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Guseva NA, Kolosov SN, Zinyakov NG, Andriyasov AV, Yin R, Scherbakova LO, Ovchinnikova EV, Nikonova ZB, Andreychuk DB, Sprygin AV, Chvala IA, Moroz NV. Analysis of Avian Orthoavulavirus 1 Detected in the Russian Federation between 2017 and 2021. Vaccines (Basel) 2023; 11:1032. [PMID: 37376421 DOI: 10.3390/vaccines11061032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Newcastle disease virus (NDV, Avian orthoavulavirus type 1, AOAV-1) is a contagious high-impact poultry pathogen with infections detected worldwide. In the present study, 19,500 clinical samples from wild bird species and poultry collected from 28 regions of Russia between 2017 and 2021 were screened for the presence of the AOAV-1 genome. NDV RNA was detected in 15 samples from wild birds and 63 samples from poultry. All isolates were screened for a partial sequence of the fusion (F) gene that included the cleavage site. Phylogenetic analysis demonstrated that lentogenic AOAV-1 I.1.1, I.1.2.1, and II genotypes were dominant among vaccine-like viruses in the territory of the Russian Federation. A vaccine-like virus with a mutated cleavage site (112-RKQGR^L-117) was detected in turkeys. Among the virulent AOAV-1 strains, viruses of the XXI.1.1, VII.1.1, and VII.2 genotypes were identified. The cleavage site of viruses of the XXI.1.1 genotype had a 112-KRQKR^F-117 amino acid sequence. The cleavage site of viruses with VII.1.1 and VII.2 genotypes had a 112-RRQKR^F-117 amino acid sequence. The data collected by the present study demonstrate the distribution and dominance of the virulent VII.1.1 genotype in the Russian Federation between 2017 and 2021.
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Affiliation(s)
- Nelly A Guseva
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Sergey N Kolosov
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Nikolay G Zinyakov
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Artem V Andriyasov
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Renfu Yin
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Lidya O Scherbakova
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Evgenia V Ovchinnikova
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Zoya B Nikonova
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Dmitry B Andreychuk
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Alexander V Sprygin
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Ilya A Chvala
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
| | - Natalia V Moroz
- Reference Laboratory for Avian Viral Diseases, FGBI "Federal Centre for Animal Health" (FGBI "ARRIAH"), 600901 Vladimir, Russia
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Wu J, Lu R, Wang J, Su J, Gu C, Xie Q, Zhu H, Xiao J, Liu W. Establishment of reverse genetics for genotype VII Newcastle disease virus and altering the cell tropism by inserting TMPRSS2 into the viral genome. Virus Genes 2023:10.1007/s11262-023-01999-9. [PMID: 37103648 PMCID: PMC10133899 DOI: 10.1007/s11262-023-01999-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 04/28/2023]
Abstract
Newcastle disease (ND) is the most important infectious disease in poultry, which is caused by avian orthoavulavirus type 1 (AOAV-1), previously known as Newcastle disease virus (NDV). In this study, an NDV strain SD19 (GenBank accession number OP797800) was isolated, and phylogenetic analysis suggested the virus belongs to the class II genotype VII. After generating wild-type rescued SD19 (rSD19), the attenuating strain (raSD19) was generated by mutating the F protein cleavage site. To explore the potential role of the transmembrane protease, serine S1 member 2 (TMPRSS2), the TMPRSS2 gene was inserted into the region between the P and M genes of raSD19 to generate raSD19-TMPRSS2. Besides, the coding sequence of the enhanced green fluorescent protein (EGFP) gene was inserted in the same region as a control (rSD19-EGFP and raSD19-EGFP). The Western blot, indirect immunofluorescence assay (IFA), and real-time quantitative PCR were employed to determine the replication activity of these constructs. The results reveal that all the rescued viruses can replicate in chicken embryo fibroblast (DF-1) cells; however, the proliferation of raSD19 and raSD19-EGFP needs additional trypsin. We next evaluated the virulence of these constructs, and our results reveal that the SD19, rSD19, and rSD19-EGFP are velogenic; the raSD19 and raSD19-EGFP are lentogenic; and the raSD19-TMPRSS2 are mesogenic. Moreover, due to the enzymatic hydrolysis of serine protease, the raSD19-TMPRSS2 can support itself to proliferate in the DF-1 cells without adding exogenous trypsin. These results may provide a new method for the NDV cell culture and contribute to ND's vaccine development.
