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Chacón JL, Chacón RD, Sánchez-Llatas CJ, Morín JG, Astolfi-Ferreira CS, Piantino Ferreira AJ. Antigenic and molecular characterization of isolates of the Brazilian genotype BR-I (GI-11) of infectious bronchitis virus supports its recognition as BR-I serotype. Avian Pathol 2023; 52:323-338. [PMID: 37477586 DOI: 10.1080/03079457.2023.2228725] [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: 04/17/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023]
Abstract
The antigenic and molecular characteristics of BR-I infectious bronchitis viruses (IBVs) isolated from Brazil are reported. IBVs isolated from commercial flocks with different clinical manifestations between 2003 and 2019 were submitted to antigenic and molecular characterization. The complete S1 glycoprotein gene of 11 field isolates was amplified and sequenced. The virus neutralization (VN) test showed 94.75% neutralization with a BR-I isolate and 30% or less against other worldwide reference strains. The nucleotide and amino acid sequence analyses revealed 84.3-100% and 83.5-100% identity among them, respectively. The identity values ranged from 57.1 to 82.6% for nucleotides and from 46.6-84.4% for amino acids compared with those of other genotypes. By phylogenetic tree analysis, the Brazilian isolates were branched into the BR-I genotype (lineage GI-11), which was differentiated from foreign reference strains. Selective pressure analyses of BR-I IBVs revealed evolution under purifying selection (negative pressure) for the complete S1 gene but four specific sites (87, 121, 279, and 542) under diversifying selection (positive pressure). Profiles of cleavage sites and potential N-glycosylation sites differed from those of other genotypes. The low molecular relationship among the Brazilian viruses and foreign serotypes was concordant with the VN test results. The low antigenic relatedness (ranging from 5.3-30% between Brazilian genotype BR-I and reference IBV serotypes of North America, Europe, and Asia) indicates that the BR-I genotype is a different serotype, referred to for the first time and hereafter as serotype BR-I. RESEARCH HIGHLIGHTSStrains of the BR-I genotype presented robust antigenic and molecular similarity.BR-I strains evolved under purifying selection mode (negative pressure).The BR-I genotype originated in Brazil and dispersed to other countries.BR-I genotype viruses can be referred to as the BR-I serotype.
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Affiliation(s)
- Jorge L Chacón
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Ruy D Chacón
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Christian J Sánchez-Llatas
- Faculty of Biology, Department of Genetics, Physiology, and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Jaime G Morín
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Claudete S Astolfi-Ferreira
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Antonio J Piantino Ferreira
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
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2
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Icochea E, González R, Castro-Sanguinetti G, Maturrano L, Alzamora L, Sesti L, Chacón J, More-Bayona J. Genetic Analysis of Infectious Bronchitis Virus S1 Gene Reveals Novel Amino Acid Changes in the GI-16 Lineage in Peru. Microorganisms 2023; 11:microorganisms11030691. [PMID: 36985264 PMCID: PMC10051523 DOI: 10.3390/microorganisms11030691] [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: 12/13/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 03/30/2023] Open
Abstract
Infectious bronchitis is a highly contagious viral disease that represents an economic threat for poultry despite the wide use of vaccination. To characterize the virus circulating in Peru, we analyzed 200 samples, including nasopharyngeal swabs and multiple tissues collected from animals suspected of being infected with infectious bronchitis virus (IBV) between January and August in 2015. All animals had at least one positive sample for IBV by RT-PCR. Out of these positive samples, eighteen (18) were selected for viral isolation and a partial S1 sequencing. Phylogenetic analysis showed that sixteen isolates clustered with members of GI-16 lineage, also known as Q1, with nucleotide homology ranging from 93% to 98%. The two remaining isolates grouped with members of the GI-1 lineage. Our study reveals circulation of GI-16 lineage during this period in poultry systems in Peru, along with GI-1 lineage (vaccine-derived). Moreover, those IBV GI-16 isolates showed unique nucleotide and amino acid changes compared to their closest relatives. Altogether, these findings reveal the circulation of GI-16 lineage while describing changes at key regions of the S protein that might be of relevance for vaccine evasion. These results highlight the importance of genetic surveillance for improving vaccination strategies against infectious bronchitis.
