indonesia, Veterinary world 10(4) (2017) 438.
- X. Li, Y. Qiu, A. Yu, T. Chai, X. Zhang, J. Liu, D. Wang, H. Wang, Z. Wang, C. Song, Degenerate primers based RT-PCR for rapid detection and differentiation of airborne chicken Newcastle disease virus in chicken houses, Journal of virological methods 158(1-2) (2009) 1-5.
- X. Yuan, Y. Wang, J. Yang, H. Xu, Y. Zhang, Z. Qin, H. Ai, J. Wang, Genetic and biological characterizations of a Newcastle disease virus from swine in china, Virology journal 9(1) (2012) 129.
- B. Sharma, M. Pokhriyal, G.K. Rai, M. Saxena, B. Ratta, M. Chaurasia, B.S. Yadav, A. Sen, B. Mondal, Isolation of Newcastle disease virus from a non-avian host (sheep) and its implications, Archives of virology 157(8) (2012) 1565-1567.
- C.B. Nelson, B.S. Pomeroy, K. Schrall, W.E. Park, R.J. Lindeman, An outbreak of conjunctivitis due to Newcastle disease virus (NDV) occurring in poultry workers, American Journal of Public Health and the Nations Health 42(6) (1952) 672-678.
- K. Ganar, M. Das, S. Sinha, S. Kumar, Newcastle disease virus: current status and our understanding, Virus research 184 (2014) 71-81.
- K.-S. Choi, E.-K. Lee, W.-J. Jeon, J.-H. Kwon, Antigenic and immunogenic investigation of the virulence motif of the Newcastle disease virus fusion protein, Journal of veterinary science 11(3) (2010) 205-211.
- M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of molecular evolution 16(2) (1980) 111-120.
- K. Tamura, G. Stecher, D. Peterson, A. Filipski, S. Kumar, MEGA6: molecular evolutionary genetics analysis version 6.0, Molecular biology and evolution 30(12) (2013) 2725-2729.
- O.R. Adianingsih, V.D. Kharisma, Study of B cell epitope conserved region of the Zika virus envelope glycoprotein to develop multi-strain vaccine, Journal of Applied Pharmaceutical Science 9(01) (2019) 098-103.
- I.A. Doytchinova, D.R. Flower, VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines, BMC bioinformatics 8(1) (2007) 4.
- H. Zahroh, A. Ma'rup, U.S.F. Tambunan, A.A. Parikesit, Immunoinformatics approach in designing epitope-based vaccine against meningitis-inducing bacteria (Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae type b), Drug target insights 10 (2016) DTI-S38458.
- X. Duan, P. Zhang, J. Ma, S. Chen, H. Hao, H. Liu, X. Fu, P. Wu, D. Zhang, W. Zhang, Characterization of genotype IX Newcastle disease virus strains isolated from wild birds in the northern Qinling Mountains, China, Virus genes 48(1) (2014) 48-55.
- L. Yu, Z. Wang, Y. Jiang, L. Chang, J. Kwang, Characterization of newly emerging Newcastle disease virus isolates from the People's Republic of China and Taiwan, Journal of clinical microbiology 39(10) (2001) 3512-3519.
References
B. Xiang, L. Han, P. Gao, R. You, F. Wang, J. Xiao, M. Liao, Y. Kang, T. Ren, Spillover of Newcastle disease viruses from poultry to wild birds in Guangdong province, southern China, Infection, Genetics and Evolution 55 (2017) 199-204.
I. Cornax, P.J. Miller, C.L. Afonso, Characterization of live LaSota vaccine strain–induced protection in chickens upon early challenge with a virulent Newcastle disease virus of heterologous genotype, Avian diseases 56(3) (2012) 464-470.
M. Mase, K. Imai, Y. Sanada, N. Sanada, N. Yuasa, T. Imada, K. Tsukamoto, S. Yamaguchi, Phylogenetic analysis of Newcastle disease virus genotypes isolated in Japan, Journal of Clinical Microbiology 40(10) (2002) 3826-3830.
E. Serrão, J. Meers, R. Pym, R. Copland, D. Eagles, J. Henning, Prevalence and incidence of Newcastle disease and prevalence of Avian Influenza infection of scavenging village chickens in Timor-Lesté, Preventive veterinary medicine 104(3-4) (2012) 301-308.