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Affiliation(s)
- Jing Wu
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Rongguang Lu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen, 518172, Guangdong, People's Republic of China
| | - Jigui Wang
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jun Su
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Chenchen Gu
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Qianqian Xie
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Hui Zhu
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jun Xiao
- Department of Geriatrics, The Eight Medical Centre, Chinese PLA General Hospital, Beijing, China.
| | - Weiquan Liu
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
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Hejazi Z, Tabatabaeizadeh S, Toroghi R, Farzin H, Saffarian P. First detection and characterisation of sub-genotype XIII.2.1 Newcastle disease virus isolated from backyard chickens in Iran. Vet Med Sci 2022; 8:2521-2531. [PMID: 36084260 PMCID: PMC9677366 DOI: 10.1002/vms3.928] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Newcastle disease (ND) is an economically significant poultry disease worldwide. During field surveillance for ND in 2010 in Iran, a backyard chicken flock showed clinical signs of ND with 100% mortality. OBJECTIVES We aimed to characterise genetically, biologically and epidemiologically an exotic virulent ND virus (NDV) detected in Iran. METHODS After observing high mortality, dead birds were sampled and then disposed of by burial, and the chicken house was disinfected. Tissue samples were molecularly tested for NDV. The genetic homogeneity of the isolate RT30/2010 was tested by plaque assay, and then a large virus plaque was used for the second step of plaque purification. Fusion and matrix complete genes were sequenced and used for genotyping and epidemiological tracing. We tested biological pathotypes using mean death time (MDT) and intracerebral pathogenicity index (ICPI) assays. RESULTS The isolate formed heterogeneous plaques in chicken embryo fibroblast cells. The second step of plaque purification produced homogeneous and large plaques. Phylogenetic analysis using both genes classified the virus into sub-genotype XIII.2.1. Nucleic acid and amino acid identities of RT30/2010 fusion gene with the closest available isolate SPVC/Karachi/NDV/43 are 97.95% and 98.73%, respectively. Isolate has 112 RRRKRF117 motif at the fusion cleavage site, and pathogenicity tests showed MDT of 56.4 h and ICPI of 1.85. CONCLUSIONS This study presents the first detection and characterisation of a velogenic NDV of sub-genotype XIII.2.1 from Iran. Our follow-up surveillance for ND shows that timely virus detection and carcass management have led to the cessation of virus transmission in Iran.
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Affiliation(s)
- Zahra Hejazi
- Department of Microbiology, Science and Research BranchIslamic Azad UniversityTehranIran
| | - Seyed‐Elias Tabatabaeizadeh
- Mashhad Branch, Razi Vaccine and Serum Research InstituteAgricultural ResearchEducation and Extension Organization (AREEO)MashhadIran
| | - Reza Toroghi
- Mashhad Branch, Razi Vaccine and Serum Research InstituteAgricultural ResearchEducation and Extension Organization (AREEO)MashhadIran
| | - Hamidreza Farzin
- Mashhad Branch, Razi Vaccine and Serum Research InstituteAgricultural ResearchEducation and Extension Organization (AREEO)MashhadIran
| | - Parvaneh Saffarian
- Department of Microbiology, Science and Research BranchIslamic Azad UniversityTehranIran
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Pelosi B. Developing a bioinformatics pipeline for comparative protein classification analysis. BMC Genom Data 2022; 23:43. [PMID: 35668373 PMCID: PMC9172112 DOI: 10.1186/s12863-022-01045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: data collection, unbalanced classification or labelling of the data.As an alternative, I propose the use of a bioinformatics pipeline to search for and classify information from protein databases. Hence, to evaluate the efficiency and accuracy of the pipeline, I focused on the carotenoid biosynthetic genes and developed a filtering approach to retrieve orthologs clusters in two well-studied plants that belong to the Brassicaceae family: Arabidopsis thaliana and Brassica rapa Pekinensis group. The result obtained has been compared with previous studies on carotenoid biosynthetic genes in B. rapa where phylogenetic analysis was conducted. RESULTS The developed bioinformatics pipeline relies on commercial software and multiple databeses including the use of phylogeny, Gene Ontology terms (GOs) and Protein Families (Pfams) at a protein level. Furthermore, the phylogeny is coupled with "population analysis" to evaluate the potential orthologs. All the steps taken together give a final table of potential orthologs. The phylogenetic tree gives a result of 43 putative orthologs conserved in B. rapa Pekinensis group. Different A. thaliana proteins have more than one syntenic ortholog as also shown in a previous finding (Li et al., BMC Genomics 16(1):1-11, 2015). CONCLUSIONS This study demonstrates that, when the biological features of proteins of interest are not specific, I can rely on a computational approach in filtering steps for classification purposes. The comparison of the results obtained here for the carotenoid biosynthetic genes with previous research confirmed the accuracy of the developed pipeline which can therefore be applied for filtering different types of datasets.
