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Patel SS, Chauhan HC, Kumar Sharma K, Patel AC, Bulbule NR, Raval SH, Shrimali MD, Kumar Mohapatra S, Patel HA. Genetic evolution of Newcastle Disease Virus sub-genotype VII.2 isolates, diagnosed from vaccinated poultry farms of Gujarat, India. Gene 2024; 930:148859. [PMID: 39151673 DOI: 10.1016/j.gene.2024.148859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 08/05/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Newcastle disease was suspected in 37 commercial poultry farms, including 12 layer and 25 broiler farms in four districts of Gujarat, India. Vaccination had been done in 32 (20 broilers and 12 layers) farms. Tissue samples from each farm were pooled as one sample. In egg embryo inoculation, HA-HI and PCR, respectively, 32/37, 29/37, and 24/37 samples were found positive. Pathotyping by mean death time calculation and primer combination PCR revealed velogenic NDV, which was later confirmed with the presence of the 112-RRQKR*F-117 sequence at the F protein cleavage site. Phylogenetic analysis of full F gene sequences (N=10) confirmed the presence of sub-genotype VII.2 in 9/10 sequences, and genotype II in one sample. These 9 sequences were only 0.7 to 2.6 % divergent with two VII.2 (=VIIi) sequences (HQ697254.1 chicken/Banjarmas/Indonesia and KU862293.1 Parakeet/Karachi/Pakistan) but had 2.2 to 3.6 % diversion from two VII.2 sequences (OR185447 and MZ546197) from India. Then branching was found from sequences of VIIh, VIIk (VII.2), and VIIa (VII.1.2), and then from sub-genotypes VII.1.1 and VII.1.2. Due to less than 5 % diversion, these sequences could not be qualified as new sub-genotype in evolutionary distance analysis. At the amino acid level, our sequences had aa N-T-I-A-L-T at 24-79-125-385-445-482. Whereas at the same positions, in most of the retrieved VII.2 sequences and vaccines, the sequence was S-A-V-T-Q/I- E/A. Two sequences revealed additional six and four amino acid differences,respectively.This indicates rapid continuous genetic evolution of sub-genotype VII.2 and partially explains vaccinal immunity escape.
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Affiliation(s)
- Sandipkumar S Patel
- College of Veterinary Science and Animal Husbandry, Kamdhenu University, Sardarkrushinagar, India
| | - Harshadkumar C Chauhan
- College of Veterinary Science and Animal Husbandry, Kamdhenu University, Sardarkrushinagar, India
| | - Kishan Kumar Sharma
- College of Veterinary Science and Animal Husbandry, Kamdhenu University, Sardarkrushinagar, India.
| | - Arunkumar C Patel
- College of Veterinary Science and Animal Husbandry, Kamdhenu University, Sardarkrushinagar, India; College of Veterinary Science and Animal Husbandry, Kamdhenu University, Anand, India
| | - Namdeo R Bulbule
- Poultry Diagnostic Research Center, Venkateshwara Hatcheries Limited, Pune, India
| | - Samir H Raval
- College of Veterinary Science and Animal Husbandry, Kamdhenu University, Sardarkrushinagar, India
| | - Mehul D Shrimali
- College of Veterinary Science and Animal Husbandry, Kamdhenu University, Sardarkrushinagar, India
| | - Sushil Kumar Mohapatra
- College of Veterinary Science and Animal Husbandry, Kamdhenu University, Sardarkrushinagar, India
| | - Harshkumar A Patel
- Passed Out M. V. Sc. Student, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Sardarkrushinagar, India
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Puro K, Sen A. Newcastle Disease in Backyard Poultry Rearing in the Northeastern States of India: Challenges and Control Strategies. Front Vet Sci 2022; 9:799813. [PMID: 35464373 PMCID: PMC9021565 DOI: 10.3389/fvets.2022.799813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/10/2022] [Indexed: 11/30/2022] Open
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Nath B, Morla S, Kumar S. Reverse Genetics and Its Usage in the Development of Vaccine Against Poultry Diseases. Methods Mol Biol 2022; 2411:77-92. [PMID: 34816399 DOI: 10.1007/978-1-0716-1888-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Vaccines are the most effective and economic way of combating poultry viruses. However, the use of traditional live-attenuated poultry vaccines has problems such as antigenic differences with the currently circulating strains of viruses and the risk of reversion to virulence. In veterinary medicine, reverse genetics is applied to solve these problems by developing genotype-matched vaccines, better attenuated and effective live vaccines, broad-spectrum vaccine vectors, bivalent vaccines, and genetically tagged recombinant vaccines that facilitate the serological differentiation of vaccinated animals from infected animals. In this chapter, we discuss reverse genetics as a tool for the development of recombinant vaccines against economically devastating poultry viruses.