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Affiliation(s)
- Eliana Icochea
- Laboratory of Avian Pathology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
| | - Rosa González
- Laboratory of Avian Pathology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
| | - Gina Castro-Sanguinetti
- Laboratory of Avian Pathology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
| | - Lenin Maturrano
- Laboratory of Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
| | - Luis Alzamora
- CEVA Animal Health, 3461 Av. República de Panamá Dpto. 1102, San Isidro, Lima 15047, Peru
| | - Luiz Sesti
- CEVA Animal Health, 3461 Av. República de Panamá Dpto. 1102, San Isidro, Lima 15047, Peru
| | - Jorge Chacón
- CEVA Animal Health, 3461 Av. República de Panamá Dpto. 1102, San Isidro, Lima 15047, Peru
| | - Juan More-Bayona
- Laboratory of Avian Pathology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
- Laboratory of Virology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
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Lunge VR, De Carli S, Fonseca ASK, Ikuta N. Avian Reoviruses in Poultry Farms from Brazil. Avian Dis 2022; 66:459-464. [PMID: 36715480 DOI: 10.1637/aviandiseases-d-22-99998] [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: 04/30/2022] [Accepted: 07/13/2022] [Indexed: 01/11/2023]
Abstract
Avian reovirus (ARV) is highly disseminated in commercial Brazilian poultry farms, causing arthritis/tenosynovitis, runting-stunting syndrome, and malabsorption syndrome in different meat- and egg-type birds (breeders, broilers, grillers, and layers). In Brazil, ARV infection was first described in broilers in the 1970s but was not considered an important poultry health problem for decades. A more concerning outcome of field infections has been observed in recent years, including condemnations at slaughterhouses because of the unsightly appearance of chicken body parts, mainly the legs. Analyses of the performance of poultry flocks have further evidenced economic losses to farms. Genetic and antigenic characterization of ARV field strains from Brazil demonstrated a high diversity of lineages circulating in the entire country, including four of the five main phylogenetic groups previously described (I, II, III, and V). It is still unclear if all of them are associated with different diseases affecting flocks' performance in Brazilian poultry. ARV infections have been controlled in Brazilian poultry farms by immunization of breeders and young chicks with classical commercial live vaccine strains (S1133, 1733, 2408, and 2177) used elsewhere in the Western Hemisphere. However, genetic and antigenic variations of the field isolates have prevented adequate protection against associated diseases, so killed autogenous vaccines are being produced from isolates obtained on specific farms. In conclusion, ARV field variants are continuously challenging poultry farming in Brazil. Epidemiological surveillance combined with molecular biological analyses from the field samples, as well as the development of vaccine strains directed toward the ARV circulating variants, are necessary to control this economically important poultry pathogen.
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Affiliation(s)
- Vagner R Lunge
- Laboratório de Diagnóstico em Medicina Veterinária, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul, Brazil, .,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil.,Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
| | - Silvia De Carli
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | | | - Nilo Ikuta
- Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
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4
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Origin of New Lineages by Recombination and Mutation in Avian Infectious Bronchitis Virus from South America. Viruses 2022; 14:v14102095. [PMID: 36298650 PMCID: PMC9609748 DOI: 10.3390/v14102095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/17/2022] Open
Abstract
The gammacoronavirus avian infectious bronchitis virus (IBV) is a highly contagious respiratory pathogen of primary economic importance to the global poultry industry. Two IBV lineages (GI-11 and GI-16) have been widely circulating for decades in South America. GI-11 is endemic to South America, and the GI-16 is globally distributed. We obtained full-length IBV genomes from Argentine and Uruguayan farms using Illumina sequencing. Genomes of the GI-11 and GI-16 lineages from Argentina and Uruguay differ in part of the spike coding region. The remaining genome regions are similar to the Chinese and Italian strains of the GI-16 lineage that emerged in Asia or Europe in the 1970s. Our findings support that the indigenous GI-11 strains recombine extensively with the invasive GI-16 strains. During the recombination process, GI-11 acquired most of the sequences of the GI-16, retaining the original S1 sequence. GI-11 strains with recombinant genomes are circulating forms that underwent further local evolution. The current IBV scenario in South America includes the GI-16 lineage, recombinant GI-11 strains sharing high similarity with GI-16 outside S1, and Brazilian GI-11 strains with a divergent genomic background. There is also sporadic recombinant in the GI-11 and GI-16 lineages among vaccine and field strains. Our findings exemplified the ability of IBV to generate emergent lineage by using the S gene in different genomic backgrounds. This unique example of recombinational microevolution underscores the genomic plasticity of IBV in South America.
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Brandão PE, Berg M, Leite BA, Silva SO, Taniwaki SA. The order of events on Avian coronavirus life cycle shapes the order of quasispecies evolution during host switches. Genet Mol Biol 2022; 45:e20220034. [PMID: 35671496 PMCID: PMC9173666 DOI: 10.1590/1678-4685-gmb-2022-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/01/2022] [Indexed: 12/02/2022] Open
Abstract
To understand the population genetics events during coronavirus host switches, the Beaudette strain of Avian coronavirus (AvCoV) adapted to BHK-21 cells was passaged 15 times in VERO cells, the virus load and the variants at each passage being determined by RT-qPCR and genome-length deep sequencing. From BHK-21 P2 to VERO P3, a trend for the extinction of variants was followed by stability up to VERO P11 and both the emergence and the rise in frequency in some variants, while the virus loads were stable up to VERO P12. At the spillover from BHK-21 to VERO cells, variants that both emerged, showed a rise in frequency or were extinguished were detected on the spike, while variants at the M gene showed the same pattern only at VERO passage 13. Furthermore, nsps 3-5, 9 and 15 variants were detected at lower passages compared to the consensus sequences, with those at nsp3 being detected in the spectra also at higher passages. This suggests that quasispecies coronavirus evolution in spillovers follows the virus life cycle, starting with the evolution of the receptor binding proteins, followed by the replicase and then proteins involved in virion assembly, keeping the general fitness of the mutant spectrum stable.