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Affiliation(s)
- Benedetta Pelosi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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5
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Characterization of Newcastle disease virus in broiler flocks with respiratory symptoms in some provinces of Iran. Mol Biol Rep 2021; 48:7281-7291. [PMID: 34623594 DOI: 10.1007/s11033-021-06728-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Newcastle disease, is one of the most important diseases of the poultry industry, has many economic losses. The aim of this study was to isolate and determine the molecular identity of Newcastle disease virus in 40 broiler flocks with respiratory symptoms in four provinces of Iran. METHODS AND RESULTS Samples of farms with respiratory symptoms were collected from different regions of Isfahan, East Azerbaijan, Golestan, and Khuzestan provinces and inoculated into 9-day-old embryonated chicken eggs. The Reverse-transcription polymerase chain reaction (RT-PCR) was performed to detect the Newcastle disease virus in allantoic fluid. Of the 40 flocks, the virus was isolated and identified in 16 flocks. The PCR products of 16 isolates were sequenced, and a phylogenetic tree was drawn. Accordingly, six isolates were in genotype II and ten isolates were in subgenotype VII.1.1 (VIId) of class II. CONCLUSION Both genotypes were present in all four provinces. The isolates of Khuzestan province showed the greatest diversity compared to the other three provinces. The similarity of isolates belonging to genotype II in this study was observed with Pakistan, China, and Nigeria, and other isolates were similar to previous isolates in Iran. Also, the highest amino acid sequence in the F-protein cleavage site was 112RRQKR/F117 for VII.1.1 (VIId) genotype isolates and 112GRQGR/L117 for II genotype isolates.
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Shafaati M, Ghorbani M, Mahmodi M, Ebadi M, Jalalirad R. Molecular evaluation and genetic characterisation of Newcastle disease virus's haemagglutinin-neuraminidase protein isolated from broiler chickens in Iran. Vet Med Sci 2021; 8:219-228. [PMID: 34606181 PMCID: PMC8788978 DOI: 10.1002/vms3.629] [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] [Indexed: 11/29/2022] Open
Abstract
Background Newcastle disease (ND) virus (NDV) is one of the major pathogens in poultry farms that causes severe economic damages to the poultry industry, especially broiler chicken and turkey farms. Despite the endemicity of ND and its many epidemics in the country, the nature of the Iranian strain of the Newcastle virus is still largely unknown. This study aimed to characterise and evaluate NDV isolates obtained from commercial poultry farms in Iran in 2019 through haemagglutinin‐neuraminidase (HN) gene sequencing. Method HN gene of each NDV isolate was amplified and sequenced using specific primers followed by phylogenetic analysis of full length of HN gene open reading frame and amino acid (aa) sequence of HN. Results Phylogenetic analysis of the HN gene showed that the virus is very closely related to genotypes VII and III. Analysis of HN gene nucleotide sequences showed that all isolates encode proteins with a length of 571 aa. Conclusion Results of the present study are useful for a better understanding of molecular epidemiology of indigenous NDV strains and determining important molecular differences between fields and commonly used vaccine strains related to main immunogenic proteins.
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Affiliation(s)
- Mohammadreza Shafaati
- Department of cellular & molecular biology, Faculty of Basic Sciences, Hamedan Branch, Islamic Azad University, Hamadan, Iran
| | - Masoud Ghorbani
- Department of Research and Development, Pasteur Institute of Iran, The production and Research Complex, 25 Kilometer Tehran-Kraj Highway, Karaj, Alborz, Iran
| | - Minoo Mahmodi
- Department of cellular & molecular biology, Faculty of Basic Sciences, Hamedan Branch, Islamic Azad University, Hamadan, Iran
| | - Mostafa Ebadi
- Department of Biology, Faculty of Sciences, Damaghan Branch, Islamic Azad University, Damghan, Semnan, Iran
| | - Reza Jalalirad
- Department of Research and Development, Pasteur Institute of Iran, The production and Research Complex, 25 Kilometer Tehran-Kraj Highway, Karaj, Alborz, Iran
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Predominance of Fourth Panzootic Newcastle Disease Virus Subgenotype VII.1.1 in Iran and Its Relation to the Genotypes Circulating in the Region. Curr Microbiol 2021; 78:3068-3078. [PMID: 34165608 DOI: 10.1007/s00284-021-02572-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Following recent Newcastle disease virus (NDV) outbreaks in Iranian poultry farms which were mostly associated with lesions of the avian gastrointestinal tract, it was speculated that the scale of the outbreaks could be attributed in part to co-circulating infectious agents or a new NDV genotype/subgenotype. This speculation was due to the isolation of a few 5th panzootic subgenotype VII.2 viruses from Iranian poultry farms in 2017. Samples from different species of commercial and domestic birds were collected from different provinces of Iran, 19 of which were selected for the current study. Phylogenetic analyses showed that the recent outbreaks have been caused by only one agent, i.e. the distinctive NDV subgenotype VII.1.1 (previously known VIIl) viruses that seem to be circulating predominantly in Iran, but have also been sporadically reported from Iraq among neighbouring countries. At most, 96.3-96.7% BLAST identity to non-Iranian VII.1.1 isolates was observed. Genetic distance values of <1% were indicative of high similarity between the isolates, but the values were approaximately 2% when the current isolates were compared to the earliest recorded Iranian VII.1.1 viruses isolated in 2010. Using Bayesian analysis, annual mutation rates of 1.7156E-3 (strict) and 1.9902E-3 (relaxed) over 11 years were obtained. In addition, we report that our laboratories have not detected any genotype XIII strains since 2011. Following up on previous reports, we concluded that currently, and except in Columbiforms, subgenotype VII.1.1 may likely be the predominant subgenotype in many bird species in Iran despite the subgenotype VII.2 being predominant in neighbouring countries.