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Affiliation(s)
- Barnali Nath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Sudhir Morla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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Marcano VC, Cardenas-Garcia S, Diel DG, Antoniassi da Silva LH, Gogal RM, Miller PJ, Brown CC, Butt SL, Goraichuk IV, Dimitrov KM, Taylor TL, Williams-Coplin D, Olivier TL, Stanton JB, Afonso CL. A Novel Recombinant Newcastle Disease Vaccine Improves Post- In Ovo Vaccination Survival with Sustained Protection against Virulent Challenge. Vaccines (Basel) 2021; 9:vaccines9090953. [PMID: 34579191 PMCID: PMC8472951 DOI: 10.3390/vaccines9090953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 01/23/2023] Open
Abstract
In ovo vaccination has been employed by the poultry industry for over 20 years to control numerous avian diseases. Unfortunately, in ovo live vaccines against Newcastle disease have significant limitations, including high embryo mortality and the inability to induce full protection during the first two weeks of life. In this study, a recombinant live attenuated Newcastle disease virus vaccine containing the antisense sequence of chicken interleukin 4 (IL-4), rZJ1*L-IL4R, was used. The rZJ1*L-IL4R vaccine was administered in ovo to naïve specific pathogen free embryonated chicken eggs (ECEs) and evaluated against a homologous challenge. Controls included a live attenuated recombinant genotype VII vaccine based on the virus ZJ1 (rZJ1*L) backbone, the LaSota vaccine and diluent alone. In the first of two experiments, ECEs were vaccinated at 18 days of embryonation (DOE) with either 104.5 or 103.5 50% embryo infectious dose (EID50/egg) and chickens were challenged at 21 days post-hatch (DPH). In the second experiment, 103.5 EID50/egg of each vaccine was administered at 19 DOE, and chickens were challenged at 14 DPH. Chickens vaccinated with 103.5 EID50/egg of rZJ1*L-IL4R had hatch rates comparable to the group that received diluent alone, whereas other groups had significantly lower hatch rates. All vaccinated chickens survived challenge without displaying clinical disease, had protective hemagglutination inhibition titers, and shed comparable levels of challenge virus. The recombinant rZJ1*L-IL4R vaccine yielded lower post-vaccination mortality rates compared with the other in ovo NDV live vaccine candidates as well as provided strong protection post-challenge.
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Affiliation(s)
- Valerie C. Marcano
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
- Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.C.B.); (J.B.S.)
| | - Stivalis Cardenas-Garcia
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
- Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.C.B.); (J.B.S.)
| | - Diego G. Diel
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
| | - Luciana H. Antoniassi da Silva
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
| | - Robert M. Gogal
- Department of Veterinary Biosciences & Diagnostic Imaging, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA;
| | - Patti J. Miller
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
| | - Corrie C. Brown
- Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.C.B.); (J.B.S.)
| | - Salman Latif Butt
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
- Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.C.B.); (J.B.S.)
- Department of Pathology, UAF Sub Campus TTS, University of Agriculture Faisalabad, Punjab 38000, Pakistan
| | - Iryna V. Goraichuk
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 83 Pushkinska St., 61023 Kharkiv, Ukraine
| | - Kiril M. Dimitrov
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
| | - Tonya L. Taylor
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
| | - Dawn Williams-Coplin
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
| | - Timothy L. Olivier
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
| | - James B. Stanton
- Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.C.B.); (J.B.S.)
| | - Claudio L. Afonso
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA; (V.C.M.); (S.C.-G.); (D.G.D.); (L.H.A.d.S.); (P.J.M.); (S.L.B.); (I.V.G.); (K.M.D.); (T.L.T.); (D.W.-C.); (T.L.O.)