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Affiliation(s)
| | - Mikael Berg
- Swedish University of Agricultural Sciences, Sweden
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6
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Marandino A, Pérez R. Genetic and Antigenic Diversity of Infectious Bronchitis Virus in South America. Avian Dis 2021; 65:624-630. [DOI: 10.1637/aviandiseases-d-21-00103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Ana Marandino
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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Haque MH, Islam MA, Karim MR, Kayesh MEH, Sarker S, Nazir KHMNH, Anwer MS. Coronavirus disease 2019 and future pandemics: Impacts on livestock health and production and possible mitigation measures. Vet World 2021; 14:2434-2443. [PMID: 34840464 PMCID: PMC8613784 DOI: 10.14202/vetworld.2021.2434-2443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
The World Health Organization declared coronavirus disease 2019 (COVID-19) a pandemic on March 11, 2020. COVID-19, the current global health emergency, is wreaking havoc on human health systems and, to a lesser degree, on animals globally. The outbreak has continued since the first report of COVID-19 in China in December 2019, and the second and third waves of the outbreak have already begun in several countries. COVID-19 is expected to have adverse effects on crop production, food security, integrated pest control, tourism, the car industry, and other sectors of the global economy. COVID-19 induces a range of effects in livestock that is reflected economically since human health and livelihood are intertwined with animal health. We summarize the potentially harmful effects of COVID-19 on livestock and possible mitigation steps in response to this global outbreak. Mitigation of the negative effects of COVID-19 and future pandemics on livestock requires the implementation of current guidelines.
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Affiliation(s)
- Md. Hakimul Haque
- Department of Veterinary and Animal Sciences, Faculty of Agriculture, Rajshahi University, Rajshahi-6205, Bangladesh
| | - Md. Aminul Islam
- Department of Medicine, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md. Rezaul Karim
- Division of Animal Health Research, Bangladesh Livestock Research Institute, Savar, Dhaka-1341, Bangladesh
| | - Mohammad Enamul Hoque Kayesh
- Department of Microbiology and Public Health, Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal-8210, Bangladesh
| | - Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia
| | | | - M. Sawkat Anwer
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, USA
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8
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de Morais HA, dos Santos AP, do Nascimento NC, Kmetiuk LB, Barbosa DS, Brandão PE, Guimarães AMS, Pettan-Brewer C, Biondo AW. Natural Infection by SARS-CoV-2 in Companion Animals: A Review of Case Reports and Current Evidence of Their Role in the Epidemiology of COVID-19. Front Vet Sci 2020; 7:591216. [PMID: 33195627 PMCID: PMC7652926 DOI: 10.3389/fvets.2020.591216] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID-19), is the causative infectious agent of the current pandemic. As researchers and health professionals are still learning the capabilities of this virus, public health concerns arise regarding the zoonotic potential of SARS-CoV-2. With millions of people detected with SARS-CoV-2 worldwide, reports of companion animals possibly infected with the virus started to emerge. Therefore, our aim is to review reported cases of animals naturally infected with SARS-CoV-2, particularly companion pets, shedding light on the role of these animals in the epidemiology of COVID-19.
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Affiliation(s)
| | - Andrea Pires dos Santos
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
| | - Naila Cannes do Nascimento
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
| | - Louise Bach Kmetiuk
- Graduate College of Parasitology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - David Soeiro Barbosa
- Department of Parasitology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Paulo Eduardo Brandão
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Christina Pettan-Brewer
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
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9
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Emergence of Avian coronavirus genotype GI-11 in Colombia. Braz J Microbiol 2020; 52:455-459. [PMID: 33104974 PMCID: PMC7586380 DOI: 10.1007/s42770-020-00394-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/17/2020] [Indexed: 11/16/2022] Open
Abstract
Avian coronavirus (AvCoV/IBV) is a virus with high morbidity, which can cause respiratory, digestive, renal, and reproductive diseases in chickens. Molecular detection and sequencing are the main tool for identification and classification of AvCoV. Thirty-six samples were collected in three broiler farms from different regions in Colombia, due to mortality increase; ten samples were positive using RT-qPCR targeted to the 5′ UTR of AvCoV, and one sample was positive and had its partial S gene sequenced. Phylogenetic analysis revealed that this strain belongs to the GI-11 lineage, similar to the Brazilian cluster. Several lineages have already been described in Colombia but, to the best of our knowledge, this is the first time that GI-11 has been detected in this country, which suggests that this subtype may be more widespread in South America than previously thought.
