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Amoia CF, Hakizimana JN, Chengula AA, Munir M, Misinzo G, Weger-Lucarelli J. Genomic Diversity and Geographic Distribution of Newcastle Disease Virus Genotypes in Africa: Implications for Diagnosis, Vaccination, and Regional Collaboration. Viruses 2024; 16:795. [PMID: 38793675 PMCID: PMC11125703 DOI: 10.3390/v16050795] [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: 04/16/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
The emergence of new virulent genotypes and the continued genetic drift of Newcastle disease virus (NDV) implies that distinct genotypes of NDV are simultaneously evolving in different geographic locations across the globe, including throughout Africa, where NDV is an important veterinary pathogen. Expanding the genomic diversity of NDV increases the possibility of diagnostic and vaccine failures. In this review, we systematically analyzed the genetic diversity of NDV genotypes in Africa using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Information published between 1999 and 2022 were used to obtain the genetic background of different genotypes of NDV and their geographic distributions in Africa. The following genotypes were reported in Africa: I, II, III, IV, V, VI, VII, VIII, XI, XIII, XIV, XVII, XVIII, XX, and XXI. A new putative genotype has been detected in the Democratic Republic of the Congo. However, of 54 African countries, only 26 countries regularly report information on NDV outbreaks, suggesting that this number may be vastly underestimated. With eight different genotypes, Nigeria is the country with the greatest genotypic diversity of NDV among African countries. Genotype VII is the most prevalent group of NDV in Africa, which was reported in 15 countries. A phylogeographic analysis of NDV sequences revealed transboundary transmission of the virus in Eastern Africa, Western and Central Africa, and in Southern Africa. A regional and continental collaboration is recommended for improved NDV risk management in Africa.
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Affiliation(s)
- Charlie F. Amoia
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, P.O. Box 3019, Morogoro 67125, Tanzania;
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania
| | - Jean N. Hakizimana
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania;
| | - Augustino A. Chengula
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, P.O. Box 3019, Morogoro 67125, Tanzania;
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK;
| | - Gerald Misinzo
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, P.O. Box 3019, Morogoro 67125, Tanzania;
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania;
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA
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Kalonda A, Saasa N, Kajihara M, Nao N, Moonga L, Ndebe J, Mori-Kajihara A, Mukubesa AN, Sakoda Y, Sawa H, Takada A, Simulundu E. Phylogenetic Analysis of Newcastle Disease Virus Isolated from Poultry in Live Bird Markets and Wild Waterfowl in Zambia. Microorganisms 2024; 12:354. [PMID: 38399757 PMCID: PMC10893471 DOI: 10.3390/microorganisms12020354] [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: 01/11/2024] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Poultry production is essential to the economy and livelihood of many rural Zambian households. However, the industry is threatened by infectious diseases, particularly Newcastle disease virus (NDV) infection. Therefore, this study employed next-generation sequencing to characterise six NDV isolates from poultry in Zambia's live bird markets (LBMs) and wild waterfowl. Four NDV isolates were detected from 410 faecal samples collected from chickens in LBMs in Lusaka and two from 2851 wild birds from Lochinvar National Park. Phylogenetic analysis revealed that the four NDVs from LBM clustered in genotype VII and sub-genotype VII.2 were closely related to viruses previously isolated in Zambia and other Southern African countries, suggesting possible local and regional transboundary circulation of the virus. In contrast, the two isolates from wild birds belonged to class I viruses, genotype 1, and were closely related to isolates from Europe and Asia, suggesting the possible introduction of these viruses from Eurasia, likely through wild bird migration. The fusion gene cleavage site motif for all LBM-associated isolates was 112RRQKR|F117, indicating that the viruses are virulent, while the isolates from wild waterfowl had the typical 112ERQER|L117 avirulent motif. This study demonstrates the circulation of virulent NDV strains in LBMs and has, for the first time, characterised NDV from wild birds in Zambia. The study further provides the first whole genomes of NDV sub-genotype VII.2 and genotype 1 from Zambia and stresses the importance of surveillance and molecular analysis for monitoring the circulation of NDV genotypes and viral evolution.
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Affiliation(s)
- Annie Kalonda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (J.N.); (A.N.M.); (H.S.); (A.T.)
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (J.N.); (A.N.M.); (H.S.); (A.T.)
| | - Masahiro Kajihara
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan; (M.K.); (N.N.)
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia;
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan; (M.K.); (N.N.)
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia;
- One Health Research Center, Hokkaido University, N18 W9, Kita-ku, Sapporo 001-0020, Japan
| | - Ladslav Moonga
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia;
| | - Joseph Ndebe
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (J.N.); (A.N.M.); (H.S.); (A.T.)
| | - Akina Mori-Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan;
| | - Andrew Nalishuwa Mukubesa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (J.N.); (A.N.M.); (H.S.); (A.T.)
| | - Yoshihiro Sakoda
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia;
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, N18 W9, Kita-ku, Sapporo 060-0818, Japan
- Division of Biological Response Analysis, Institute for Vaccine Research and Development (IVReD), Hokkaido University, N21 W11, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (J.N.); (A.N.M.); (H.S.); (A.T.)
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan; (M.K.); (N.N.)
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia;
- One Health Research Center, Hokkaido University, N18 W9, Kita-ku, Sapporo 001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Division of Biological Response Analysis, Institute for Vaccine Research and Development (IVReD), Hokkaido University, N21 W11, Kita-ku, Sapporo 001-0020, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Global Virus Network, 725 W Lombard Street, Baltimore, MD 21201, USA
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (J.N.); (A.N.M.); (H.S.); (A.T.)
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- One Health Research Center, Hokkaido University, N18 W9, Kita-ku, Sapporo 001-0020, Japan
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan;
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (J.N.); (A.N.M.); (H.S.); (A.T.)
- Macha Research Trust, Choma 20100, Zambia
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Ather S, Wajid A, Batool A, Noureen A, Ain Q, Ayub G, Molouki A, Sultan IN, Mahmood S, Hanif A, Ahmed N. Genomic and comparative clinico-pathological assessment of two Pakistani pigeon-derived newcastle disease virus sub-genotypes XXI.1.1 and XXI.1.2 isolated in 2017. Comp Immunol Microbiol Infect Dis 2023; 94:101957. [PMID: 36808017 DOI: 10.1016/j.cimid.2023.101957] [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: 09/28/2022] [Revised: 01/07/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
Pigeon paramyxovirus type-1 (PPMV-1) is an antigenic-variant of Newcastle disease virus (NDV) which is associated with infection in Columbidae family. In this study, we isolated two pigeon-derived strains pi/Pak/Lhr/SA_1/17 (designed as SA_1) and pi/Pak/Lhr/SA_2/17 (designed as SA_2) from diseased pigeons collected in Punjab province in 2017. We performed the whole genome, phylogenetic analysis and comparative clinico-pathological evaluation of two viruses in pigeons. Phylogenetic analysis based on fusion (F) gene and complete genome sequences showed that SA_1 belonged to sub-genotype XXI.1.1 and SA_2 clustered in sub-genotype XXI.1.2. SA_1 and SA_2 viruses contributed to morbidity and mortality in pigeons. Remarkably, although the two viruses resulted in comparatively similar pattern of pathogenesis and replication ability in various tissues of infected pigeons, SA_2 could cause more severe histopathological lesions and had comparatively high replication ability in pigeons than SA_1. Moreover, pigeons infected with SA_2 had higher shedding efficiency than that of pigeons infected with SA_1. Moreover, several aa substitutions in the major functional domains of the F and HN proteins might be contributed to the pathogenic differences between the two isolates in pigeons. Overall, these findings provide us with important insight into the epidemiology and evolution of PPMV-1 in Pakistan and laid the foundation for the further elucidation of the mechanism underlying the pathogenic difference of PPMV-1 in pigeons.
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Affiliation(s)
- Safa Ather
- Department of Molecular Biology, Virtual University of Pakistan, Pakistan
| | - Abdul Wajid
- Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan.
| | - Andleeb Batool
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Aasma Noureen
- Department of Biology, Virtual University of Pakistan, Pakistan
| | - Quratul Ain
- Department of Biotechnology, Virtual University of Pakistan, Pakistan
| | - Goher Ayub
- Department of Biotechnology, Virtual University of Pakistan, Pakistan
| | - Aidin Molouki
- Department of Poultry Diseases, RAZI vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Imrana Niaz Sultan
- Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Sara Mahmood
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Atif Hanif
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Nazeer Ahmed
- Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
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Wodajo W, Mohammed N, Tora E, Seyoum W. Sero-prevalence of Newcastle disease and associated risk factors in chickens at backyard chicken production Kindo Koisha, Wolaita zone, Southern Ethiopia. Front Vet Sci 2023; 9:1089931. [PMID: 36699327 PMCID: PMC9868296 DOI: 10.3389/fvets.2022.1089931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Newcastle disease (ND) is a serious infectious disease of poultry caused by virulent strains of Avian Paramyxovirus-1 and has a substantial impact on villages where people's livelihood depends upon poultry farming in several developing countries including Ethiopia. In the district of the study area, no previous studies have been conducted. Thus, the aim of the present study was to estimate individual and household flock level seroprevalence and risk factors for ND in unvaccinated backyard chickens in Kindo Koisha district, Wolaita zone, Ethiopia. A cross-sectional study design was conducted. For the study, household flocks were sampled as a cluster, and backyard chickens within the cluster with an age of more than 3 months were sampled. A total of 598 blood samples were collected from 86 household flocks during the study period. Serum samples were tested for ND antibodies using an Indirect-Enzyme Linked Immuno Sorbent Assay. The overall seroprevalence of ND virus at individual and flock level was 17.06% (95% CI: 14.25-20.29%) and 73.26% (95% CI: 62.79-81.64%), respectively. The ND seropositivity and associated risk factors were assessed at the individual bird and flock level by using ordinary and mixed effect logistic regression, respectively. Ordinary logistic regression revealed that crossbreed chickens had significantly higher odds of ND seropositivity than local breeds, with an odds ratio of 2.15 (95% CI: 1.54-3.00; p < 0.001). The odds of ND seropositivity was significantly higher in backyard chickens which belongs flock size >9 in comparison to <9 with an odds ratio of 3.7 (95% CI: 1.12-12.30; p < 0.031). The potential flock level risk factors related to ND seropositivity in this study were flock size, chicken house cleaning frequency, water source for chickens, dead chicken disposal practice, and distance to the next neighbor household, mixing with wild birds and owning pets. In conclusion, the current study generates significant information on the seroprevalence and the potential risk factors associated with ND at individual and flock level in Kindo Koisha district, Wolaita zone. Consequently, ND vaccination campaigns should be launched, and effective extension programs should also be provided to raise awareness about the disease.