- Correspondence:
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Song X, Liu L, Hu W, Liang X, He C, Yin L, Ye G, Zou Y, Li L, Tang H, Jia R, Yin Z. Identification of the amino acids residues involved in hemagglutinin-neuraminidase of Newcastle disease virus binding to sulfated Chuanmingshen violaceum polysaccharides. Poult Sci 2021; 100:101255. [PMID: 34198092 PMCID: PMC8255242 DOI: 10.1016/j.psj.2021.101255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022] Open
Abstract
The antiviral mechanism of sulfated polysaccharides is supposed to prevent virus entry, which is mediated by the interactions of anionic charges on sulfated polysaccharides with positively charged domains of viral envelope glycoproteins, leading to shielding of the functional domain involved in virus attachment to cell surface receptors. But, few direct evidences were reported. In the previous study, we found that sulfated Chuanmingshen violaceum polysaccharides (sCVPS) possessed remarkable inhibitory effect against Newcastle disease virus (NDV) through inhibition of NDV attachment to host cells. Whether sCVPS bound to hemagglutinin-neuraminidase (HN) leading to inhibition of NDV attachment needs to be further clarified. The present study conducted site-directed mutagenesis of possible positively charged residues of HN, and found that mutants R197G, H199G, R363G, and R523G could significantly decrease the inhibitory effects of sCVPS on receptor binding ability through hemadsorption assay, especially R363G which suggested that binding to R363 is more effective to shield the sialic acid binding sites. Dual mutants (R363G/R197G, R363G/H199G and R363G/R523G) induced more decreased inhibitory effect of sCVPS than single mutants. The immunofluorescence study using FITC-labeled sCVPS found that the fluorescence intensity of mutants R363G and R363G/H199G were significantly decreased. The binding kinetics of sCVPS to HN measured by surface plasmon resonance indicated that sCVPS had a higher binding affinity for wild-type HN than mutants R363G and R363G/H199G. Plaque reduction study was performed using recombinant NDV with mutant HNR363G and HNR363G/H199G, which showed significantly decreased inhibitory effects of sCVPS against mutant NDV adsorption to BHK-21 cells. These results suggested that the residues R197, H199, R363, and R523 were the binding sites for sCVPS, especially R363 act as the main interaction site. The present study provided direct evidence for the theory that antiviral mechanism of sulfated polysaccharides attributed to anionic groups binding to the positively charged residues of viral proteins which led to the shielding of receptor binding sites.
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Affiliation(s)
- Xu Song
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lin Liu
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Wei Hu
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaoxia Liang
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Changliang He
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lizi Yin
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Gang Ye
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yuanfeng Zou
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lixia Li
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Huaqiao Tang
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Renyong Jia
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China
| | - Zhongqiong Yin
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130 China.
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Tavassoli A, Soleymani S, Haghparast A, Hashemi Tabar G, Bassami MR, Dehghani H. Reverse Genetics Assembly of Newcastle Disease Virus Genome Template Using Asis-Sal-Pac BioBrick Strategy. Biol Proced Online 2020; 22:9. [PMID: 32377174 PMCID: PMC7193399 DOI: 10.1186/s12575-020-00119-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/18/2020] [Indexed: 11/25/2022] Open
Abstract
Background The BioBrick construction as an approach in synthetic biology provides the ability to assemble various gene fragments. To date, different BioBrick strategies have been exploited for assembly and cloning of a variety of gene fragments. We present a new BioBrick strategy, here referred as Asis-Sal-Pac BioBrick, which we used for the assembly of NDV as a candidate for single-stranded non-segmented, negative-sense RNA genome viruses. Results In the present study, we isolated three NDVs from clinical samples which were classified into the VIId genotype based on their pathogenicity and phylogenetic analyses. Then, SalI, AsisI, and PacI enzymes were used to design and develop a novel BioBrick strategy, which enabled us to assemble the NDV genome, adopting the “rule of six”. In this method, in each assembly step, the restriction sites in the newly formed destination plasmid are reproduced, which will be used for the next insertion. In this study using two overlapping PCRs, the cleavage site of the F gene was also modified from 112RRQKRF117to 112GRQGRL117 in order to generate the attenuated recombinant NDV. Finally, in order to construct the recombinant NDV viruses, the plasmids harboring the assembled full-length genome of the NDV and the helper plasmids were co-transfected into T7-BHK cells. The rescue of the recombinant NDVwas confirmed by RT-PCR and HA tests. Conclusions These findings suggest that the combination of reverse genetic technology and BioBrick assembly have the potential to be applied for the development of novel vaccine candidates. This promising strategy provides an effective and reliable approach to make genotype-matched vaccines against specific NDV strains or any other virus.