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10
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Three Amino Acid Changes in Avian Coronavirus Spike Protein Allow Binding to Kidney Tissue. J Virol 2020; 94:JVI.01363-19. [PMID: 31694947 PMCID: PMC6955270 DOI: 10.1128/jvi.01363-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/25/2019] [Indexed: 01/03/2023] Open
Abstract
Infectious bronchitis virus is the causative agent of infectious bronchitis in chickens. Upon infection of chicken flocks, the poultry industry faces substantial economic losses by diminished egg quality and increased morbidity and mortality of infected animals. While all IBV strains infect the chicken respiratory tract via the ciliated epithelial layer of the trachea, some strains can also replicate in the kidneys, dividing IBV into the following two pathotypes: nonnephropathogenic (example, IBV-M41) and nephropathogenic viruses (including IBV-QX). Here, we set out to identify the determinants for the extended nephropathogenic tropism of IBV-QX. Our data reveal that each pathotype makes use of a different sialylated glycan ligand, with binding sites on opposite sides of the attachment protein. This knowledge should facilitate the design of antivirals to prevent coronavirus infections in the field. Infectious bronchitis virus (IBV) infects ciliated epithelial cells in the chicken respiratory tract. While some IBV strains replicate locally, others can disseminate to various organs, including the kidney. Here, we elucidate the determinants for kidney tropism by studying interactions between the receptor-binding domain (RBD) of the viral attachment protein spike from two IBV strains with different tropisms. Recombinantly produced RBDs from the nephropathogenic IBV strain QX and from the nonnephropathogenic strain M41 bound to the epithelial cells of the trachea. In contrast, only QX-RBD binds more extensively to cells of the digestive tract, urogenital tract, and kidneys. While removal of sialic acids from tissues prevented binding of all proteins to all tissues, binding of QX-RBD to trachea and kidney could not be blocked by preincubation with synthetic alpha-2,3-linked sialic acids. The lack of binding of QX-RBD to a previously identified IBV-M41 receptor was confirmed by enzyme-linked immunosorbent assay (ELISA), demonstrating that tissue binding of QX-RBD is dependent on a different sialylated glycan receptor. Using chimeric RBD proteins, we discovered that the region encompassing amino acids 99 to 159 of QX-RBD was required to establish kidney binding. In particular, QX-RBD amino acids 110 to 112 (KIP) were sufficient to render IBV-M41 with the ability to bind to kidney, while the reciprocal mutations in IBV-QX abolished kidney binding completely. Structural analysis of both RBDs suggests that the receptor-binding site for QX is located at a different location on the spike than that of M41. IMPORTANCE Infectious bronchitis virus is the causative agent of infectious bronchitis in chickens. Upon infection of chicken flocks, the poultry industry faces substantial economic losses by diminished egg quality and increased morbidity and mortality of infected animals. While all IBV strains infect the chicken respiratory tract via the ciliated epithelial layer of the trachea, some strains can also replicate in the kidneys, dividing IBV into the following two pathotypes: nonnephropathogenic (example, IBV-M41) and nephropathogenic viruses (including IBV-QX). Here, we set out to identify the determinants for the extended nephropathogenic tropism of IBV-QX. Our data reveal that each pathotype makes use of a different sialylated glycan ligand, with binding sites on opposite sides of the attachment protein. This knowledge should facilitate the design of antivirals to prevent coronavirus infections in the field.
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11
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Viral agents related to enteric disease in commercial chicken flocks, with special reference to Latin America. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s0043933913000858] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Chacón RD, Astolfi-Ferreira CS, Chacón JL, Nuñez LFN, De la Torre DI, Piantino Ferreira AJ. A seminested RT-PCR for molecular genotyping of the Brazilian BR-I Infectious Bronchitis Virus Strain (GI-11). Mol Cell Probes 2019; 47:101426. [PMID: 31365883 DOI: 10.1016/j.mcp.2019.101426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 10/26/2022]
Abstract
Infectious bronchitis (IB) is one of the avian diseases with the greatest impact on poultry farming worldwide. In Brazil, strain BR-I (GI-11) is the most prevalent in poultry flocks. The present study aimed to develop a seminested RT-PCR assay specific for the diagnosis of BR-I IBV in Brazilian samples, targeting subunit 1 of the S gene. The detection limit of this assay was 10 copies of the IBV genome. In this study, 62.24% of 572 organ pools from the 5 regions of Brazil tested positive in a 3'UTR screening, and 84.83% were typed as BR-I IBV. BR-I was detected in the respiratory, digestive and urogenital tracts in pooled samples from all Brazilian geographical regions and in all the breeding systems analyzed. Specificity and sensitivity tests as well as phylogenetic analysis successfully confirmed the expected clustering of the sequences detected by this assay with the BR-I (GI-11) group. The nested PCR described in this study represents a suitable and valuable tool in the diagnosis, epidemiology, monitoring and vaccination decisions of IBV.
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Affiliation(s)
- Ruy D Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, SP, Brazil
| | | | | | - Luis F N Nuñez
- Facultad de Ciencias de la Salud, Carrera de Medicina Veterinaria, Universidad de Las Américas, Quito, Ecuador
| | - David I De la Torre
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, SP, Brazil
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13
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Khanh NP, Tan SW, Yeap SK, Lee HJ, Choi KS, Hair-Bejo M, Bich TN, Omar AR. Comparative Pathogenicity of Malaysian QX-like and Variant Infectious Bronchitis Virus Strains in Chickens at Different Age of Exposure to the Viruses. J Comp Pathol 2018; 161:43-54. [PMID: 30173857 DOI: 10.1016/j.jcpa.2018.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/20/2018] [Accepted: 04/30/2018] [Indexed: 02/05/2023]
Abstract
Infectious bronchitis viruses (IBVs) circulating in Malaysia are classified into two groups as Malaysian QX-like and variant strains. In this study, the pathogenicity of IBS130/2015 (QX-like) and IBS037A/2014 (variant) IBVs in 1-day-old and 30-day-old specific pathogen free (SPF) chickens was characterized. Both strains caused respiratory and kidney infections based on immunohistochemistry (IHC), real-time quantitative polymerase chain reaction (qPCR) and a ciliostasis study; however, the results showed that the QX-like strain was more pathogenic, caused higher mortality and showed higher tissue tropism for the kidney than the variant strain. In contrast, despite causing low or no mortality depending on the age of the infected chickens, the Malaysian variant strain showed high tissue tropism for the respiratory tract compared with the QX-like strain. IHC and qPCR indicated the presence of both IBV strains in the epithelial lining of villi in the jejunum and the caecal tonsil; however, no pathological changes were detected in these organs. Both the Malaysian QX-like and variant IBV strains are able to infect the respiratory tract and kidney of chickens irrespective of age.