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Molouki A, Soltani M, Akhijahani MM, Merhabadi MHF, Abtin A, Shoushtari A, Langeroudi AG, Lim SHE, Allahyari E, Abdoshah M, Pourbakhsh SA. Circulation of at Least Six Distinct Groups of Pigeon-Derived Newcastle Disease Virus in Iran Between 1996 and 2019. Curr Microbiol 2021; 78:2672-2681. [PMID: 34008101 DOI: 10.1007/s00284-021-02505-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/18/2020] [Indexed: 11/24/2022]
Abstract
According to the latest Newcastle disease virus (NDV) classification system, Iranian PPMV-1 isolates were classified as either XXI.1.1 or XXI.2 subgenotypes only. However, a few recent studies have suggested the possible existence of other Iranian PPMV-1 genotypes/subgenotypes. Recently, we isolated a PPMV-1 closely related to the African origin subgenotype VI.2.1.2 from an ill captive pigeon in a park aviary in central Tehran (Pg/IR/AMMM160/2019). This subgenotype had never been reported from Iran or neighboring countries. We also isolated a subgenotype VII.1.1 NDV (Pg/IR/AMMM117/2018), usually reported from non-pigeon birds in Iran. The nucleotide distance of AMMM117 was 1.0-2.5% compared to other Iranian subgenotypes VII.1.1 isolates. However, usually the same year VII.1.1 viruses that we isolate from Iranian poultry farms show negligible distances (0.0-0.5%). More isolates are required to study if this difference is due to subgenotype VII.1.1 being circulated and mutated in pigeons. Here, we also characterized two other isolates, namely Pg/IR/AMMM168/2019 and Pg/IR/MAM39/2017. The latter is the first Iranian subgenotype XXI.1.1 to be featured in the NDV datasets of the international NDV consortium. We also investigated the phylogenetic relation of all the published Iranian pigeon-derived NDV to date and updated the grouping according to the latest classification system. We have concluded that at least six different groups of pigeon-derived NDV have been circulating in Iran since 1996, four of which have been reported from just one city over the last seven years. This study suggests that the Iranian pigeon-origin NDV have been more diverse than the Iranian poultry-derived NDV in recent years.
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Affiliation(s)
- Aidin Molouki
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Mohammad Soltani
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran.