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Affiliation(s)
- Wondimu Wodajo
- Wolaita Sodo Regional Veterinary Laboratory, Department of Microbiology, Wolaita Sodo, Ethiopia
| | - Nejib Mohammed
- Department of Animal Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Ephrem Tora
- Department of Animal Sciences, Arba Minch University, Arba Minch, Ethiopia,*Correspondence: Ephrem Tora ✉
| | - Wasihun Seyoum
- Department of Animal Sciences, Arba Minch University, Arba Minch, Ethiopia
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Epidemiology of Newcastle disease in poultry in Africa: systematic review and meta-analysis. Trop Anim Health Prod 2022; 54:214. [PMID: 35705876 DOI: 10.1007/s11250-022-03198-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/25/2022] [Indexed: 10/18/2022]
Abstract
The present study intended to determine the prevalence of Newcastle disease in unvaccinated backyard poultry in Africa. Using the PRISMA approach, a systematic review and meta-analysis of 107 epidemiological studies was conducted. The meta-analysis identified significant variation of both seroprevalence (I2 = 99.38, P = 0.00) and Newcastle disease virus prevalence (I2 = 99.52, P = 0.00) reported in various studies included in this review. Publication bias was not detected in either case. Seroprevalence of Newcastle disease was 40.2 (95%CI 32.9-47.8). Seroprevalence was significantly influenced by sampling frame and the African region where the studies were conducted. The prevalence of Newcastle disease virus (NDV) was 12% (95%CI 7.3-17.8), and the variation was influenced by sampling frame, diagnostic test, and regions where the studies were conducted. Also, Newcastle disease (ND) accounted for 33.1% (95%CI 11.9-58.1) of sick chickens. Results also indicated that genotypes VI and VII are widely distributed in all countries included in the study. However, genotype V is restricted in East Africa, and genotypes XIV, XVII, and XVIII are restricted in West and Central Africa. On the other hand, genotype XI occurs in Madagascar only. In addition, virulent genotypes were isolated from apparently healthy and sick birds. It is concluded that several genotypes of NDV are circulating and maintained within the poultry population. African countries should therefore strengthen surveillance systems, be able to study the viruses circulating in their territories, and establish control programs.
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Naguib MM, Höper D, Elkady MF, Afifi MA, Erfan A, Abozeid HH, Hasan WM, Arafa AS, Shahein M, Beer M, Harder TC, Grund C. Comparison of genomic and antigenic properties of Newcastle Disease virus genotypes II, XXI and VII from Egypt do not point to antigenic drift as selection marker. Transbound Emerg Dis 2021; 69:849-863. [PMID: 33955204 DOI: 10.1111/tbed.14121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/12/2021] [Accepted: 04/20/2021] [Indexed: 01/27/2023]
Abstract
Newcastle disease (ND), caused by avian orthoavulavirus type-1 (NDV), is endemic in poultry in many regions of the world and causes continuing outbreaks in poultry populations. In the Middle East, genotype XXI, used to be present in poultry in Egypt but has been replaced by genotype VII. We investigated whether virus evolution contributed to superseding and focussed on the antigenic sites within the hemagglutinin-neuraminidase (HN) spike protein. Full-length sequences of an NDV genotype VII isolate currently circulating in Egypt was compared to a genotype XXI isolate that was present as co-infection with vaccine-type viruses (II) in a historical virus isolated in 2011. Amino acid differences in the HN glycoprotein for both XXI and VII viruses amounted to 11.7% and 11.9%, respectively, compared to the La Sota vaccine type. However, mutations within the globular head (aa 126-570), bearing relevant antigenic sites, were underrepresented (a divergence of 8.8% and 8.1% compared to 22.4% and 25.6% within the protein domains encompassing cytoplasmic tail, transmembrane part and stalk regions (aa 1-125) for genotypes XXI and VII, respectively). Nevertheless, reaction patterns of HN-specific monoclonal antibodies inhibiting receptor binding revealed differences between vaccine-type viruses and genotype XXI and VII viruses for epitopes located in the head domain. Accordingly, compared to Egyptian vaccine-type isolates and the La Sota vaccine reference strain, single aa substitutions in 6 of 10 described neutralizing epitopes of HN were found. However, the same alterations in neutralization sensitive epitopes were present in old genotype XXI as well as in newly emerged genotype VII isolates. In addition, isolates were indistinguishable by polyclonal chicken sera raised against different genotypes including vaccine viruses. These findings suggest that factors other than antigenic differences within the HN protein account for facilitating the spread of genotype VII versus genotype XXI viruses in Egypt.
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Affiliation(s)
- Mahmoud M Naguib
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald Insel-Riems, Germany
| | - Magdy F Elkady
- Department of poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Manal A Afifi
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Ahmed Erfan
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Hassanein H Abozeid
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Wafaa M Hasan
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Abdel-Satar Arafa
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Momtaz Shahein
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald Insel-Riems, Germany
| | - Timm C Harder
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald Insel-Riems, Germany
| | - Christian Grund
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald Insel-Riems, Germany
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Jadhav A, Zhao L, Liu W, Ding C, Nair V, Ramos-Onsins SE, Ferretti L. Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections. Viruses 2020; 12:v12111305. [PMID: 33202558 PMCID: PMC7698180 DOI: 10.3390/v12111305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/31/2020] [Accepted: 11/06/2020] [Indexed: 12/19/2022] Open
Abstract
Newcastle disease virus (NDV) infections are well known to harbour quasispecies, due to the error-prone nature of the RNA polymerase. Quasispecies variants in the fusion cleavage site of the virus are known to significantly change its virulence. However, little is known about the genomic patterns of diversity and selection in NDV viral swarms. We analyse deep sequencing data from in vitro and in vivo NDV infections to uncover the genomic patterns of diversity and the signatures of selection within NDV swarms. Variants in viruses from in vitro samples are mostly localised in non-coding regions and 3′ and 5′ untranslated regions (3′UTRs or 5′UTRs), while in vivo samples contain an order of magnitude more variants. We find different patterns of genomic divergence and diversity among NDV genotypes, as well as differences in the genomic distribution of intra-host variants among in vitro and in vivo infections of the same strain. The frequency spectrum shows clear signatures of intra-host purifying selection in vivo on the matrix protein (M) coding gene and positive or diversifying selection on nucleocapsid (NP) and haemagglutinin-neuraminidase (HN). The comparison between within-host polymorphisms and phylogenetic divergence reveals complex patterns of selective pressure on the NDV genome at between- and within-host level. The M sequence is strongly constrained both between and within hosts, fusion protein (F) coding gene is under intra-host positive selection, and NP and HN show contrasting patterns: HN RNA sequence is positively selected between hosts while its protein sequence is positively selected within hosts, and NP is under intra-host positive selection at the RNA level and negative selection at the protein level.
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Affiliation(s)
- Archana Jadhav
- Viral Oncogenesis Group, The Pirbright Institute, Pirbright, Woking GU24 0NF, Surrey, UK; (A.J.); (V.N.)
| | - Lele Zhao
- Nuffield Department of Medicine, Li Ka Shing Centre for Health Information and Discovery, Big Data Institute, University of Oxford, Oxford OX3 7LF, UK;
| | - Weiwei Liu
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (W.L.); (C.D.)
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (W.L.); (C.D.)
| | - Venugopal Nair
- Viral Oncogenesis Group, The Pirbright Institute, Pirbright, Woking GU24 0NF, Surrey, UK; (A.J.); (V.N.)
- UK-China Centre of Excellence on Avian Disease Research, Pirbright, Woking GU24 0NF, Surrey, UK
| | - Sebastian E. Ramos-Onsins
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, 08193 Bellaterra, Spain
- Correspondence: (S.E.R.-O.); (L.F.)
| | - Luca Ferretti
- Nuffield Department of Medicine, Li Ka Shing Centre for Health Information and Discovery, Big Data Institute, University of Oxford, Oxford OX3 7LF, UK;
- Correspondence: (S.E.R.-O.); (L.F.)
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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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9
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Genomic and Pathogenic Characteristics of Virulent Newcastle Disease Virus Isolated from Chicken in Live Bird Markets and Backyard Flocks in Kenya. Int J Microbiol 2020; 2020:4705768. [PMID: 32908524 PMCID: PMC7450340 DOI: 10.1155/2020/4705768] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022] Open
Abstract
Newcastle disease (ND) causes significant economic losses in the poultry industry in developing countries. In Kenya, despite rampant annual ND outbreaks, implementation of control strategies is hampered by a lack of adequate knowledge on the circulating and outbreak causing-NDV strains. This study reports the first complete genome sequences of NDV from backyard chicken in Kenya. The results showed that all three isolates are virulent, as assessed by the mean death time (MDT) and intracerebral pathogenicity index (ICPI) in specific antibody negative (SAN) embryonated eggs and 10-day-old chickens, respectively. Also, the polybasic amino acid sequence at the fusion-protein cleavage site had the motif 112RRQKRFV118. Histopathological findings in four-week-old SPF chicken challenged with the NDV isolates KE001, KE0811, and KE0698 showed multiple organ involvement at five days after infection with severe effects seen in lymphoid tissues and blood vessels. Analysis of genome sequences obtained from the three isolates showed that they were 15192 base pair (bp) in length and had genomic features consistent with other NDV strains, the functional sites within the coding sequence being highly conserved in the sequence of the three isolates. Amino acid residues and substitutions in the structural proteins of the three isolates were similar to the newly isolated Tanzanian NDV strain (Mbeya/MT15). A similarity matrix showed a high similarity of the isolates to NDV strains of class II genotype V (89–90%) and subgenotype Vd (95–97%). Phylogenetic analysis confirmed that the three isolates are closely related to NDV genotype V strains but form a distinct cluster together with NDV strains from the East African countries of Uganda and Tanzania to form the newly characterized subgenotype Vd. Our study provides the first description of the genomic and pathological characteristics of NDV of subgenotype Vd and lays a baseline in understanding the evolutionary dynamics of NDV and, in particular, Genotype V. This information will be useful in the development of specific markers for detection of viruses of genotype V and generation of genotype matched vaccines.