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Affiliation(s)
- Amin Tavassoli
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Safoura Soleymani
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Alireza Haghparast
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.,2Immunology Section, Department of Pathobiology , Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Gholamreza Hashemi Tabar
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Mohammad Reza Bassami
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Hesam Dehghani
- 1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.,3Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.,4Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
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7
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Dimitrov KM, Abolnik C, Afonso CL, Albina E, Bahl J, Berg M, Briand FX, Brown IH, Choi KS, Chvala I, Diel DG, Durr PA, Ferreira HL, Fusaro A, Gil P, Goujgoulova GV, Grund C, Hicks JT, Joannis TM, Torchetti MK, Kolosov S, Lambrecht B, Lewis NS, Liu H, Liu H, McCullough S, Miller PJ, Monne I, Muller CP, Munir M, Reischak D, Sabra M, Samal SK, Servan de Almeida R, Shittu I, Snoeck CJ, Suarez DL, Van Borm S, Wang Z, Wong FYK. Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 74:103917. [PMID: 31200111 PMCID: PMC6876278 DOI: 10.1016/j.meegid.2019.103917] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 02/07/2023]
Abstract
Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.
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Affiliation(s)
- Kiril M Dimitrov
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA.
| | - Celia Abolnik
- Department of Production Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, Pretoria 0110, South Africa
| | - Claudio L Afonso
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA.
| | - Emmanuel Albina
- CIRAD, UMR ASTRE, F-97170 Petit-Bourg, Guadeloupe, France; ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France
| | - Justin Bahl
- Center for Ecology of Infectious Disease, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden
| | - Francois-Xavier Briand
- ANSES, Avian and Rabbit Virology Immunology and Parasitology Unit, National reference laboratory for avian Influenza and Newcastle disease, BP 53, 22440 Ploufragan, France
| | - Ian H Brown
- OIE/FAO International Reference Laboratory for Newcastle Disease, Animal and Plant Health Agency (APHA -Weybridge), Addlestone KT15 3NB, UK
| | - Kang-Seuk Choi
- Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs (MAFRA), 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea
| | - Ilya Chvala
- Federal Governmental Budgetary Institution, Federal Centre for Animal Health, FGI ARRIAH, Vladimir 600901, Russia
| | - Diego G Diel
- Department of Veterinary and Biomedical Sciences, Animal Disease, Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD, USA
| | - Peter A Durr
- CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia
| | - Helena L Ferreira
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA; University of Sao Paulo, ZMV, FZEA, Pirassununga 13635900, Brazil
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, Legnaro 35020, Italy
| | - Patricia Gil
- ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France; CIRAD, UMR ASTRE, F-34398 Montpellier, France
| | - Gabriela V Goujgoulova
- National Diagnostic and Research Veterinary Medical Institute, 15 Pencho Slaveikov blvd., Sofia 1606, Bulgaria
| | - Christian Grund
- Friedrich-Loeffler-Institut, 17493 Greifswald, Insel Riems, Germany
| | - Joseph T Hicks
- Center for Ecology of Infectious Disease, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Tony M Joannis
- Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Diagnostics and Biologics, Veterinary Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010, USA
| | - Sergey Kolosov
- Federal Governmental Budgetary Institution, Federal Centre for Animal Health, FGI ARRIAH, Vladimir 600901, Russia
| | - Bénédicte Lambrecht
- Infectious Diseases in Animals, SCIENSANO, Groeselenberg 99, 1180, Ukkel, Brussels, Belgium
| | - Nicola S Lewis