| | - Mohsen Mahmoudzadeh Akhijahani
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Mohammad Hossein Fallah Merhabadi
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Alireza Abtin
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Abdelhamid Shoushtari
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Arash Ghalyanchi Langeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Swee Hua Erin Lim
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, 41012, Abu Dhabi, United Arab Emirates
| | | | - Mohammad Abdoshah
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Seyed Ali Pourbakhsh
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
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Nooruzzaman M, Mumu TT, Kabiraj CK, Hasnat A, Rahman MM, Chowdhury EH, Dimitrov KM, Islam MR. Genetic and biological characterization of Newcastle disease viruses circulating in Bangladesh during 2010-2017: further genetic diversification of class II genotype XIII in Southcentral Asia. J Gen Virol 2021; 102. [PMID: 33507145 DOI: 10.1099/jgv.0.001554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Newcastle disease virus (NDV) is endemic in Bangladesh and is a major threat to commercial poultry operations. While complete fusion (F) genes are recommended for molecular characterization and classification of NDV isolates, heretofore, only partial F gene data have been available for Bangladeshi NDVs. To this end, we obtained the full-length F gene coding sequences of 11 representative NDVs isolated in Bangladesh between 2010 and 2017. In addition, one of the viruses (MK934289/chicken/Bangladesh/C161/2010) was used in an experimental infection of chickens to establish the viral pathotype and study gross and microscopic lesions. Phylogenetic analysis provided evidence that all studied Bangladeshi isolates belong to genotype XIII.2 of class II NDVs. Six of the viruses were isolated between 2010 and 2017 and grouped together with isolates from neighbouring India during 2013-2016. Another four Bangladeshi isolates (2010-2016) formed a separate monophyletic branch within XIII.2 and showed high nucleotide distance from the isolates from India and the other six Bangladeshi viruses within the sub-genotype; however, none of these groups fulfils all classification criteria to be named as a separate sub-genotype. The eleventh Bangladeshi virus studied here (C162) was genetically more distant from the remaining isolates. It out-grouped the viruses from sub-genotypes XIII.2.1 and XIII.2.2 and showed more than 9.5 % nucleotide distance from all genotype XIII sub-genotypes. This isolate may represent an NDV variant that is evolving independently from the other viruses in the region. The experimental infection in chickens revealed that the tested isolate (C161) is a velogenic viscerotropic virus. Massive haemorrhages, congestion and necrosis in different visceral organs, and lymphoid depletion in lymphoid tissues, typical for infection with velogenic NDV, were observed. Our findings demonstrate the endemic circulation of sub-genotype XIII.2 in Southcentral Asia and further genetic diversification of these viruses in Bangladesh and neighbouring India. This constant evolution of the viruses may lead to the establishment of new genetic groups in the region. Additional historical and prospective virus and surveillance data from the region and neighbouring countries will allow a more detailed epidemiological inference.
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Affiliation(s)
- Mohammed Nooruzzaman
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Tanjin Tamanna Mumu
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Congriev Kumar Kabiraj
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Azmary Hasnat
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Mijanur Rahman
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Emdadul Haque Chowdhury
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Kiril M Dimitrov
- Texas A&M Veterinary Medical Diagnostic Laboratory, 483 Agronomy Rd, College Station, TX 77843-4471, USA
| | - Mohammad Rafiqul Islam
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
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Toroghi R, Salamatian I, Bassami MR, Irankhah N, Emarloo A, Mahouti A, Ghavi S. Implementation of high-level biosecurity measures can reduce the baseline antibody titers of Newcastle disease in non-integrated layer flocks in northeast Iran. WORLD POULTRY SCI J 2020. [DOI: 10.1080/00439339.2020.1823301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- R. Toroghi
- Department of Veterinary Research and Biotechnology, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization, Mashhad, Iran
- Veterinary Diagnostic Laboratory, MAAD Professional Poultry Hospital, Mashhad, Iran
| | - I. Salamatian
- Department of Veterinary Research and Biotechnology, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization, Mashhad, Iran
- Veterinary Diagnostic Laboratory, MAAD Professional Poultry Hospital, Mashhad, Iran
| | - M. R. Bassami
- Veterinary Diagnostic Laboratory, MAAD Professional Poultry Hospital, Mashhad, Iran
- Division of Poultry Diseases, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - N. Irankhah
- Veterinary Diagnostic Laboratory, MAAD Professional Poultry Hospital, Mashhad, Iran
| | - A. Emarloo
- Veterinary Diagnostic Laboratory, MAAD Professional Poultry Hospital, Mashhad, Iran
| | - A. Mahouti
- Veterinary Diagnostic Laboratory, MAAD Professional Poultry Hospital, Mashhad, Iran
| | - S. Ghavi
- Veterinary Diagnostic Laboratory, MAAD Professional Poultry Hospital, Mashhad, Iran
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Esmaeelzadeh Dizaji R, Ghalyanchilangeroudi A, Vasfi Marandi M, Hosseini H, Karimi V, Ziafatikafi Z, Molouki A, Fallah Mehrabadi MH. Complete genome sequence of a subgenotype XXI.1.1 pigeon paramyxovirus type 1 virus (PPMV‑1) isolated from Iran in 2018 and phylogenetic analysis of a possible novel, but unassigned, PPMV-1 group isolated in 2014. Comp Immunol Microbiol Infect Dis 2020; 73:101565. [PMID: 33126169 DOI: 10.1016/j.cimid.2020.101565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 10/03/2020] [Accepted: 10/08/2020] [Indexed: 11/30/2022]
Abstract
Newcastle disease (ND) is one of the most serious infectious and contagious viral diseases in avian species. Recently, several ND outbreaks in pigeon caused by pigeon paramyxovirus serotype-1 (PPMV-1) have been reported from Iran, but unfortunately, phylogenetic studies have been mostly conducted on partial sequence of NDV fusion (F) gene. In addition, a complete genome data of Iranian PPMV-1 strains are not available. In the present study, a PPMV-1, named Avian avulavirus 1/pigeon/Iran/UT-EGV/2018, isolated from an infected pigeon, was subjected to whole-genome sequencing. The isolate showed an MDT of 74 h, thus categorizing it as mesogenic. The phylogenetic analysis based on the F gene sequence revealed the isolate belongs to XXI.1.1 subgenotype (min 0.9 % and max 3 %). To our knowledge, our study is the first study to publish the complete genome of a PPMV-1 from Iran. According to BLAST results, the whole genome of UT-EGV had high homology with some Russian, Egyptian and Ukrainian strains (the highest was 96.55 %). Additionally, we conducted a phylogenetic analysis on five PPMV-1 that we isolated in 2014 to find that they may belong to a completely unreported subgenotype (6 % distance when compared as a group). The information obtained from this study can be useful in preventive measures, including constructing an effective vaccine against PPMV-1 in Iran.