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Affiliation(s)
- N P Khanh
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia; Faculty of Agriculture and Applied Biology, Can Tho University, Xuan Khanh, Ninh Kieu, Can Tho, Viet Nam
| | - S W Tan
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - S K Yeap
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - H J Lee
- Avian Disease Division, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - K S Choi
- Avian Disease Division, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea
| | - M Hair-Bejo
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia; Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - T N Bich
- Faculty of Agriculture and Applied Biology, Can Tho University, Xuan Khanh, Ninh Kieu, Can Tho, Viet Nam
| | - A R Omar
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia; Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
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14
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Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks. Vet Sci 2018; 5:vetsci5020038. [PMID: 29596389 PMCID: PMC6024555 DOI: 10.3390/vetsci5020038] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 02/04/2023] Open
Abstract
Enteric viruses play an important role in the Brazilian poultry industry due to the economic impact of resulting low yields of broilers, layers, and breeders. The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The aim of this study was to identify single and multiple infections using data obtained from 270 samples from eleven Brazilian states, corresponding to the period between 2010 and 2017. This was accompanied by an analysis of the relationship between the age of birds, clinical signs, and geographical distribution, using Polymerase Chain Reaction (PCR) and Reverse Transcription-PCR (RT-PCR) techniques. Twenty-five profiles of virus combinations were detected. Single infections were encountered in 86.3% of samples, and multiple infections were present in the remaining 13.7%. Both single and multiple infections affected all kinds of commercial chickens with digestive problems, stunting syndrome, decreases in egg and meat production, increased mortality, and respiratory signs. FAdV-I, ChPV, CAstV, ANV, and ARtV were mostly detected in young broilers, in contrast with IBV, which was detected in hens from one to greater than 51 weeks of age. These results exhibit the complexity of enteric diseases and the still poorly understood role of each pathogen as a unique etiological agent.
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15
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Saraiva GL, Santos MR, Pereira CG, Vidigal PMP, Fietto JLR, de Oliveira Mendes TA, Bressan GC, Soares-Martins JAP, de Almeida MR, Silva-Júnior A. Evaluation of the genetic variability found in Brazilian commercial vaccines for infectious bronchitis virus. Virus Genes 2018; 54:77-85. [PMID: 29128885 PMCID: PMC7089498 DOI: 10.1007/s11262-017-1515-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 10/17/2017] [Indexed: 11/02/2022]
Abstract
Infectious bronchitis virus (IBV) is currently one of the most important pathogens in the poultry industry. The H120 and Ma5 are the only viral strains approved by the Brazilian government as the constituent of vaccines. Despite the systematic vaccination in Brazil, IBV has not yet been controlled and diseases associated with this virus have been reported in vaccinated chickens. Here, we investigated the genetic variability of H120 and Ma5 strains present in the IBV vaccines from different Brazilian manufacturers. We performed DNA sequencing analyses of the S1 spike glycoprotein gene to investigate its genetic variability and the presence of viral subpopulations among vaccines, between batches, and also in each vaccine after a single passage was performed in chicken embryonated eggs. Our results revealed up to 13 amino acid substitutions among vaccines and some of them were localized in regions of the S1 glycoprotein that play a role in virus-host interaction. Secondary nucleotide peaks identified in the chromatogram for the S1 gene sequence revealed that all original vaccines (H120 and Ma5) were composed by different subpopulations of IBV. Moreover, new viral subpopulations were also found in vaccines after a single passage in chicken embryonated eggs. These findings indicate that H120 and Ma5 viral strains used in vaccines market in Brazil can still mutate very rapidly during replication, leading to amino acid substitutions in proteins involved in the stimulation of the immune response, such as the S1 glycoprotein. Therefore, our data suggest that the genetic variability of these viral strains should be taken into consideration to ensure an effective immune response against IBV.
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Affiliation(s)
- Giuliana Loreto Saraiva
- Laboratório de Virologia Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
- Laboratório de Infectologia Molecular Animal, Instituto de Biotecnologia Aplicada a Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Marcus Rebouças Santos
- Laboratório de Virologia Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Claiton Gonçalves Pereira
- Laboratório de Virologia Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBiomol), Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Juliana Lopes Rangel Fietto
- Laboratório de Infectologia Molecular Animal, Instituto de Biotecnologia Aplicada a Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Tiago Antonio de Oliveira Mendes
- Laboratório de Infectologia Molecular Animal, Instituto de Biotecnologia Aplicada a Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Gustavo Costa Bressan
- Laboratório de Infectologia Molecular Animal, Instituto de Biotecnologia Aplicada a Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Jamária A P Soares-Martins
- Department of Mathematics and Science, Waukesha County Technical College, 800 Main Street, Pewaukee, WI, 53072, USA
| | - Márcia Rogéria de Almeida
- Laboratório de Infectologia Molecular Animal, Instituto de Biotecnologia Aplicada a Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Abelardo Silva-Júnior
- Laboratório de Virologia Animal, Departamento de Veterinária, Universidade Federal de Viçosa, Av. PH Rolfs, s/n, Viçosa, MG, 36570-900, Brazil.