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10
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Ferreira HL, Suarez DL. Single-Nucleotide Polymorphism Analysis to Select Conserved Regions for an Improved Real-Time Reverse Transcription-PCR Test Specific for Newcastle Disease Virus. Avian Dis 2020; 63:625-633. [PMID: 31865677 DOI: 10.1637/aviandiseases-d-19-00071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 08/12/2019] [Indexed: 11/05/2022]
Abstract
A bioinformatics approach using single-nucleotide polymorphism (SNP) analysis was performed to improve the current real-time reverse transcription-PCR (RRT-PCR) tests for the rapid detection of Newcastle disease virus (NDV). In total, 422 NDV complete genomes were analyzed using the Virus Pathogen Resource to compare the conservation of the primer and probe sequences and to select regions to develop new RRT-PCR tests. The sensitivity and specificity of the three new RRT-PCR tests targeting the nucleoprotein (NP) and polymerase (L) genes were optimized and were compared with established tests for NDV detection. The SNP analysis was also used to identify the number of mismatches between selected primers/probes and the NDV complete genome sequences. The SNP analysis, averaged over the entire primer or probe, showed the primer/probe sequences of three new tests were more conserved than the primer/probe sequences of the commonly used test targeting the matrix (M) gene. The M RRT-PCR test was compared with the new tests on a panel of 46 viruses, comprising 31 NDV isolates. Limit of detection (LOD) varied from 1.3 to 3.7 log 50% egg-infective doses using five isolates from different genotypes by all tests. The two RRT-PCR tests targeting the L and M genes detected three out of five isolates with the lowest LOD. The NP and M RRT-PCR tests had the lowest and highest rates of genetic variants, respectively, among all probes. Because currently used tests are likely to miss some isolates, the availability of validated alternative tests provides alternatives for detection of viral variants that can be rapidly deployed to diagnostic laboratories.
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Affiliation(s)
- H L Ferreira
- U.S. National Poultry Research Center, Southeast Poultry Research Laboratory 934 College Station Road, Athens, GA 30605.,University of Sao Paulo, ZMV- FZEA, Pirassununga-SP, 13635900, Brazil
| | - D L Suarez
- U.S. National Poultry Research Center, Southeast Poultry Research Laboratory 934 College Station Road, Athens, GA 30605,
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11
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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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12
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Ferreira HL, Taylor TL, Absalon AE, Dimitrov KM, Cortés-Espinosa DV, Butt SL, Marín-Cruz JL, Goraichuk IV, Volkening JD, Suarez DL, Afonso CL. Presence of Newcastle disease viruses of sub-genotypes Vc and VIn in backyard chickens and in apparently healthy wild birds from Mexico in 2017. Virus Genes 2019; 55:479-489. [PMID: 30976951 DOI: 10.1007/s11262-019-01663-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/04/2019] [Indexed: 12/20/2022]
Abstract
Virulent Newcastle disease viruses (NDV) have been present in Mexico since 1946, and recently, multiple outbreaks have been reported in the country. Here, we characterized eleven NDV isolated from apparently healthy wild birds and backyard chickens in three different locations of Jalisco, Mexico in 2017. Total RNA from NDV was reverse-transcribed, and 1285 nucleotides, which includes 3/4 of the fusion gene, was amplified and sequenced using a long-read MinION sequencing method. The sequences were 99.99-100% identical to the corresponding region obtained using the Illumina MiSeq. Phylogenetic analysis using MinION sequences demonstrated that nine virulent NDV from wild birds belonged to sub-genotypes Vc and VIn, and two backyard chicken isolates were of sub-genotype Vc. The sub-genotype Vc viruses had nucleotide sequence identity that ranged from 97.7 to 98% to a virus of the same sub-genotype isolated from a chicken in Mexico in 2010. Three viruses from pigeons had 96.3-98.7% nucleotide identity to sub-genotype VIn pigeon viruses, commonly referred to as pigeon paramyxovirus, isolated in the USA during 2000-2016. This study demonstrates that viruses of sub-genotype Vc are still present in Mexico, and the detection of this sub-genotype in both chickens and wild birds suggests that transmission among these species may represent a biosecurity risk. This is the first detection and complete genome sequencing of genotype VI NDV from Mexico. In addition, the utilization of an optimized long-read sequencing method for rapid virulence and genotype identification using the Oxford nanopore MinION system is demonstrated.
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Affiliation(s)
- H L Ferreira
- Southeast Poultry Research Laboratory, US National Poultry Research Center, 934 College Station Rd, Athens, GA, 30605, USA.,University of Sao Paulo, ZMV- FZEA, Pirassununga, 13635900, Brazil
| | - T L Taylor
- Southeast Poultry Research Laboratory, US National Poultry Research Center, 934 College Station Rd, Athens, GA, 30605, USA
| | - A E Absalon
- Vaxbiotek S.C, San Lorenzo No. 122-7, CP. 72700, Cuautlancingo, Puebla, Mexico
| | - K M Dimitrov
- Southeast Poultry Research Laboratory, US National Poultry Research Center, 934 College Station Rd, Athens, GA, 30605, USA
| | - D V Cortés-Espinosa
- Instituto Politécnico Nacional/CIBA-Tlaxcala, Carr. Est. Santa Ines Tecuexcomac Km 1.5, Tepetitla, Tlaxcala, Mexico
| | - S L Butt
- Southeast Poultry Research Laboratory, US National Poultry Research Center, 934 College Station Rd, Athens, GA, 30605, USA.,Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - J L Marín-Cruz
- Consorcio consultivo empresarial S.C., Lasallistas No. 120 Col. Rosario, San Juan De Los Lagos, Jalisco, Mexico
| | - I V Goraichuk
- Southeast Poultry Research Laboratory, US National Poultry Research Center, 934 College Station Rd, Athens, GA, 30605, USA.,National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 83, Pushkinska Street, Kharkiv, 61023, Ukraine
| | - J D Volkening
- BASE2BIO, 1945, Arlington Drive, Oshkosh, WI, 54904, USA
| | - D L Suarez
- Southeast Poultry Research Laboratory, US National Poultry Research Center, 934 College Station Rd, Athens, GA, 30605, USA
| | - C L Afonso
- Southeast Poultry Research Laboratory, US National Poultry Research Center, 934 College Station Rd, Athens, GA, 30605, USA.
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13
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Pathogenicity and transmission of virulent Newcastle disease virus from the 2018-2019 California outbreak and related viruses in young and adult chickens. Virology 2019; 531:203-218. [PMID: 30928699 DOI: 10.1016/j.virol.2019.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/12/2019] [Accepted: 03/19/2019] [Indexed: 11/22/2022]
Abstract
In May of 2018, virulent Newcastle disease virus was detected in sick, backyard, exhibition chickens in southern California. Since, the virus has affected 401 backyard and four commercial flocks, and one live bird market in California, and one backyard flock in Utah. The pathogenesis and transmission potential of this virus, along with two genetically related and widely studied viruses, chicken/California/2002 and chicken/Belize/2008, were evaluated in both 3-week- and 62-week-old chickens given a low, medium, or high challenge dose. All three viruses were highly virulent causing clinical signs, killing all the chickens in the medium and high dose groups, and efficiently transmitting to contacts. The three viruses also replicated in the reproductive tract of the adult hens. Virus shedding for all viruses was detected 24 hours after challenge, peaking with high titers at day 4 post challenge. Although not genetically identical, the studied isolates were shown to be phenotypically very similar, which allows the utilization of the available literature in the control of the current outbreak.
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14
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Wei T, Deng Q, Zhai G, He C, Li H, Zhang Y, Zeng R, Mo M, Huang T, Wei P. Re-emergence of a genotype VIII virulent Newcastle disease virus isolated from Chinese game fowl after 13 years. Transbound Emerg Dis 2019; 66:1077-1084. [PMID: 30658009 DOI: 10.1111/tbed.13129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/08/2018] [Accepted: 01/05/2019] [Indexed: 11/28/2022]
Abstract
Circulation of dominant genotypes VI and VII of Newcastle disease virus (NDV) is causing significant economic losses to the poultry industry in China. However, reports of Newcastle disease (ND) outbreaks caused by genotype VIII strains of NDV are rare. In this study, a virulent genotype VIII strain of NDV, designated GXGB2011, was isolated from a vaccinated game fowl flock showing clinic signs of infection in Pinxiang county, Guangxi, China. The whole genome of the isolate was completely sequenced and was found to be comprised of 15,192 nucleotides (nt), encoding the six structural proteins in the order of 3'-NP-P-M-F-HN-L-5'. The pattern of cleavage site 112 RRQKR↓F117 in the fusion (F) protein and the intracerebral pathogenicity index (ICPI) value of 1.5 showed that the strain GXGB2011 was a velogenic NDV. The results of the challenge experiment with the 5-week-old SPF chickens showed that the strain was highly pathogenic with 100% morbidity and mortality of the challenged birds. Based on the detection of virus in different organs of the infected birds, the highest viral load in caecal tonsils was observed and viral levels in immune organs were higher than those in the respiratory organs. Bayesian reconstruction of complete genomes based on the sequences of 66 NDV reference strains showed that the strain belonged to the genotype VIII of NDV. Phylogenetic analysis showed that the strain was more closely related to the foreign strains gamefowl/U.S.(CA)/24225/98, 1ITTY94060 and IT-147/94 rather than to the first domestic strains of the emergence genotype VIII in Qinghai, China during 1979-1985. In summary, the results of the study demonstrated the re-emergence of a highly pathogenic virulent isolate of genotype VIII of NDV. These results indicate the risk that this genotype VIII of NDV may spread to commercial chickens from game fowl.