B. Nath, S. Kumar, Emerging variant of genotype XIII Newcastle disease virus from Northeast India, Acta tropica 172 (2017) 64-69.
S.S. Ewies, A. Ali, S.M. Tamam, H.M. Madbouly, Molecular characterization of Newcastle disease virus (genotype VII) from broiler chickens in Egypt, Beni-Suef University journal of basic and applied sciences 6(3) (2017) 232-237.
A. Wiseman, E.M. Berman, E. Klement, Risk factors for Newcastle disease in broiler farms in Israel, Preventive veterinary medicine 149 (2018) 92-97
S. Xiao, A. Paldurai, B. Nayak, A. Samuel, E.E. Bharoto, T.Y. Prajitno, P.L. Collins, S.K. Samal, Complete genome sequences of Newcastle disease virus strains circulating in chicken populations of Indonesia, Am Soc Microbiol, 2012.
D.D. Putri, E. Handharyani, R.D. Soejoedono, A. Setiyono, N.L.P.I. Mayasari, O.N. Poetri, Pathotypic characterization of Newcastle disease virus isolated from vaccinated chicken in West Java, Indonesia, Veterinary world 10(4) (2017) 438.
X. Li, Y. Qiu, A. Yu, T. Chai, X. Zhang, J. Liu, D. Wang, H. Wang, Z. Wang, C. Song, Degenerate primers based RT-PCR for rapid detection and differentiation of airborne chicken Newcastle disease virus in chicken houses, Journal of virological methods 158(1-2) (2009) 1-5.
X. Yuan, Y. Wang, J. Yang, H. Xu, Y. Zhang, Z. Qin, H. Ai, J. Wang, Genetic and biological characterizations of a Newcastle disease virus from swine in china, Virology journal 9(1) (2012) 129.
B. Sharma, M. Pokhriyal, G.K. Rai, M. Saxena, B. Ratta, M. Chaurasia, B.S. Yadav, A. Sen, B. Mondal, Isolation of Newcastle disease virus from a non-avian host (sheep) and its implications, Archives of virology 157(8) (2012) 1565-1567.
C.B. Nelson, B.S. Pomeroy, K. Schrall, W.E. Park, R.J. Lindeman, An outbreak of conjunctivitis due to Newcastle disease virus (NDV) occurring in poultry workers, American Journal of Public Health and the Nations Health 42(6) (1952) 672-678.
K. Ganar, M. Das, S. Sinha, S. Kumar, Newcastle disease virus: current status and our understanding, Virus research 184 (2014) 71-81.
K.-S. Choi, E.-K. Lee, W.-J. Jeon, J.-H. Kwon, Antigenic and immunogenic investigation of the virulence motif of the Newcastle disease virus fusion protein, Journal of veterinary science 11(3) (2010) 205-211.
M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of molecular evolution 16(2) (1980) 111-120.
K. Tamura, G. Stecher, D. Peterson, A. Filipski, S. Kumar, MEGA6: molecular evolutionary genetics analysis version 6.0, Molecular biology and evolution 30(12) (2013) 2725-2729.
O.R. Adianingsih, V.D. Kharisma, Study of B cell epitope conserved region of the Zika virus envelope glycoprotein to develop multi-strain vaccine, Journal of Applied Pharmaceutical Science 9(01) (2019) 098-103.
I.A. Doytchinova, D.R. Flower, VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines, BMC bioinformatics 8(1) (2007) 4.
H. Zahroh, A. Ma'rup, U.S.F. Tambunan, A.A. Parikesit, Immunoinformatics approach in designing epitope-based vaccine against meningitis-inducing bacteria (Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae type b), Drug target insights 10 (2016) DTI-S38458.
X. Duan, P. Zhang, J. Ma, S. Chen, H. Hao, H. Liu, X. Fu, P. Wu, D. Zhang, W. Zhang, Characterization of genotype IX Newcastle disease virus strains isolated from wild birds in the northern Qinling Mountains, China, Virus genes 48(1) (2014) 48-55.
L. Yu, Z. Wang, Y. Jiang, L. Chang, J. Kwang, Characterization of newly emerging Newcastle disease virus isolates from the People's Republic of China and Taiwan, Journal of clinical microbiology 39(10) (2001) 3512-3519.