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Affiliation(s)
- Reza Esmaeelzadeh Dizaji
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Arash Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mehdi Vasfi Marandi
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Hossein Hosseini
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University, Karaj Branch, Karaj, Iran
| | - Vahid Karimi
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Zahra Ziafatikafi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Aidin Molouki
- Department of Poultry Diseases, RAZI Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Mohammad Hossein Fallah Mehrabadi
- Department of Poultry Diseases, RAZI Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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12
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Li SY, You GJ, Du JT, Xia J, Wen YP, Huang XB, Zhao Q, Han XF, Yan QG, Wu R, Cao SJ, Huang Y. A class Ⅰ lentogenic newcastle disease virus strain confers effective protection against the prevalent strains. Biologicals 2019; 63:74-80. [PMID: 31753578 DOI: 10.1016/j.biologicals.2019.11.001] [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: 04/04/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022] Open
Abstract
The traditional vaccine strains, such as LaSota, do not completely prevent the shedding of NDV. An ideal vaccine which could not only prevent the clinical signs, but significantly reduce the shedding of NDV is urgently needed for the eradication of ND. In this study, an NDV isolate APMV-1/Chicken/China (SC)/PT3/2016 (hereafter referred as PT3) was identified as a class Ⅰ NDV and a lentogenic strain. The antigenic relationship between PT3 and 3 other NDV strains, including vaccine strain LaSota and 2 prevalent genotype Ⅶd and Ⅵb strains were analyzed. The protective efficacy of PT3 and LaSota against challenge with genotype Ⅶd and Ⅵb strains were assessed. The antigenic analysis result showed that 4 strains belong to the single serotype and the PT3 antiserum exhibited the highest HI titer against 3 other NDV strains. The results of protective efficacy showed that both of LaSota and PT3 could provide 100% survivability for infected chickens. However, PT3 performed better in inducing higher humoral responses and reducing virus shedding than the LaSota strain. Lentogenic strains from Class I NDV appear to be promising vaccine candidates for the control of ND, and allows for the easy discrimination of field NDV and vaccine strains.
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Affiliation(s)
- Shu-Yun Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Guo-Jin You
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Ji-Teng Du
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Jing Xia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Yi-Ping Wen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Xiao-Bo Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Qing Zhao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Xin-Feng Han
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Qi-Gui Yan
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Rui Wu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - San-Jie Cao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
| | - Yong Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Wenjiang, Chengdu, Sichuan, 611130, PR China.
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13
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Development of Avian Avulavirus 1 Epitope-Based Vaccine Pattern Based on Epitope Prediction and Molecular Docking Analysis: An Immunoinformatic Approach. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09952-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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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: 217] [Impact Index Per Article: 43.4] [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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15
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Teng JLL, Wernery U, Lee HH, Joseph S, Fung J, Elizabeth SK, Yeong KY, Kinne J, Chan KH, Lau SKP, Woo PCY. First Isolation and Rapid Identification of Newcastle Disease Virus from Aborted Fetus of Dromedary Camel Using Next-Generation Sequencing. Viruses 2019; 11:v11090810. [PMID: 31480604 PMCID: PMC6783818 DOI: 10.3390/v11090810] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/23/2019] [Accepted: 08/30/2019] [Indexed: 02/07/2023] Open
Abstract
Newcastle disease virus (NDV) causes morbidities and mortalities in wild and domestic birds globally. For humans, exposure to infected birds can cause conjunctivitis and influenza-like symptoms. NDV infections in mammals are rarely reported. In this study, using next-generation sequencing, an NDV was identified and isolated from Vero cells inoculated with the nasal swab of an aborted dromedary fetus in Dubai, during the time when an NDV outbreak occurred in a pigeon farm located in close proximity to the dairy camel farm where the mother of the aborted dromedary fetus resided, and there were a lot of pigeons in the camel farm. Genome analysis revealed that the structurally and functionally important features of other NDVs were also present in this dromedary NDV genome. Phylogenetic analysis based on the nucleotide sequences of fusion protein (F), hemagglutinin-neuraminidase protein (HN) and complete polyprotein showed that the virus belonged to sub-genotype VIg of class II NDV and is most closely related to pigeon NDVs in Egypt in the same year. The present study is the first that demonstrated isolation of NDV in dromedaries. Further study is warranted to investigate the relationship between NDV infection and abortion.