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16
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Carranza C, Astolfi-Ferreira CS, Santander Parra SH, Nuñez LFN, Penzes Z, Chacón JL, Sesti L, Chacón RD, Piantino Ferreira AJ. Genetic characterisation and analysis of infectious bronchitis virus isolated from Brazilian flocks between 2010 and 2015. Br Poult Sci 2017; 58:610-623. [PMID: 28805451 DOI: 10.1080/00071668.2017.1365116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
1. Infectious bronchitis virus (IBV) variants in Brazil were isolated during 2010-2015 for epidemiological and molecular analysis to characterise the different variants and perform a bioinformatic analysis to compare with sequences of variants collected over the previous 40 years. 2. Of the 453 samples examined, 61.4% were positive for IBV and 75.9% of these were considered to have the BR-I genotype and were detected in birds of all ages distributed in all five Brazilian regions. 3. The ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS), i.e. dN/dS, revealed a predominance of codons with non-synonymous substitutions in the first third of the S1 gene and a dN/dS ratio of 0.67. Additionally, prediction of N-glycosylation sites showed that most of the BR-I variants (from 2003 to early 2014) had an extra site at amino acid position 20, whereas the newest variants lacked this extra site. 4. These results suggest that Brazilian IBV variants probably underwent drastic mutations at various points between 1983 and 2003 and that the selection processes became silent after achieving a sufficiently effective antigenic structure for invasion and replication in their hosts. Brazilian IBV genotype BR-I is currently the predominant genotype circulating in Brazil and South America.
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Affiliation(s)
- Claudia Carranza
- a Department of Pathology, School of Veterinary Medicine , University of São Paulo , São Paulo , Brazil
| | | | - Silvana H Santander Parra
- a Department of Pathology, School of Veterinary Medicine , University of São Paulo , São Paulo , Brazil
| | - Luis F N Nuñez
- a Department of Pathology, School of Veterinary Medicine , University of São Paulo , São Paulo , Brazil
| | | | | | - Luiz Sesti
- c CEVA Animal Health , Campinas , Brazil
| | - Ruy D Chacón
- a Department of Pathology, School of Veterinary Medicine , University of São Paulo , São Paulo , Brazil
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17
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Torres CA, Listorti V, Lupini C, Franzo G, Drigo M, Catelli E, Brandão PE, Cecchinato M. Gamma and Deltacoronaviruses in quail and pheasants from Northern Italy1. Poult Sci 2017; 96:717-722. [PMID: 27738120 PMCID: PMC7107168 DOI: 10.3382/ps/pew332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/06/2016] [Indexed: 02/03/2023] Open
Abstract
In view of the restricted knowledge on the diversity of coronaviruses in poultry other than chicken, this study aimed to investigate the genetic diversity of coronaviruses in quail, pheasant, and partridge from two regions of Northern Italy. To this end, pools of tracheal and cloacal swabs from European quail (Coturnix Coturnix) and intestinal tract from pheasants (Phasianus Colchicus) and partridge (Perdix Perdix) flocks, with or without enteric signs, were collected during 2015. Avian coronavirus (Gammacoronavirus) was detected in quail not vaccinated against Infectious Bronchitis Virus (IBV) and in pheasants vaccinated with an IBV Massachusetts serotype. Based on DNA sequences for the gene encoding the S protein, the avian coronaviruses detected in the quail and pheasant are related to the IBV 793B and Massachusetts types, respectively. However, RNA-dependent RNA polymerase (RdRp) analyses showed the susceptibility of quail also to Deltacoronaviruses, suggesting that quail and pheasant avian coronaviruses share spike genes identical to chicken IBV spike genes and quail might host Deltacoronavirus.
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Affiliation(s)
- C A Torres
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando, Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil.,Coronavirus Research Group, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil
| | - V Listorti
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50, 40064, Ozzano Emilia (BO), Italy
| | - C Lupini
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50, 40064, Ozzano Emilia (BO), Italy
| | - G Franzo
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell'università, 16, 35020, Legnaro (PD), Italy
| | - M Drigo
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell'università, 16, 35020, Legnaro (PD), Italy
| | - E Catelli
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50, 40064, Ozzano Emilia (BO), Italy
| | - P E Brandão
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando, Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil.,Coronavirus Research Group, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil
| | - M Cecchinato
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell'università, 16, 35020, Legnaro (PD), Italy
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18
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Torres CA, Hora AS, Tonietti PO, Taniwaki SA, Cecchinato M, Villarreal LYB, Brandão PE. Gammacoronavirus and Deltacoronavirus in Quail. Avian Dis 2017; 60:656-61. [PMID: 27610726 DOI: 10.1637/11412-032316-reg.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This paper expands on a previous report about coronaviruses in quail. After surveillance carried out in 2009 and 2010, some farmers started vaccinating quail with the Massachusetts avian infectious bronchitis virus serotype. The samples for this study were collected in 2013 from São Paulo state in southeastern Brazil. Pools of trachea, lungs, reproductive tract, kidneys, and enteric contents from quail and laying hens kept in the same farms and from quail-only farms as well as from both healthy birds and those showing infectious bronchitis-like symptoms were sampled in this study. The samples were screened using nested RT-PCR targeting the 3'-untranslated region of the Gammacoronavirus genus. Based on the DNA sequence for the RNA-dependent RNA polymerase (RdRp) gene, the strains isolated from quail clustered within either the Gammacoronavirus or Deltacoronavirus genus, and sequences from both genera were found in one quail sample. The phylogeny based on the partial S1 subunit sequence showed that the gammacoronaviruses detected in quail and layers belonged to the Brazil type. These results suggest that quail are susceptible to Gammacoronavirus and Deltacoronavirus viruses and indicate that the Massachusetts vaccination was not controlling IBV in quail or chickens.