- OIE/FAO International Reference Laboratory for Newcastle Disease, Animal and Plant Health Agency (APHA -Weybridge), Addlestone KT15 3NB, UK; Royal Veterinary College, University of London, 4 Royal College Street, London NW1 0TU, UK
| | - Haijin Liu
- College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi 712100, PR China
| | - Hualei Liu
- China Animal Health and Epidemiology Center (CAHEC), 369 Nanjing Road, Qingdao 266032, China
| | - Sam McCullough
- CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia
| | - Patti J Miller
- Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Road, Athens, GA 30602, USA
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, Legnaro 35020, Italy
| | - Claude P Muller
- Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Dilmara Reischak
- Ministério da Agricultura, Pecuária e Abastecimento, Laboratório Federal de Defesa Agropecuário, Campinas, SP 13100-105, Brazil
| | - Mahmoud Sabra
- Department of Poultry Diseases, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Siba K Samal
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Renata Servan de Almeida
- ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France; CIRAD, UMR ASTRE, F-34398 Montpellier, France
| | - Ismaila Shittu
- Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Chantal J Snoeck
- Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - David L Suarez
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA
| | - Steven Van Borm
- Infectious Diseases in Animals, SCIENSANO, Groeselenberg 99, 1180, Ukkel, Brussels, Belgium
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center (CAHEC), 369 Nanjing Road, Qingdao 266032, China
| | - Frank Y K Wong
- CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia
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8
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A comparative genomic and evolutionary analysis of circulating strains of Avian avulavirus 1 in Pakistan. Mol Genet Genomics 2019; 294:1289-1309. [PMID: 31147843 DOI: 10.1007/s00438-019-01580-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/20/2019] [Indexed: 01/10/2023]
Abstract
Newcastle disease, caused by Avian avulavirus 1 (AAvV 1), is endemic to many developing countries around the globe including Pakistan. Frequent epidemics are not uncommon even in vaccinated populations and are largely attributed to the genetic divergence of prevailing isolates and their transmission in the environment. With the strengthening of laboratory capabilities in Pakistan, a number of genetically diverse AAvV 1 strains have recently been isolated and individually characterized in comparison with isolates reported elsewhere in the world. However, there lacks sufficient comparative genomic and phylogenomic analyses of field circulating strains that can elucidate the evolutionary dynamics over a period of time. Herein, we enriched the whole genome sequences of AAvV reported so far (n = 35) from Pakistan and performed comparative genomic, phylogenetic and evolutionary analyses. Based on these analyses, we found only isolates belonging to genotypes VI, VII and XIII of AAvV 1 in a wide range of avian and human hosts. Comparative phylogeny revealed the concurrent circulation of avulaviruses representing different sub-genotypes such as VIg, VIm, VIIa, VIIb, VIIe, VIIf, VIIi, XIIIb and XIIId. We found that the isolates of genotype VII were more closely associated with viruses of genotype XIII than genotype VI. An inter-genotype comparative residue analysis revealed a few substitutions in structurally and functionally important motifs. Putative recombination events were reported for only one of the captive-wild bird (pheasant)-origin isolates. The viruses of genotype VII had a high genetic diversity as compared to isolates from genotypes VI and XIII and, therefore, have more potential to evolve over a period of time. Taken together, the current study provides an insight into the genetic diversity and evolutionary dynamics of AAvV 1 strains circulating in Pakistan. Such findings are expected to facilitate better intervention strategies for the prevention and control of ND in disease-endemic countries across the globe particularly Pakistan.