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Affiliation(s)
- Jade Lee Lee Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai 00000, United Arab Emirates.
| | - Hwei Huih Lee
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Sunitha Joseph
- Central Veterinary Research Laboratory, Dubai 00000, United Arab Emirates
| | - Joshua Fung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | | | - Kai Yan Yeong
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Joerg Kinne
- Central Veterinary Research Laboratory, Dubai 00000, United Arab Emirates
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Susanna Kar Pui Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Patrick Chiu Yat Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
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16
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Aziz-Ul-Rahman, Rohaim MA, El Naggar RF, Mustafa G, Chaudhry U, Shabbir MZ. Comparative clinico-pathological assessment of velogenic (sub-genotype VIIi) and mesogenic (sub-genotype VIm) Avian avulavirus 1 in chickens and pigeons. Avian Pathol 2019; 48:610-621. [PMID: 31403322 DOI: 10.1080/03079457.2019.1648751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Newcastle disease (ND), caused by virulent Avian avulavirus 1 (AAvV 1), affects a wide range of avian species worldwide. Recently, several AAvVs of diverse genotypes have emerged with varying genomic and residue substitutions, and subsequent clinical impact on susceptible avian species. We assessed the clinico-pathological influence of two different AAvV 1 pathotypes [wild bird originated-velogenic strain (sub-genotype VIIi, MF437287) and feral pigeon originated-mesogenic strain (sub-genotype VIm, KU885949)] in commercial broiler chickens and pigeons. The velogenic strain caused 100% mortality in both avian species while the mesogenic strain caused 0% and 30% mortality in chickens and pigeons, respectively. Both strains showed tissue tropism for multiple tissues including visceral organs; however, minor variances were observed according to host and pathotype. The observed gross and microscopic lesions were typical of AAvV 1 infection. Utilizing oropharyngeal and cloacal swabs, a comparable pattern of viral shedding was observed for both strains from each of the infected individuals of both avian species. The study concludes a varying susceptibility of chickens and pigeons to different wild bird-originated AAvV 1 pathotypes and, therefore, suggests continuous monitoring and surveillance of currently prevailing strains for effective control of the disease worldwide, particularly in disease-endemic countries.
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Affiliation(s)
- Aziz-Ul-Rahman
- Department of Microbiology, University of Veterinary and Animal Sciences , Lahore Pakistan.,Quality Operation Laboratory, University of Veterinary and Animal Sciences , Lahore Pakistan
| | - Mohammed A Rohaim
- Department of Virology, Faculty of Veterinary Medicine, Cairo University , Giza , Egypt.,Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University , Lancaster , UK
| | - Rania F El Naggar
- Department of Virology, Faculty of Veterinary Medicine, University of Sadat City , Sadat , Egypt
| | - Ghulam Mustafa
- Department of Pathology, University of Veterinary and Animal Sciences , Lahore , Pakistan
| | - Umer Chaudhry
- Roslin Institute, Easter Bush Veterinary Centre, University of Edinburgh , Roslin, Midlothian , UK
| | - Muhammad Zubair Shabbir
- Quality Operation Laboratory, University of Veterinary and Animal Sciences , Lahore Pakistan
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17
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Enhanced phylogenetic resolution of Newcastle disease outbreaks using complete viral genome sequences from formalin-fixed paraffin-embedded tissue samples. Virus Genes 2019; 55:502-512. [PMID: 31089865 DOI: 10.1007/s11262-019-01669-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
Abstract
Highly virulent Newcastle disease virus (NDV) causes Newcastle disease (ND), which is a threat to poultry production worldwide. Effective disease management requires approaches to accurately determine sources of infection, which involves tracking of closely related viruses. Next-generation sequencing (NGS) has emerged as a research tool for thorough genetic characterization of infectious organisms. Previously formalin-fixed paraffin-embedded (FFPE) tissues have been used to conduct retrospective epidemiological studies of related but genetically distinct viruses. However, this study extends the applicability of NGS for complete genome analysis of viruses from FFPE tissues to track the evolution of closely related viruses. Total RNA was obtained from FFPE spleens, lungs, brains, and small intestines of chickens in 11 poultry flocks during disease outbreaks in Pakistan. The RNA was randomly sequenced on an Illumina MiSeq instrument and the raw data were analyzed using a custom data analysis pipeline that includes de novo assembly. Genomes of virulent NDV were detected in 10/11 birds: eight nearly complete (> 95% coverage of concatenated coding sequence) and two partial genomes. Phylogeny of the NDV complete genome coding sequences was compared to current methods of analysis based on the full and partial fusion genes and determined that the approach provided a better phylogenetic resolution. Two distinct lineages of sub-genotype VIIi NDV were identified to be simultaneously circulating in Pakistani poultry. Non-targeted NGS of total RNA from FFPE tissues coupled with de novo assembly provided a reliable, safe, and affordable method to conduct epidemiological and evolutionary studies to facilitate management of ND in Pakistan.