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Affiliation(s)
| | - Qiaomu Deng
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Guosheng Zhai
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Chengwei He
- Pingxiang Customs P. R. China, Pingxiang, Guangxi, China
| | - Haiqiong Li
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Yuanqin Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Rongling Zeng
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Meilan Mo
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Teng Huang
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Ping Wei
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
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15
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Rasambainarivo F, Goodman SM. Disease Risk to Endemic Animals From Introduced Species on Madagascar. FOWLER'S ZOO AND WILD ANIMAL MEDICINE CURRENT THERAPY, VOLUME 9 2019. [PMCID: PMC7173427 DOI: 10.1016/b978-0-323-55228-8.00043-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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16
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Soltani M, Peighambari SM, Pourbakhsh SA, Ashtari A, Rezaei Far A, Abdoshah M. Molecular characterization of haemagglutinin-neuraminidase gene among virulent Newcastle disease viruses isolated in Iran. IRANIAN JOURNAL OF VETERINARY RESEARCH 2019; 20:1-8. [PMID: 31191692 PMCID: PMC6509910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 06/11/2018] [Accepted: 10/16/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Virulent Newcastle disease virus (vNDV) causes great economic losses to the poultry industry throughout the world. Despite the endemicity of Newcastle disease (ND) and occurrence of recurrent outbreaks, the nature and genetic features of circulating NDV strains in Iran are largely unknown. Aims: This study was conducted to characterize 13 NDV isolates obtained from different outbreaks in various regions of Iran during 1999-2000 by sequencing and phylogenetic analysis of complete coding sequences of haemagglutinin-neuraminidase (HN) gene. METHODS All isolates were analyzed based on the previously determined in vivo pathogenicity indices and amino acid (aa) sequences of fusion (F) protein cleavage site (FPCS). RESULTS Phylogenetic analysis based on the HN gene coding region revealed a very close relationship of these viruses with the recently defined genotype XIII, and more specifically, subgenotype XIIIa viruses. Analysis of HN gene nucleotide (nt) sequences revealed that all studied isolates encode for a protein length of 571 aa and there is no C-terminal extension on HN aa sequences. Sequence analysis revealed multiple aa residue substitutions at antigenic sites or neutralizing epitopes on the HN glycoprotein of studied viruses compared with commonly used vaccinal strains. CONCLUSION In this study, molecular characterization of vNDV isolates, obtained from commercial poultry farms in Iran, were conducted through complete sequencing and analysis of HN gene. Isolation and molecular characterization of further NDV isolates from other parts of Iran and from neighboring countries in the region will be helpful to identify the nature and origin of indigenous viruses.
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Affiliation(s)
- M. Soltani
- Graduated from Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - S. M. Peighambari
- Department of Avian Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - S. A. Pourbakhsh
- Avian Diseases Research and Diagnosis Department, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - A. Ashtari
- Avian Diseases Research and Diagnosis Department, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - A. Rezaei Far
- Graduated from Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - M. Abdoshah
- Quality Control Management, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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17
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Genotype Diversity of Newcastle Disease Virus in Nigeria: Disease Control Challenges and Future Outlook. Adv Virol 2018; 2018:6097291. [PMID: 30631359 PMCID: PMC6304561 DOI: 10.1155/2018/6097291] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/28/2018] [Indexed: 11/17/2022] Open
Abstract
Newcastle disease (ND) is one of the most important avian diseases with considerable threat to the productivity of poultry all over the world. The disease is associated with severe respiratory, gastrointestinal, and neurological lesions in chicken leading to high mortality and several other production related losses. The aetiology of the disease is an avian paramyxovirus type-1 or Newcastle disease virus (NDV), whose isolates are serologically grouped into a single serotype but genetically classified into a total of 19 genotypes, owing to the continuous emergence and evolution of the virus. In Nigeria, molecular characterization of NDV is generally very scanty and majorly focuses on the amplification of the partial F gene for genotype assignment. However, with the introduction of the most objective NDV genotyping criteria which utilize complete fusion protein coding sequences in phylogenetic taxonomy, the enormous genetic diversity of the virus in Nigeria became very conspicuous. In this review, we examine the current ecological distribution of various NDV genotypes in Nigeria based on the available complete fusion protein nucleotide sequences (1662 bp) in the NCBI database. We then discuss the challenges of ND control as a result of the wide genetic distance between the currently circulating NDV isolates and the commonest vaccines used to combat the disease in the country. Finally, we suggest future directions in the war against the economically devastating ND in Nigeria.
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18
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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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Molecular Characterization of Newcastle Disease Virus from Backyard Poultry Farms and Live Bird Markets in Kenya. Int J Microbiol 2018; 2018:2368597. [PMID: 30154854 PMCID: PMC6098844 DOI: 10.1155/2018/2368597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 01/23/2023] Open
Abstract
Newcastle disease (ND) is a serious disease of poultry that causes significant economic losses. Despite rampant ND outbreaks that occur annually in Kenya, the information about the NDV circulating in Kenya is still scarce. We report the first countrywide study of NDV in Kenya. Our study is aimed at evaluating the genetic characteristics of Newcastle disease viruses obtained from backyard poultry in farms and live bird markets in different regions of Kenya. We sequenced and analyzed fusion (F) protein gene, including the cleavage site, of the obtained viruses. We aligned and compared study sequences with representative NDV of different genotypes from GenBank. The fusion protein cleavage site of all the study sequences had the motif 112RRQKRFV118 indicating their velogenic nature. Phylogenetic analysis revealed that the NDV from various sites in Kenya was highly similar genetically and that it clustered together with NDV of genotype V. The study samples were 96% similar to previous Ugandan and Kenyan viruses grouped in subgenotype Vd This study points to possible circulation of NDV of similar genetic characteristics between backyard poultry farms and live bird markets in Kenya. The study also suggests the possible spread of velogenic NDV between Kenya and Uganda possibly through cross-border live bird trade. Our study provides baseline information on the genetic characteristics of NDV circulating in the Kenyan poultry population. This highlights the need for the ND control programmes to place more stringent measures on cross-border trade of live bird markets and poultry products to prevent the introduction of new strains of NDV that would otherwise be more difficult to control.
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Wanyana A, Mugimba KK, Bosco OJ, Kirunda H, Nakavuma JL, Teillaud A, Ducatez MF, Byarugaba DK. Genotypic characterisation of Avian paramyxovirus type-1 viruses isolated from aquatic birds in Uganda. ACTA ACUST UNITED AC 2018; 85:e1-e7. [PMID: 30035597 PMCID: PMC6238811 DOI: 10.4102/ojvr.v85i1.1510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/21/2017] [Accepted: 05/16/2018] [Indexed: 11/16/2022]
Abstract
Avian paramyxovirus type-1 (APMV-1) viruses of the lentogenic pathotypes are often isolated from wild aquatic birds and may mutate to high pathogenicity when they cross into poultry and cause debilitating Newcastle disease. This study characterised AMPV-1 isolated from fresh faecal droppings from wild aquatic birds roosting sites in Uganda. Fresh faecal samples from wild aquatic birds at several waterbodies in Uganda were collected and inoculated into 9–10-day-old embryonated chicken eggs. After isolation, the viruses were confirmed as APMV-1 by APMV-1-specific polymerase chain reaction (PCR). The cleavage site of the fusion protein gene for 24 representative isolates was sequenced and phylogenetically analysed and compared with representative isolates of the different APMV-1 genotypes in the GenBank database. In total, 711 samples were collected from different regions in the country from which 72 isolates were recovered, giving a prevalence of 10.1%. Sequence analysis of 24 isolates revealed that the isolates were all lentogenic, with the typical 111GGRQGR’L117 avirulent motif. Twenty-two isolates had similar amino acid sequences at the cleavage site, which were different from the LaSota vaccine strain by a silent nucleotide substitution T357C. Two isolates, NDV/waterfowl/Uganda/MU150/2011 and NDV/waterfowl/Uganda/MU186/2011, were different from the rest of the isolates in a single amino acid, with aspartate and alanine at positions 124 and 129, respectively. The results of this study revealed that Ugandan aquatic birds indeed harbour APMV-1 that clustered with class II genotype II strains and had limited genetic diversity.
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Affiliation(s)
- Agnes Wanyana
- College of Veterinary Medicine, Makerere University.
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Liu H, de Almeida RS, Gil P, Majó N, Nofrarías M, Briand FX, Jestin V, Albina E. Can genotype mismatch really affect the level of protection conferred by Newcastle disease vaccines against heterologous virulent strains? Vaccine 2018; 36:3917-3925. [PMID: 29843999 DOI: 10.1016/j.vaccine.2018.05.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/10/2018] [Accepted: 05/17/2018] [Indexed: 10/24/2022]
Abstract
Newcastle disease (ND), caused by virulent class II avian paramyxovirus 1 (Newcastle disease virus, NDV), occurs sporadically in poultry despite their having been immunized with commercial vaccines. These vaccines were all derived from NDV strains isolated around 70 years ago. Since then, class II NDV strains have evolved into 18 genotypes. Whether the vaccination failure results from genotype mismatches between the currently used vaccine strains and field-circulating velogenic strains or from an impaired immune response in the vaccination remains unclear. To test the first hypothesis, we performed a heterologous genotype II vaccine/genotype XI challenge in one-day old specific pathogen free (SPF) chicks and reproduced viral shedding. We then produced two attenuated strains of genotype II and XI by reverse genetics and used them to immunize two-week old SPF chickens that were subsequently challenged with velogenic strains of genotypes II, VII and XI. We found that both vaccines could induce antibodies with hemagglutination inhibition titers higher than 6.5 log2. Vaccination also completely prevented disease, viral shedding in swabs, and blocked viral replication in tissues from different genotypes in contrast to unvaccinated chickens that died shortly after challenge. Taken together, our results support the hypothesis that, in immunocompetent poultry, genotype mismatch is not the main reason for vaccination failure.
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Affiliation(s)
- Haijin Liu
- CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France; Department of Avian Disease, College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Renata Servan de Almeida
- CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Patricia Gil
- CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Natàlia Majó
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus UAB, 08193 Bellaterra, Spain; Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193 Bellaterra, Spain
| | - Miquel Nofrarías
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus UAB, 08193 Bellaterra, Spain
| | | | | | - Emmanuel Albina
- CIRAD, UMR ASTRE, F-34398 Montpellier, France; CIRAD, UMR ASTRE, F-97170 Petit-Bourg, Guadeloupe, France.