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Affiliation(s)
- C A Torres
- A Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil.,B Coronavirus Research Group, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil
| | - A S Hora
- A Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil.,B Coronavirus Research Group, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil
| | - P O Tonietti
- A Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil
| | - S A Taniwaki
- A Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil
| | - M Cecchinato
- D Department of Animal Medicine, Production and Health, University of Padua, Viale dell'università, 16, 35020, Legnaro (PD), Italy
| | - L Y B Villarreal
- B Coronavirus Research Group, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil.,C MSD Animal Health, Av. Doutor Chucri Zaidan, 246, CEP 04583-110, São Paulo, SP, Brazil
| | - P E Brandão
- A Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil.,B Coronavirus Research Group, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508 270, São Paulo, SP, Brazil
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19
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Marandino A, Tomás G, Panzera Y, Greif G, Parodi-Talice A, Hernández M, Techera C, Hernández D, Pérez R. Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages. INFECTION GENETICS AND EVOLUTION 2017; 54:245-250. [PMID: 28705717 PMCID: PMC7106025 DOI: 10.1016/j.meegid.2017.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 01/28/2023]
Abstract
Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing. The strains here sequenced are the first obtained in South America for the infectious bronchitis virus and provide new insights into the origin, spreading and evolution of viral variants. The complete genome of the GI-11 and GI-16 strains have 27,621 and 27,638 nucleotides, respectively, and possess the same genomic organization. Phylogenetic incongruence analysis reveals that both strains have a mosaic genome that arose by recombination between Euro Asiatic strains of the GI-16 lineage and ancestral South American GI-11 viruses. The recombination occurred in South America and produced two viral variants that have retained the full-length S1 sequences of the parental lineages but are extremely similar in the rest of their genomes. These recombinant virus have been extraordinary successful, persisting in the continent for several years with a notorious wide geographic distribution. Our findings reveal a singular viral dynamics and emphasize the importance of complete genomic characterization to understand the emergence and evolutionary history of viral variants. Genomic analysis was performed in two main lineages of Infectious bronchitis virus. Lineages differ in their S1 sequences but are similar in the rest of the genome. Genomic similarity between both lineages arise by inter-lineage recombination. Inter-lineage recombination occurred in South America between European/Asiatic and local strain. Recombinant forms have persisted in the continent for several years with wide geographic distribution.
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Affiliation(s)
- Ana Marandino
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Yanina Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Greif
- Unidad de Biología Molecular, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Adriana Parodi-Talice
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Unidad de Biología Molecular, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Martín Hernández
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Claudia Techera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Diego Hernández
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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20
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Bande F, Arshad SS, Omar AR, Hair-Bejo M, Mahmuda A, Nair V. Global distributions and strain diversity of avian infectious bronchitis virus: a review. Anim Health Res Rev 2017; 18:70-83. [PMID: 28776490 DOI: 10.1017/s1466252317000044] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The poultry industry faces challenge amidst global food security crisis. Infectious bronchitis is one of the most important viral infections that cause huge economic loss to the poultry industry worldwide. The causative agent, infectious bronchitis virus (IBV) is an RNA virus with great ability for mutation and recombination; thus, capable of generating new virus strains that are difficult to control. There are many IBV strains found worldwide, including the Massachusetts, 4/91, D274, and QX-like strains that can be grouped under the classic or variant serotypes. Currently, information on the epidemiology, strain diversity, and global distribution of IBV has not been comprehensively reported. This review is an update of current knowledge on the distribution, genetic relationship, and diversity of the IBV strains found worldwide.