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18
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Esmaelizad M, Mayahi V. Analysis of natural recombination and host-related evolutionary dynamics of avian avulavirus 1 isolates based on positive and negative selection from 1948 to 2017. Arch Virol 2019; 164:717-724. [DOI: 10.1007/s00705-018-04130-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/08/2018] [Indexed: 12/26/2022]
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19
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Epidemiological and genetic analysis of Avian avulavirus-1 in Israel reveals parallel circulating strains and a new sub-genotype within genotype VI. INFECTION GENETICS AND EVOLUTION 2018; 66:159-170. [DOI: 10.1016/j.meegid.2018.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/08/2018] [Accepted: 09/17/2018] [Indexed: 11/23/2022]
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20
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Gowthaman V, Ganesan V, Gopala Krishna Murthy TR, Nair S, Yegavinti N, Saraswathy PV, Suresh Kumar G, Udhayavel S, Senthilvel K, Subbiah M. Molecular phylogenetics of Newcastle disease viruses isolated from vaccinated flocks during outbreaks in Southern India reveals circulation of a novel sub‐genotype. Transbound Emerg Dis 2018; 66:363-372. [DOI: 10.1111/tbed.13030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/29/2018] [Accepted: 09/24/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Vasudevan Gowthaman
- Poultry Disease Diagnosis and Surveillance Laboratory Veterinary College and Research Institute Campus Tamil Nadu Veterinary and Animal Sciences University Namakkal India
| | | | | | - Sowmya Nair
- National Institute of Animal Biotechnology Hyderabad India
| | | | | | - Ganesan Suresh Kumar
- Poultry Disease Diagnosis and Surveillance Laboratory Veterinary College and Research Institute Campus Tamil Nadu Veterinary and Animal Sciences University Namakkal India
| | - Shanmugasunderam Udhayavel
- Poultry Disease Diagnosis and Surveillance Laboratory Veterinary College and Research Institute Campus Tamil Nadu Veterinary and Animal Sciences University Namakkal India
| | - Kandasamy Senthilvel
- Poultry Disease Diagnosis and Surveillance Laboratory Veterinary College and Research Institute Campus Tamil Nadu Veterinary and Animal Sciences University Namakkal India
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21
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Prevalence of avian influenza, Newcastle disease, and infectious bronchitis viruses in broiler flocks infected with multifactorial respiratory diseases in Iran, 2015-2016. Trop Anim Health Prod 2018; 51:689-695. [PMID: 30377950 PMCID: PMC7088748 DOI: 10.1007/s11250-018-1743-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/18/2018] [Indexed: 11/04/2022]
Abstract
In this study, the prevalence and spatial distribution of Newcastle disease, infectious bronchitis, and avian influenza have been evaluated in commercial broiler farms in 31 provinces in Iran. In this survey, a total of 233 affected broiler chicken farms were sampled. The infectious bronchitis virus (alone) was detected with highest frequency in 60 farms, and separately or combined with other agents, in 110 farms; Newcastle disease virus, separately, was detected in 28 farms, and in 63 farms separately or combined with other infectious agents; and avian influenza H9N2 was detected in 22 farms separately and in 51 farms separately or concomitant with other infectious agents. The sample tested negative for all H5 serotypes. The results of the present study show that the most prevalent avian viral infectious disease contributing to respiratory syndromes in broiler farms in Iran was infectious bronchitis due to infectious bronchitis virus serotypes variant 2 and 793/B. On the other hand, combined with the alternation of dominant viruses and circulating strains, flocks are exposed to unremitting anamorphic viral infections. Thus, the permanent monitoring of cases that have occurred and the review of vaccination plans of affected flocks every year are some of the necessary measures needed for strategic control of respiratory syndrome in broilers. It is noteworthy that execution of epidemiologic examinations on the cogent factors of prevalence of this syndrome and defeat of vaccination strategy in the flocks is urgent and has to be fulfilled on the definite causes of time.
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