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Evaluating the efficacy of LaSota vaccination induced protection in chickens upon challenge with a genotype IV strain of Newcastle disease virus. Virusdisease 2018; 28:328-336. [PMID: 29291221 DOI: 10.1007/s13337-017-0396-2] [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: 04/11/2017] [Accepted: 08/28/2017] [Indexed: 10/18/2022] Open
Abstract
Newcastle disease (ND) is a major risk to the poultry industry which results in severe economic loss throughout the world even with vaccination. The vaccine viruses that are used in many countries include the LaSota and other live viruses that were isolated in the early and late 1950s. Reports from several laboratories including ours indicate a greater variance of the circulating strains and recent classification indicates the existence of XVIII different genotypes of NDV strains. The efficiency of the LaSota vaccination in inducing protective immunity to different heterologous strains has been a question and its efficacy upon exposure to a virulent genotype IV strain has not been reported after 1989 world-wide except for India. Serum antibody negative (SAN) chicks of either sex obtained by hatching specific-pathogen-free (SPF) eggs were vaccinated with increasing doses of the vaccine virus from 101 to 107 EID50 per bird delivered through occulo-nasal route and challenged 20 days later with NDV-2K3 (genotype IV) strain of virus isolated in the year 2000 from pigeon in India. The birds were monitored for serum antibody titers and following challenge for morbidity, mortality, viral load in the cloacal swab and different tissues. We could clearly show that a minimum vaccine titre of 104 EID50 could establish protective antibody levels and also prevent viral replication post challenge upon exposure to the virulent genotype IV strain. We conclude based on our results and previous observation that there do exist differences in the levels of the antibody that could limit viral replication and shedding upon exposure to different heterologous genotype of NDV. Developing a strain matched vaccine might less potential to result in better protection by limiting the viral shedding.
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23
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Phylogenetic analysis of Newcastle disease viruses from Bangladesh suggests continuing evolution of genotype XIII. Arch Virol 2017; 162:3177-3182. [DOI: 10.1007/s00705-017-3479-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/09/2017] [Indexed: 01/01/2023]
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24
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Identification and pathotypical analysis of a novel VIk sub-genotype Newcastle disease virus obtained from pigeon in China. Virus Res 2017; 238:1-7. [PMID: 28554562 DOI: 10.1016/j.virusres.2017.05.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 11/21/2022]
Abstract
Newcastle disease virus (NDV) can lead to a devastating disease to various avian species including pigeons. Genotype VI NDV is a major cause of Newcastle disease (ND) in Columbiformes (i.e. pigeons and doves). Here, we analyzed the genetic diversity of genotype VI based on the complete F gene sequences of 2 pigeon-origin isolates in northeastern China in 2015, along with 238 genotype VI strains available in GenBank. The phylogenetic tree and evolutionary distances revealed that the 2 new isolates were clustered into a new sub-genotype herein proposed as VIk. Although the 2 isolates contain the 113RQKRF117 cleavage site, a feature generally associated with virulent NDV strains, the values of ICPI and MDT showed lentogenic characteristics. The challenge experiment demonstrated that the isolate Pigeon/China/Jilin/NG05/2015 was pathogenic to pigeons, causing lesions in multiple tissues and organs. The emergence and spread of the sub-genotype VIk viruses illustrated that the genotype VI NDV was undergoing evolutionary changes. It is necessary to pay close attention and carry out epidemiological surveillance in pigeons.
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25
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Molini U, Aikukutu G, Khaiseb S, Cattoli G, Dundon WG. First genetic characterization of newcastle disease viruses from Namibia: identification of a novel VIIk subgenotype. Arch Virol 2017; 162:2427-2431. [PMID: 28470419 DOI: 10.1007/s00705-017-3389-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
The complete sequences of the fusion (F) protein genes of six Newcastle disease virus (NDV) isolates from backyard poultry in Namibia in 2016 have been determined. The F gene cleavage site motif for all of the isolates was 112RRQKRF117, indicating that the viruses are virulent. A phylogenetic analysis using the full F gene sequence revealed that the viruses belong to a novel subgenotype, VIIk. This is the first genetic characterization of NDV isolates from Namibia, and the findings have important implications for Newcastle disease management and control in the region.
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Affiliation(s)
- Umberto Molini
- Central Veterinary Laboratory (CVL), 24 Goethe Street, P. Box 18137, Windhoek, Namibia
| | - Gottlieb Aikukutu
- Central Veterinary Laboratory (CVL), 24 Goethe Street, P. Box 18137, Windhoek, Namibia
| | - Siegfried Khaiseb
- Central Veterinary Laboratory (CVL), 24 Goethe Street, P. Box 18137, Windhoek, Namibia
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria
| | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria. .,APHL Joint FAO/IAEA Division, IAEA Laboratories, Seibersdorf, 2444, Austria.
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26
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Abolnik C. History of Newcastle disease in South Africa. ACTA ACUST UNITED AC 2017; 84:e1-e7. [PMID: 28281777 PMCID: PMC6238702 DOI: 10.4102/ojvr.v84i1.1306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/05/2016] [Indexed: 11/09/2022]
Abstract
Poultry production in South Africa, a so-called developing country, may be seen as a gradient between two extremes with highly integrated commercial enterprises with world-class facilities on one hand and unimproved rural chickens kept by households and subsistence farmers on the other. Although vaccination against Newcastle disease is widely applied to control this devastating infection, epizootics continue to occur. Since the first official diagnosis in 1945, through the sporadic outbreaks of the 1950s and early 1960s, to serious epizootics caused by genotype VIII (late 1960s–2000), genotype VIIb (1993–1999), genotype VIId (2003–2012) and most recently genotype VIIh (2013 to present), South Africa’s encounters with exotic Newcastle disease follow global trends. Importation – probably illegal – of infected poultry, poultry products or exotic birds and illegal swill dumping are likely routes of entry. Once the commercial sector is affected, the disease spreads rapidly within the region via transportation routes. Each outbreak genotype persisted for about a decade and displaced its predecessor.
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Affiliation(s)
- Celia Abolnik
- Department of Production Animal Studies, University of Pretoria.
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Rezaei Far A, Peighambari SM, Pourbakhsh SA, Ashtari A, Soltani M. Co-circulation of genetically distinct groups of avian paramyxovirus type 1 in pigeon Newcastle disease in Iran. Avian Pathol 2016; 46:36-43. [PMID: 27314285 DOI: 10.1080/03079457.2016.1203068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Pigeons are considered as one of the major natural reservoirs in the epidemiology of Newcastle disease (ND). In this study, the partial sequence of fusion protein gene of 17 pigeon-origin ND viruses (NDVs) isolated during 2012-2013 in Iran was analysed. Since the studied isolates showed F0 protein cleavage sites compatible with velogenic NDVs, all were considered as virulent NDVs. Two isolates carried 112RRQKRF117 as the cleavage site motif, whereas the rest demonstrated 112KRQKRF117 motif which just recently has been reported among Iranian virulent NDVs. Phylogenetic analysis divided all these diverse isolates in two distinct clusters within class II genotype VI. Based on the partial fusion protein gene sequence, 15 out of 17 isolates showed the highest genetic identity to subgenotype VIb/2 and the other two isolates were placed in a distinct genetic group of genotype VI. Based on recent findings, at least two different sublineages of genotype VI are causing the ND outbreaks in the pigeon population and are circulating simultaneously along with virulent NDVs of genotype VII in various species in Iran. The continuing circulation of a diverse group of virulent NDVs as an enzootic in widespread species such as pigeon can cause outbreaks in commercial poultry flocks and also failure in controlling programmes. Therefore, the constant monitoring and awareness of the virus characteristics should be considered in controlling programmes against ND in Iran.
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Affiliation(s)
- A Rezaei Far
- a Department of Avian Diseases, Faculty of Veterinary Medicine , University of Tehran , Tehran , Iran
| | - S M Peighambari
- a Department of Avian Diseases, Faculty of Veterinary Medicine , University of Tehran , Tehran , Iran
| | - S A Pourbakhsh
- b Avian Diseases Research and Diagnosis Department , Razi Vaccine and Serum Research Institute , Alborz , Iran
| | - A Ashtari
- b Avian Diseases Research and Diagnosis Department , Razi Vaccine and Serum Research Institute , Alborz , Iran
| | - M Soltani
- a Department of Avian Diseases, Faculty of Veterinary Medicine , University of Tehran , Tehran , Iran
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Shittu I, Joannis TM, Odaibo GN, Olaleye OD. Newcastle disease in Nigeria: epizootiology and current knowledge of circulating genotypes. Virusdisease 2016; 27:329-339. [PMID: 28004012 DOI: 10.1007/s13337-016-0344-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/24/2016] [Indexed: 10/21/2022] Open
Abstract
Over the years, Newcastle disease (ND) has defied all available control measures. The disease has remained at the forefront of infectious diseases afflicting poultry production after avian influenza. Despite the continuous global use of million doses of ND vaccine annually, the causative pathogen, avian paramyxovirus type 1 also known as Newcastle disease virus (NDV) has continued to evolve causing, even more, a threat not only to the unvaccinated but the vaccinated flocks inclusive. The disease has been well studied in the developed countries where the virus is found in circulation. However, limited information exists on the epizootiology and circulating genotypes of the virus in developing countries where the majority of the flocks are raised on the extensive management system. Identification of virulent NDV in apparently healthy free-range ducks in this system calls for concern and pragmatic approach to investigate factor(s) that favour the virus inhabiting the ducks without clinical manifestation of the disease. Recently, novel genotypes (XIV, XVII, and XVIII) with peculiarity to West and Central African countries have been discovered and due to lack or poor surveillance system possibility of hitherto unreported genotypes are likely. This review elucidates and discusses available literature on the diversity of the circulating NDV genotypes across the West Africa countries and the epizootiology (molecular) of the disease in Nigeria with the view of identifying gaps in knowledge that can assist in the development of effective vaccines and control strategies to combat the peril of the disease.