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9
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Intracellular fixation buffer inactivates Newcastle disease virus in chicken allantoic fluid, macrophages and splenocytes. J Virol Methods 2017; 251:1-6. [PMID: 28969954 DOI: 10.1016/j.jviromet.2017.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 11/20/2022]
Abstract
Inactivation of Newcastle disease virus (NDV) has been routinely achieved with heat, β-propiolactone, binary ethylenimine, ultraviolet light and formalin. However, these strategies have not been tested for cell surface ligand or receptor phenotype in viral-infected chicken immune cells. To study the capacity of fixation buffers to preserve surface markers while inactivating NDV, a primary splenocyte culture was infected with NDV and incubated with a commercial intracellular fixation buffer (ICB), formulated with 4% formaldehyde. Splenocytes were fixed with a 1:2 dilution of ICB in phosphate buffered saline (PBS) for 45min at 23°C or 4°C and inactivation of NDV was tested in addition to recognition of antigens by antibodies in fixed and non-fixed splenocytes via flow cytometric analysis. The binding and percentage of splenic CD4+ and CD8+ cells were not affected. In addition, NDV titers as high as 109.5 and 107.6 EID50 in allantoic fluid (AF) and macrophages, respectively, were successfully inactivated after 45min at 23°C and 4°C, confirming the ICB's effectiveness in inactivating high concentrations of NDV. In conclusion, high concentrations of NDV in AF, chicken splenocytes, and macrophages can be inactivated using ICB. Additionally, this method did not compromise cell phenotyping of enriched chicken splenocytes.
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10
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Emerging variant of genotype XIII Newcastle disease virus from Northeast India. Acta Trop 2017; 172:64-69. [PMID: 28450210 DOI: 10.1016/j.actatropica.2017.04.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 01/12/2023]
Abstract
Northeast India with its rich and diverse avifauna acts as a hotbed for emerging virulent Newcastle disease virus (NDV) strains. The present work describes the molecular and pathogenic characterization of NDV strain isolated from Pandu, Assam, India. Clinicopathological and genetic analysis showed the virulent nature of NDV strain Pandu. On molecular phylogenetic and evolutionary distance analysis, the NDV strain Pandu formed a distinct clade within the genotype XIII of class II NDV, suggesting a new sub-genotype XIIIc. The accumulation of mutations in the NDV strain Pandu makes it divergent enough to be considered as a new sub-genotype. The proposed NDV sub-genotype XIIIc consists of strains recently reported from eastern and northeastern India.
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11
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Emergence of a deviating genotype VI pigeon paramyxovirus type-1 isolated from India. Arch Virol 2017; 162:2169-2174. [PMID: 28349356 DOI: 10.1007/s00705-017-3340-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/17/2017] [Indexed: 01/13/2023]
Abstract
Pigeon paramyxovirus type 1 (PPMV-1) is an antigenic variant of avian paramyxovirus type 1 (APMV-1), which infects pigeons. The virus causes high morbidity and mortality, creating an alarming state for the poultry industry. The present work describes the molecular and pathogenic characterization of a PPMV-1 strain isolated from pigeon in Bhopal, India. Complete genome sequence analysis revealed a genome of 15,192 nucleotides encoding six genes organized in the order 3'-N-P-M-F-HN-L-5'. The fusion gene sequence analysis showed the presence of multiple basic amino acids 112R-R-Q-K-R-F117 at the cleavage site corresponding to pathogenic strains. The mean death time and intracerebral pathogenicity index values indicated a mesogenic nature for the PPMV-1 isolate. On phylogenetic analysis, the strain clustered with genotype VI viruses, including isolates from pigeon and dove. The Bhopal strain showed significant intra and inter-genotype evolutionary distance, suggesting the emergence of a new sub-genotype, VIj.
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12
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Das M, Kumar S. Evidence of independent evolution of genotype XIII Newcastle disease viruses in India. Arch Virol 2016; 162:997-1007. [PMID: 28035479 DOI: 10.1007/s00705-016-3182-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
Abstract
Despite the prevalence of Newcastle disease virus (NDV) outbreaks in India through the decades, there has been little genetic characterisation of the virulent strains circulating in Northeast India. In 2014, a poultry farm in the Kamrup district of Assam reported an ND outbreak. In this study, genetic analysis and clinicopathological tests showed the virulent nature of the isolate Kamrup. Based on prudent classification criteria, the virulent strain Kamrup was found to be most closely related to members of genotype XIII of class II NDV. A phylogenetic analysis of NDV strains suggested three sub-genotypes: XIIIa, XIIIb and XIIIc. NDV strain Kamrup belonged to sub-genotype XIIIc. Sub-genotype XIIIc isolates were similar to the 1982 isolate from cockatoo and appeared to have evolved parallel to the preceding genotype XIII viruses circulating in India. The high genetic diversity and frequency of mutations observed in the envelope glycoproteins of strain Kamrup demonstrate the evolution of the pandemic genotype XIII NDV in India, which further undermines and complicates of NDV management in India.