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Affiliation(s)
- Ismaila Shittu
- Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, Virology Division, National Veterinary Research Institute, Vom, Nigeria ; Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State Nigeria
| | - Tony M Joannis
- Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, Virology Division, National Veterinary Research Institute, Vom, Nigeria
| | - Georgina N Odaibo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State Nigeria
| | - Olufemi D Olaleye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State Nigeria
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Dimitrov KM, Bolotin V, Muzyka D, Goraichuk IV, Solodiankin O, Gerilovych A, Stegniy B, Goujgoulova GV, Silko NY, Pantin-Jackwood MJ, Miller PJ, Afonso CL. Repeated isolation of virulent Newcastle disease viruses of sub-genotype VIId from backyard chickens in Bulgaria and Ukraine between 2002 and 2013. Arch Virol 2016; 161:3345-3353. [DOI: 10.1007/s00705-016-3033-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/25/2016] [Indexed: 10/21/2022]
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Phylogenetic analysis of Newcastle disease viruses isolated from commercial poultry in Mozambique (2011-2016). Virus Genes 2016; 52:748-53. [PMID: 27277578 DOI: 10.1007/s11262-016-1362-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/02/2016] [Indexed: 10/21/2022]
Abstract
The complete sequence of the fusion (F) protein gene from 11 Newcastle disease viruses (NDVs) isolated from commercial poultry in Mozambique between 2011 and 2016 has been generated. The F gene cleavage site motif for all 11 isolates was (112)RRRKRF(117) indicating that the viruses are virulent. A phylogenetic analysis using the full F gene sequence revealed that the viruses clustered within genotype VIIh and showed a higher similarity to NDVs from South Africa, China and Southeast Asia than to viruses previously described in Mozambique in 1994, 1995 and 2005. The identification of these new NDVs has important implications for Newcastle disease management and control in Mozambique.
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COMPLETE GENOMIC SEQUENCE OF VIRULENT PIGEON PARAMYXOVIRUS IN LAUGHING DOVES (STREPTOPELIA SENEGALENSIS) IN KENYA. J Wildl Dis 2016; 52:599-608. [PMID: 27224210 DOI: 10.7589/2015-07-199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Following mass deaths of Laughing Doves (Streptopelia senegalensis) in different localities throughout Kenya, internal organs obtained during necropsy of two moribund birds were sampled and analyzed by next generation sequencing. We isolated the virulent strain of pigeon paramyxovirus type-1 (PPMV-1), PPMV1/Laughing Dove/Kenya/Isiolo/B2/2012, which had a characteristic fusion gene motif (110)GGRRQKRF(117). We obtained a partial full genome of 15,114 nucleotides. The phylogenetic relationship based on the fusion gene and genomic sequence grouped our isolate as class II genotype VI, a group of viruses commonly isolated from wild birds but potentially lethal to Chickens ( Gallus gallus domesticus ). The fusion gene isolate clustered with PPMV-I strains from pigeons (Columbidae) in Nigeria. The complete genome showed a basal and highly divergent lineage to American, European, and Asian strains, indicating a divergent evolutionary pathway. The isolated strain is highly virulent and apparently species-specific to Laughing Doves in Kenya. Risk of transmission of such a strain to poultry is potentially high whereas the cyclic epizootic in doves is a threat to conservation of wild Columbidae in Kenya.
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Damena D, Fusaro A, Sombo M, Belaineh R, Heidari A, Kebede A, Kidane M, Chaka H. Characterization of Newcastle disease virus isolates obtained from outbreak cases in commercial chickens and wild pigeons in Ethiopia. SPRINGERPLUS 2016; 5:476. [PMID: 27217991 PMCID: PMC4835400 DOI: 10.1186/s40064-016-2114-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 04/06/2016] [Indexed: 12/18/2022]
Abstract
Newcastle disease (ND), caused by virulent avian paramyxovirus type 1, is one of the most important diseases responsible for devastating outbreaks in poultry flocks in Ethiopia. However, the information about genetic characteristics of the Newcastle disease viruses (NDVs) circulating in commercial chickens and wild birds is scarce. In this study, we characterized isolates obtained from ND suspected outbreaks during 2012–2014 from poultry farms (n = 8) and wild pigeons (n = 4). The NDVs isolated from pathological specimens, through inoculation in embryonated chicken eggs, were characterized biologically by conventional intracerebral pathogenicity indices (ICPI), and genetically on the basis of Phylogenic analysis of partial F-gene sequences (260 bp) encompassing the cleavage site. The ICPI values of isolates from chickens ranged from 0.9 to 1.8; whereas, the ICPI of pigeon isolates was 1.4. All isolates contained multiple basic amino acids at the deduced cleavage site of fusion protein, which is a typical feature of virulent viruses. Phylogenic analysis of the partial cleavage site of F-gene (260 bp) indicated that all the sequences of viruses obtained from pigeons were identical and clustered within the genotype VIh while the sequences of viruses obtained from chickens were clustered together within the genotype VIf. The similarity between the viruses obtained from chickens and those obtained from pigeons ranged from 82.5 to 85.6 %. This suggests that different sub genotypes of genotype VI are circulating in chicken and wild pigeon population in Ethiopia. This warrants further study to understand the role of wild birds in the epidemiology of NDV in Ethiopia and as well highlights the importance of continuous surveillances both in wild birds and domestic poultry.
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Affiliation(s)
- Delesa Damena
- National Animal Health Diagnostic and Investigation Center, P.O. Box 04, Sebeta, Ethiopia
| | - Alice Fusaro
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, OIE/FAO and National Reference Laboratory for Newcastle Disease and Avian Influenza, OIE Collaborating Center for Diseases at the Human-Animal Interface, Legnaro, Padova Italy
| | - Melaku Sombo
- National Animal Health Diagnostic and Investigation Center, P.O. Box 04, Sebeta, Ethiopia
| | - Redeat Belaineh
- National Animal Health Diagnostic and Investigation Center, P.O. Box 04, Sebeta, Ethiopia
| | - Alireza Heidari
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, OIE/FAO and National Reference Laboratory for Newcastle Disease and Avian Influenza, OIE Collaborating Center for Diseases at the Human-Animal Interface, Legnaro, Padova Italy
| | - Abera Kebede
- National Animal Health Diagnostic and Investigation Center, P.O. Box 04, Sebeta, Ethiopia
| | - Menbere Kidane
- National Animal Health Diagnostic and Investigation Center, P.O. Box 04, Sebeta, Ethiopia
| | - Hassen Chaka
- National Animal Health Diagnostic and Investigation Center, P.O. Box 04, Sebeta, Ethiopia
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Newcastle Disease Viruses Causing Recent Outbreaks Worldwide Show Unexpectedly High Genetic Similarity to Historical Virulent Isolates from the 1940s. J Clin Microbiol 2016; 54:1228-35. [PMID: 26888902 DOI: 10.1128/jcm.03044-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/07/2016] [Indexed: 11/20/2022] Open
Abstract
Virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), a devastating disease of poultry and wild birds. Phylogenetic analyses clearly distinguish historical isolates (obtained prior to 1960) from currently circulating viruses of class II genotypes V, VI, VII, and XII through XVIII. Here, partial and complete genomic sequences of recent virulent isolates of genotypes II and IX from China, Egypt, and India were found to be nearly identical to those of historical viruses isolated in the 1940s. Phylogenetic analysis, nucleotide distances, and rates of change demonstrate that these recent isolates have not evolved significantly from the most closely related ancestors from the 1940s. The low rates of change for these virulent viruses (7.05 × 10(-5) and 2.05 × 10(-5) per year, respectively) and the minimal genetic distances existing between these and historical viruses (0.3 to 1.2%) of the same genotypes indicate an unnatural origin. As with any other RNA virus, Newcastle disease virus is expected to evolve naturally; thus, these findings suggest that some recent field isolates should be excluded from evolutionary studies. Furthermore, phylogenetic analyses show that these recent virulent isolates are more closely related to virulent strains isolated during the 1940s, which have been and continue to be used in laboratory and experimental challenge studies. Since the preservation of viable viruses in the environment for over 6 decades is highly unlikely, it is possible that the source of some of the recent virulent viruses isolated from poultry and wild birds might be laboratory viruses.
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Valastro V, Holmes EC, Britton P, Fusaro A, Jackwood MW, Cattoli G, Monne I. S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification. INFECTION GENETICS AND EVOLUTION 2016; 39:349-364. [PMID: 26883378 PMCID: PMC7172980 DOI: 10.1016/j.meegid.2016.02.015] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/27/2016] [Accepted: 02/10/2016] [Indexed: 01/01/2023]
Abstract
Infectious bronchitis virus (IBV) is the causative agent of a highly contagious disease that results in severe economic losses to the global poultry industry. The virus exists in a wide variety of genetically distinct viral types, and both phylogenetic analysis and measures of pairwise similarity among nucleotide or amino acid sequences have been used to classify IBV strains. However, there is currently no consensus on the method by which IBV sequences should be compared, and heterogeneous genetic group designations that are inconsistent with phylogenetic history have been adopted, leading to the confusing coexistence of multiple genotyping schemes. Herein, we propose a simple and repeatable phylogeny-based classification system combined with an unambiguous and rationale lineage nomenclature for the assignment of IBV strains. By using complete nucleotide sequences of the S1 gene we determined the phylogenetic structure of IBV, which in turn allowed us to define 6 genotypes that together comprise 32 distinct viral lineages and a number of inter-lineage recombinants. Because of extensive rate variation among IBVs, we suggest that the inference of phylogenetic relationships alone represents a more appropriate criterion for sequence classification than pairwise sequence comparisons. The adoption of an internationally accepted viral nomenclature is crucial for future studies of IBV epidemiology and evolution, and the classification scheme presented here can be updated and revised novel S1 sequences should become available.
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Affiliation(s)
- Viviana Valastro
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy; University of Padova, Padova, Italy.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paul Britton
- Pirbright Institute, Compton Laboratory, Compton, UK
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Mark W Jackwood
- Department of Population Health, College of Veterinary Medicine, Poultry Diagnostic and Research Center, University of Georgia, Athens, GA 30602, USA
| | - Giovanni Cattoli
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
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Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus). INFECTION GENETICS AND EVOLUTION 2016; 39:22-34. [PMID: 26792710 DOI: 10.1016/j.meegid.2016.01.008] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/08/2016] [Accepted: 01/09/2016] [Indexed: 12/16/2022]
Abstract
Newcastle disease is caused by virulent forms of avian paramyxovirus of serotype 1 (APMV-1) and has global economic importance. The disease reached panzootic proportions within two decades after first being identified in 1926 in the United Kingdom and Indonesia and still remains endemic in many countries across the world. Here we review information on the host, temporal, and geographic distribution of APMV-1 genetic diversity based on the evolutionary systematics of the complete coding region of the fusion gene. Strains of APMV-1 are phylogenetically separated into two classes (class I and class II) and further classified into genotypes based on genetic differences. Class I viruses are genetically less diverse, generally present in wild waterfowl, and are of low virulence. Class II viruses are genetically and phenotypically more diverse, frequently isolated from poultry with occasional spillovers into wild birds, and exhibit a wider range of virulence. Waterfowl, cormorants, and pigeons are natural reservoirs of all APMV-1 pathotypes, except viscerotropic velogenic viruses for which natural reservoirs have not been identified. Genotypes I and II within class II include isolates of high and low virulence, the latter often being used as vaccines. Viruses of genotypes III and IX that emerged decades ago are now isolated rarely, but may be found in domestic and wild birds in China. Containing only virulent viruses and responsible for the majority of recent outbreaks in poultry and wild birds, viruses from genotypes V, VI, and VII, are highly mobile and have been isolated on different continents. Conversely, virulent viruses of genotypes XI (Madagascar), XIII (mainly Southwest Asia), XVI (North America) and XIV, XVII and XVIII (Africa) appear to have a more limited geographic distribution and have been isolated predominantly from poultry.
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Elmardi N, Bakheit M, Khalafalla A. Phylogenetic analysis of some Newcastle disease virus isolates from the Sudan. Open Vet J 2016; 6:89-97. [PMID: 27419101 PMCID: PMC4935765 DOI: 10.4314/ovj.v6i2.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 05/30/2016] [Indexed: 02/05/2023] Open
Abstract
A reverse transcription-polymerase chain reaction (RT-PCR) was used to amplify 1412 bp of the fusion protein gene (F gene) of four Newcastle disease virus (NDV) isolates; two velogenic (TY-1/90 and DIK-90) and two lentogenic isolates (Dongla 88/1 and GD.S.1). Following sequencing, nucleotide sequences were annotated and 894 bp were compared phylogenetically with those from strains previously reported in the Sudan and the virus strains published on the GenBank. It could be demonstrated that TY-1/90 and DIK-90 strains belong to the genotype VI of NDV and are in close genetic relationship to sub- genotype VIb. TY-1/90 and DIK-90 strains were observed to be genetically unrelated to the earlier Sudanese isolates of 1970/80s and the late of 2000s suggesting a different origin. The close genetic relationship to the European and African pigeon paramyxovirus type 1 (PPMV-1) suggests a common ancestor. Dongola, GD.S.1 strains were classified into genotype II that comprises non-pathogenic lentogenic NDV strains. The present genetic classification of NDV isolates of the Sudan provides valuable information on genotypes of NDV. Further molecular epidemiological investigations of the recent outbreaks of Newcastle disease in the Sudan are needed in order to improve the efficiency of control strategies and vaccine development.
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Affiliation(s)
- N.A. Elmardi
- Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 1334, Khartoum North, Sudan
| | - M.A. Bakheit
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 1334, Khartoum North, Sudan
| | - A.I. Khalafalla
- Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 1334, Khartoum North, Sudan
- Corresponding Author: Abdelmalik Ibrahim Khalafalla. Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 1334 Khartoum North, Sudan. E-mail:
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Fuller C, Löndt B, Dimitrov KM, Lewis N, van Boheemen S, Fouchier R, Coven F, Goujgoulova G, Haddas R, Brown I. An Epizootiological Report of the Re-emergence and Spread of a Lineage of Virulent Newcastle Disease Virus into Eastern Europe. Transbound Emerg Dis 2015; 64:1001-1007. [PMID: 26671034 DOI: 10.1111/tbed.12455] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Indexed: 11/28/2022]
Abstract
A number of contemporary outbreaks of Newcastle disease (ND) in Israel, Turkey, Georgia and Bulgaria have all been caused by a very similar viruses related to lineage 5a (genotype VIIa). Comparison with published ND virus (NDV) sequences suggests that this virus strain originated in South-East Asia and on introduction has circulated widely in backyard poultry in the Middle East and into Eastern Europe. An intracerebral pathogenicity index of 1.9 was obtained for a representative isolate from Bulgaria. In addition, the International Reference Laboratory for ND has characterized a molecular epidemiologically linked virus that has been reported to have caused disease in well-vaccinated broiler chickens in Pakistan. In the 1990s, another strain from the 5a lineage NDV was introduced into Europe and spread across the continent causing numerous outbreaks up to 1999. Despite improved controls, including good diagnostic tests and widespread vaccination, in commercial poultry, the novel circulating NDV strains described here have been established widely in the region and represent an increased risk for similar disease outbreak events to reoccur within the EU.
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Affiliation(s)
- C Fuller
- Animal and Plant Health Agency, Weybridge, UK
| | - B Löndt
- Animal and Plant Health Agency, Weybridge, UK
| | - K M Dimitrov
- National Diagnostic Research Veterinary Medical Institute, Sofia, Bulgaria
| | - N Lewis
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - R Fouchier
- Viroscience lab, Erasmus MC, Rotterdam, The Netherlands
| | - F Coven
- Bornova Veterinary Control Institute, Izmir, Turkey
| | - G Goujgoulova
- National Diagnostic Research Veterinary Medical Institute, Sofia, Bulgaria
| | - R Haddas
- Division of Avian Diseases, Kimron Veterinary Institute, Beit-Dagan, Israel
| | - I Brown
- Animal and Plant Health Agency, Weybridge, UK
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Miller PJ, Haddas R, Simanov L, Lublin A, Rehmani SF, Wajid A, Bibi T, Khan TA, Yaqub T, Setiyaningsih S, Afonso CL. Identification of new sub-genotypes of virulent Newcastle disease virus with potential panzootic features. INFECTION GENETICS AND EVOLUTION 2014; 29:216-29. [PMID: 25445644 DOI: 10.1016/j.meegid.2014.10.032] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 10/25/2014] [Accepted: 10/30/2014] [Indexed: 11/29/2022]
Abstract
Virulent Newcastle disease virus (NDV) isolates from new sub-genotypes within genotype VII are rapidly spreading through Asia and the Middle East causing outbreaks of Newcastle disease (ND) characterized by significant illness and mortality in poultry, suggesting the existence of a fifth panzootic. These viruses, which belong to the new sub-genotypes VIIh and VIIi, have epizootic characteristics and do not appear to have originated directly from other genotype VII NDV isolates that are currently circulating elsewhere, but are related to the present and past Indonesian NDV viruses isolated from wild birds since the 80s. Viruses from sub-genotype VIIh were isolated in Indonesia (2009-2010), Malaysia (2011), China (2011), and Cambodia (2011-2012) and are closely related to the Indonesian NDV isolated in 2007, APMV1/Chicken/Karangasem, Indonesia (Bali-01)/2007. Since 2011 and during 2012 highly related NDV isolates from sub-genotype VIIi have been isolated from poultry production facilities and occasionally from pet birds, throughout Indonesia, Pakistan and Israel. In Pakistan, the viruses of sub-genotype VIIi have replaced NDV isolates of genotype XIII, which were commonly isolated in 2009-2011, and they have become the predominant sub-genotype causing ND outbreaks since 2012. In a similar fashion, the numbers of viruses of sub-genotype VIIi isolated in Israel increased in 2012, and isolates from this sub-genotype are now found more frequently than viruses from the previously predominant sub-genotypes VIId and VIIb, from 2009 to 2012. All NDV isolates of sub-genotype VIIi are approximately 99% identical to each other and are more closely related to Indonesian viruses isolated from 1983 through 1990 than to those of genotype VII, still circulating in the region. Similarly, in addition to the Pakistani NDV isolates of the original genotype XIII (now called sub-genotype XIIIa), there is an additional sub-genotype (XIIIb) that was initially detected in India and Iran. This sub-genotype also appears to have as an ancestor a NDV strain from an Indian cockatoo isolated in 1982. These data suggest the existence of a new panzootic composed of viruses of subgenotype VIIi and support our previous findings of co-evolution of multiple virulent NDV genotypes in unknown reservoirs, e.g. as recorded with the virulent NDV identified in Dominican Republic in 2008. The co-evolution of at least three different sub-genotypes reported here and the apparent close relationship of some of those genotypes from ND viruses isolated from wild birds, suggests that identifying wild life reservoirs may help predict new panzootics.
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Affiliation(s)
- Patti J Miller
- Southeast Poultry Research Laboratory, Agricultural Research Service-United States Department of Agriculture (USDA), Athens, GA 30605, USA
| | - Ruth Haddas
- Kimron Veterinary Institute, Bet Dagan 50250, Israel
| | - Luba Simanov
- Kimron Veterinary Institute, Bet Dagan 50250, Israel
| | | | - Shafqat Fatima Rehmani
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Out Fall Road, Lahore, Pakistan
| | - Abdul Wajid
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Out Fall Road, Lahore, Pakistan
| | - Tasra Bibi
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Out Fall Road, Lahore, Pakistan
| | - Taseer Ahmad Khan
- Poultry Research Laboratory, Department of Physiology, University of Karachi, Karachi, Pakistan
| | - Tahir Yaqub
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Out Fall Road, Lahore, Pakistan
| | - Surachmi Setiyaningsih
- Department of Infectious Diseases & Veterinary Public Health, Faculty of Veterinary Medicine-Bogor Agricultural University, Jl. Agatis, IPB Dramaga, Bogor 16680, Indonesia
| | - Claudio L Afonso
- Southeast Poultry Research Laboratory, Agricultural Research Service-United States Department of Agriculture (USDA), Athens, GA 30605, USA.