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Affiliation(s)
- Moushumee Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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13
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Morla S, Shah M, Kaore M, Kurkure NV, Kumar S. Molecular characterization of genotype XIIIb Newcastle disease virus from central India during 2006–2012: Evidence of its panzootic potential. Microb Pathog 2016; 99:83-86. [DOI: 10.1016/j.micpath.2016.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 11/28/2022]
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Effects of Chicken Interferon Gamma on Newcastle Disease Virus Vaccine Immunogenicity. PLoS One 2016; 11:e0159153. [PMID: 27409587 PMCID: PMC4943709 DOI: 10.1371/journal.pone.0159153] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/28/2016] [Indexed: 02/06/2023] Open
Abstract
More effective vaccines are needed to control avian diseases. The use of chicken interferon gamma (chIFNγ) during vaccination is a potentially important but controversial approach that may improve the immune response to antigens. In the present study, three different systems to co-deliver chIFNγ with Newcastle disease virus (NDV) antigens were evaluated for their ability to enhance the avian immune response and their protective capacity upon challenge with virulent NDV. These systems consisted of: 1) a DNA vaccine expressing the Newcastle disease virus fusion (F) protein co-administered with a vector expressing the chIFNγ gene for in ovo and booster vaccination, 2) a recombinant Newcastle disease virus expressing the chIFNγ gene (rZJ1*L/IFNγ) used as a live vaccine delivered in ovo and into juvenile chickens, and 3) the same rZJ1*L/IFNγ virus used as an inactivated vaccine for juvenile chickens. Co-administration of chIFNγ with a DNA vaccine expressing the F protein resulted in higher levels of morbidity and mortality, and higher amounts of virulent virus shed after challenge when compared to the group that did not receive chIFNγ. The live vaccine system co-delivering chIFNγ did not enhanced post-vaccination antibody response, nor improved survival after hatch, when administered in ovo, and did not affect survival after challenge when administered to juvenile chickens. The low dose of the inactivated vaccine co-delivering active chIFNγ induced lower antibody titers than the groups that did not receive the cytokine. The high dose of this vaccine did not increase the antibody titers or antigen-specific memory response, and did not reduce the amount of challenge virus shed or mortality after challenge. In summary, regardless of the delivery system, chIFNγ, when administered simultaneously with the vaccine antigen, did not enhance Newcastle disease virus vaccine immunogenicity.
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Isolation of novel variants of infectious bursal disease virus from different outbreaks in Northeast India. Microb Pathog 2016; 93:131-6. [PMID: 26854869 DOI: 10.1016/j.micpath.2016.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 02/03/2016] [Accepted: 02/03/2016] [Indexed: 11/21/2022]
Abstract
Infectious bursal disease virus (IBDV) is a highly infectious disease of young chicken that predominantly affects the immune system. In the present study, we are reporting first comprehensive study of IBDV outbreaks from the Northeastern part of India. Northeast India shares a porous border with four different countries; and as a rule any outbreak in the neighboring countries substantially affects the poultry population in the adjoining states. Nucleotide sequence analysis of the VP2 gene of the IBDV isolates from the Northeastern part of India suggested the extreme virulent nature of the virus. The virulent marker amino acids (A222, I242, Q253, I256 and S299) in the hypervariable region of the Northeastern isolates were found identical with the reported very virulent strains of IBDV. A unique insertion of I/L294V was recorded in all the isolates of the Northeastern India. The study will be useful in understanding the circulating pathotypes of IBDV in India.
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16
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Kumar S, Koul M. Newcastle disease virus: A constant threat to the poultry industry in India. Vaccine 2016; 34:597-598. [DOI: 10.1016/j.vaccine.2015.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/05/2015] [Accepted: 12/10/2015] [Indexed: 02/06/2023]
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