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Byarugaba DK, Mugimba KK, Omony JB, Okitwi M, Wanyana A, Otim MO, Kirunda H, Nakavuma JL, Teillaud A, Paul MC, Ducatez MF. High pathogenicity and low genetic evolution of avian paramyxovirus type I (Newcastle disease virus) isolated from live bird markets in Uganda. Virol J 2014; 11:173. [PMID: 25273689 PMCID: PMC4190331 DOI: 10.1186/1743-422x-11-173] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 09/23/2014] [Indexed: 12/18/2022] Open
Abstract
Background Newcastle disease is still a serious disease of poultry especially in backyard free-range production systems despite the availability of cross protective vaccines. Healthy-looking poultry from live bird markets have been suspected as a major source of disease spread although limited studies have been conducted to ascertain the presence of the virulent strains in the markets and to understand how they are related to outbreak strains. Methods This study evaluated the occurrence of Newcastle disease virus in samples collected from poultry in live bird markets across Uganda. The isolates were pathoyped using standard methods (mean death time (MDT), intracelebral pathogenicity index (ICPI), and sequencing of the fusion protein cleavage site motif) and also phylogenetically analysed after sequencing of the full fusion and hemagglutin-neuraminidase genes. The isolates were classified into genotypes and subgenotypes based on the full fusion protein gene classification system and compared with other strains in the region and world-wide. Results Virulent avian paramyxovirus type I (APMV-1) (Newcastle disease virus) was isolated in healthy-looking poultry in live bird markets. The viruses belonged to a new subgenotype, Vd, in genotype V, and clustered together with Tanzania and Kenya strains. They harbored low genetic diversity. Conclusion The occurrence of virulent AMPV-1 strains in live bird markets may serve as sources of Newcastle disease outbreaks in non-commercial farms.
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Affiliation(s)
- Denis K Byarugaba
- College of Veterinary Medicine, Makerere University, P,O, Box 7062, Kampala, Uganda.
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Khulape SA, Gaikwad SS, Chellappa MM, Mishra BP, Dey S. Genetic characterization and pathogenicity assessment of Newcastle disease virus isolated from wild peacock. Virus Genes 2014; 49:449-55. [PMID: 25260553 DOI: 10.1007/s11262-014-1116-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/16/2014] [Indexed: 11/26/2022]
Abstract
The continued spread and occurrence of Newcastle disease virus (NDV) has posed potential threat to domestic poultry industry around the globe. Mainly, wild avian species has always been implicated for the natural reservoir for virus and spread of the disease. In the present study, we report the isolation of Newcastle disease virus (NDV/Peacock/India/2012) in necropsy brain tissue sample of wild peacock from North India. Complete genome of the virus was found to be 15,186 nucleotides (nts) with six genes in order of 3'-N-P-M-F-HN-L-5', which was limited by 55-nts leader region at the 3' end and a 114-nts trailer sequence at 5' end. Sequence analysis of fusion protein revealed the dibasic amino acid cleavage site (112)R-R-Q-K-R-F(117), a characteristic motif of virulent virus. Phylogenetic analysis placed the isolate in genotype II of Newcastle disease virus showing the lowest mean percent divergence (6 %) with other genotype II counterparts. The isolate was characterized as mesogenic (intermediate pathotype) based on the mean death time (63 h) in embryonated chicken eggs and the intra-cerebral pathogenicity index (1.40) in day-old chicks. The report emphasizes the dynamic ecology of NDV strains circulating in a wild avian host during the outbreak of 2012 in North India. Further the genotypic and pathotypical characterizations of the isolate could help in development of homologous vaccine against NDV strain circulating in avian population.
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Affiliation(s)
- Sagar A Khulape
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
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Mulisa DD, W/Kiros MK, Alemu RB, Keno MS, Furaso A, Heidari A, Chibsa TR, Chunde HC. Characterization of Newcastle Disease Virus and poultry-handling practices in live poultry markets, Ethiopia. SPRINGERPLUS 2014; 3:459. [PMID: 25279281 PMCID: PMC4162888 DOI: 10.1186/2193-1801-3-459] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/18/2014] [Indexed: 12/11/2022]
Abstract
Newcastle disease represents the most severe poultry disease responsible for marked economic losses in Ethiopia. To provide a molecular characterization of Newcastle disease viruses circulating in this country, a cross sectional survey was conducted at five selected live poultry market sites in Addis Ababa. In addition, baseline data on the live poultry market system were acquired through a detailed questionnaire submitted to poultry traders. We identified 44/146 positive samples, 29 of which were virulent strains belonging to sub-genotype VIf. The very poor biosecurity practices, which have resulted from responses of the participants, suggest that they might have had a heavy impact in the spread of the disease. This study provides important information on epidemiology and control of NDV in Ethiopia and highlights the importance of implementing surveillances and biosecurity practices in live poultry markets.
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Affiliation(s)
| | | | | | - Melaku Sombo Keno
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Alice Furaso
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, OIE/FAO and National Reference Laboratory for Newcastle Disease and Avian Influenza, OIE collaborating Center for Diseases at the Human-Animal Interface, Legnaro, Padova, Italy
| | - Alireza Heidari
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, OIE/FAO and National Reference Laboratory for Newcastle Disease and Avian Influenza, OIE collaborating Center for Diseases at the Human-Animal Interface, Legnaro, Padova, Italy
| | | | - Hassen Chaka Chunde
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
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Paldurai A, Xiao S, Kim SH, Kumar S, Nayak B, Samal S, Collins PL, Samal SK. Effects of naturally occurring six- and twelve-nucleotide inserts on Newcastle disease virus replication and pathogenesis. PLoS One 2014; 9:e103951. [PMID: 25093330 PMCID: PMC4122465 DOI: 10.1371/journal.pone.0103951] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/03/2014] [Indexed: 01/10/2023] Open
Abstract
Newcastle disease virus (NDV) isolates contain genomes of 15,186, 15,192 or 15,198 nucleotides (nt). The length differences reflect a 6-nt insert in the 5′ (downstream) non-translated region (NTR) of the N gene (15,192-nt genome) or a 12-nt insert in the ORF encoding the P and V proteins (causing a 4-amino acid insert; 15,198-nt genome). We evaluated the role of these inserts in the N and P genes on viral replication and pathogenicity by inserting them into genomes of two NDV strains that have natural genome lengths of 15,186 nt and represent two different pathotypes, namely the mesogenic strain Beaudette C (BC) and the velogenic strain GB Texas (GBT). Our results showed that the 6-nt and 12-nt inserts did not detectably affect N gene expression or P protein function. The inserts had no effect on the replication or virulence of the highly virulent GBT strain but showed modest degree of attenuation in mesogenic strain BC. We also deleted a naturally-occurring 6-nt insertion in the N gene from a highly virulent 15,192-nt genome-length virus, strain Banjarmasin. This resulted in reduced replication in vitro and reduced virulence in vivo. Thus, although these inserts had no evident effect on gene expression, protein function, or replication in vivo, they did affect virulence in two of the three tested strains.
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Affiliation(s)
- Anandan Paldurai
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Sa Xiao
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Shin-Hee Kim
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Sachin Kumar
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Baibaswata Nayak
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Sweety Samal
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Peter L. Collins
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Siba K. Samal
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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Empirical analysis suggests continuous and homogeneous circulation of Newcastle disease virus in a wide range of wild bird species in Africa. Epidemiol Infect 2014; 143:1292-303. [PMID: 25090191 DOI: 10.1017/s095026881400185x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Newcastle disease (ND) is one of the most important poultry diseases worldwide and can lead to annual losses of up to 80% of backyard chickens in Africa. All bird species are considered susceptible to ND virus (NDV) infection but little is known about the role that wild birds play in the epidemiology of the virus. We present a long-term monitoring of 9000 wild birds in four African countries. Overall, 3·06% of the birds were PCR-positive for NDV infection, with prevalence ranging from 0% to 10% depending on the season, the site and the species considered. Our study shows that ND is circulating continuously and homogeneously in a large range of wild bird species. Several genotypes of NDV circulate concurrently in different species and are phylogenetically closely related to strains circulating in local domestic poultry, suggesting that wild birds may play several roles in the epidemiology of different NDV strains in Africa. We recommend that any strategic plan aiming at controlling ND in Africa should take into account the potential role of the local wild bird community in the transmission of the disease.
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Brown PA, Lemaitre E, Briand FX, Courtillon C, Guionie O, Allée C, Toquin D, Bayon-Auboyer MH, Jestin V, Eterradossi N. Molecular comparisons of full length metapneumovirus (MPV) genomes, including newly determined French AMPV-C and -D isolates, further supports possible subclassification within the MPV Genus. PLoS One 2014; 9:e102740. [PMID: 25036224 PMCID: PMC4103871 DOI: 10.1371/journal.pone.0102740] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/20/2014] [Indexed: 01/12/2023] Open
Abstract
Four avian metapneumovirus (AMPV) subgroups (A-D) have been reported previously based on genetic and antigenic differences. However, until now full length sequences of the only known isolates of European subgroup C and subgroup D viruses (duck and turkey origin, respectively) have been unavailable. These full length sequences were determined and compared with other full length AMPV and human metapneumoviruses (HMPV) sequences reported previously, using phylogenetics, comparisons of nucleic and amino acid sequences and study of codon usage bias. Results confirmed that subgroup C viruses were more closely related to HMPV than they were to the other AMPV subgroups in the study. This was consistent with previous findings using partial genome sequences. Closer relationships between AMPV-A, B and D were also evident throughout the majority of results. Three metapneumovirus "clusters" HMPV, AMPV-C and AMPV-A, B and D were further supported by codon bias and phylogenetics. The data presented here together with those of previous studies describing antigenic relationships also between AMPV-A, B and D and between AMPV-C and HMPV may call for a subclassification of metapneumoviruses similar to that used for avian paramyxoviruses, grouping AMPV-A, B and D as type I metapneumoviruses and AMPV-C and HMPV as type II.
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Affiliation(s)
- Paul A. Brown
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
| | - Evelyne Lemaitre
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
| | - François-Xavier Briand
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
| | - Céline Courtillon
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
| | - Olivier Guionie
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
| | - Chantal Allée
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
| | - Didier Toquin
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
| | - Marie-Hélène Bayon-Auboyer
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
| | - Véronique Jestin
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
| | - Nicolas Eterradossi
- French Agency for Food, Environmental and Occupational Health Safety (ANSES), Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), Université Européenne de Bretagne, Ploufragan/Plouzané laboratory, Ploufragan, France
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