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Affiliation(s)
- Faruku Bande
- Department of Veterinary Pathology and Microbiology,Faculty of Veterinary Medicine,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Siti Suri Arshad
- Department of Veterinary Pathology and Microbiology,Faculty of Veterinary Medicine,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Abdul Rahman Omar
- Department of Veterinary Pathology and Microbiology,Faculty of Veterinary Medicine,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Mohd Hair-Bejo
- Department of Veterinary Pathology and Microbiology,Faculty of Veterinary Medicine,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Aliyu Mahmuda
- Department of Microbiology and Parasitology,Faculty of Medicine and Health Sciences,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Venugopal Nair
- Avian Oncogenic Virus Group,The Pirbright Institute,Working,Guildford,Surrey,GU24 0NF,UK
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21
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Fraga APD, Ikuta N, Fonseca ASK, Spilki FR, Balestrin E, Rodrigues CD, Canal CW, Lunge VR. A Real-Time Reverse-Transcription Polymerase Chain Reaction for Differentiation of Massachusetts Vaccine and Brazilian Field Genotypes of Avian Infectious Bronchitis Virus. Avian Dis 2016; 60:16-21. [PMID: 26953939 DOI: 10.1637/11262-081815-regr.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The avian infectious bronchitis virus is classified into serotypes or genotypes (or both) in different poultry-producing countries of the world. In Brazil, Massachusetts type (Mass), used as a live vaccine, and local field Brazilian variants (genotypes; BR) predominate in the commercial poultry flocks. This study describes the development and validation of two real-time reverse-transcription polymerase chain reactions (RT-qPCR) for the specific detection of Mass and BR genotypes in allantoic fluids and clinical samples. Genotype-specific primers, combined with a generic probe targeted to the S1 gene, originated Mass RT-qPCR and BR RT-qPCR-specific assays. Analytical sensitivity and linearity of these assays were determined in comparison with an IBV generic real-time RT-PCR based on the 5' untranslated region (5'UTR RT-qPCR). Mass RT-qPCR detected five Mass field isolates, three vaccine samples, and one coinfected sample (BR and Mass) while BR RT-qPCR detected 16 BR field isolates. Both assays were linear (R(2) > 0.98), reproducible, and as sensitive as the classical 5'UTR RT-qPCR used to detect IBV. In the analysis of 141 IBV clinical samples, 8 were positive for Mass RT-qPCR, 76 for BR RT-qPCR, and 2 for both assays. In the remaining 55 samples, 25 were positive only for 5'UTR RT-qPCR and 30 were negative for the three assays. In conclusion, both assays were able to detect Mass and BR genotypes, allowing rapid and easy IBV molecular typing from allantoic fluids and clinical samples.
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Affiliation(s)
- Aline Padilha de Fraga
- A Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil - ULBRA, Canoas, 92425-900, Rio Grande do Sul, Brazil.,B Simbios Biotecnologia, Cachoeirinha, 94940-030, Rio Grande do Sul, Brazil
| | - Nilo Ikuta
- A Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil - ULBRA, Canoas, 92425-900, Rio Grande do Sul, Brazil.,B Simbios Biotecnologia, Cachoeirinha, 94940-030, Rio Grande do Sul, Brazil
| | | | | | - Eder Balestrin
- A Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil - ULBRA, Canoas, 92425-900, Rio Grande do Sul, Brazil
| | - Carolina Dias Rodrigues
- A Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil - ULBRA, Canoas, 92425-900, Rio Grande do Sul, Brazil
| | - Cláudio Wageck Canal
- D Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, 91540-000, Rio Grande do Sul, Brazil
| | - Vagner Ricardo Lunge
- A Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil - ULBRA, Canoas, 92425-900, Rio Grande do Sul, Brazil.,B Simbios Biotecnologia, Cachoeirinha, 94940-030, Rio Grande do Sul, Brazil
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22
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Lobani AM, Gharaibeh SM, Al-Majali AM. Relationship between different enteric viral infections and the occurrence of diarrhea in broiler flocks in Jordan. Poult Sci 2016; 95:1257-61. [PMID: 27190109 PMCID: PMC7107110 DOI: 10.3382/ps/pew054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/14/2016] [Indexed: 11/20/2022] Open
Abstract
The aim of this study is to determine if enteric viruses are the cause of diarrhea in broiler flocks in Jordan. Intestinal content samples were collected from 101 broiler flocks from several regions of Jordan to detect the presence of astrovirus, coronavirus, reovirus, and rotavirus, by using reverse transcriptase polymerase chain reaction (RT-PCR). Forty-six of these flocks were clinically healthy with no enteric disease, and the other 55 flocks were clinically suffering from diarrhea. The samples were collected between 5 and 16 d of age. The results show that 79% of total 101 flocks tested were infected with one or more of the above enteric viruses. Coronavirus was the most common virus, detected in 56.4% of these flocks, with astrovirus in 29.7% of the flocks, and rotavirus (9.9%) and reovirus (5.6%) being the least common. None of these flocks were found to be infected with all four viruses, but one of the flocks was found to be infected with astrovirus, coronavirus, and rotavirus simultaneously. Individual infection was noted with astrovirus, coronavirus and rotavirus but not with reovirus, whereas all flocks infected with reovirus were also infected with coronavirus. There was no statistical evidence to link these viruses as the main cause of diarrhea in the flocks tested. This is the first study in Jordan to detect all of these viruses and to correlate their presence with diarrhea in chicken flocks.
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Affiliation(s)
- A M Lobani
- Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - S M Gharaibeh
- Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - A M Al-Majali
- Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
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23
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Marandino A, Tomás G, Hernández M, Panzera Y, Craig MI, Vagnozzi A, Vera F, Techera C, Grecco S, Banda A, Hernández D, Pérez R. Development of RT-qPCR assays for the specific identification of two major genotypes of avian infectious bronchitis virus. J Virol Methods 2016; 235:21-25. [PMID: 27181213 DOI: 10.1016/j.jviromet.2016.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 11/30/2022]
Abstract
Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus (27.6kb) that causes one of the most persistent respiratory disease in poultry. The virus is classified in genotypes with different epidemiological relevance and clinical implications. The present study reports the development and validation of specific RT-qPCR assays for the detection of two major IBV genotypes: South America I (SAI) and Asia/South America II (A/SAII). The SAI genotype is an exclusive and widespread South American lineage while the A/SAII genotype is distributed in Asia, Europe and South America. Both identification assays employ TaqMan probes that hybridize with unique sequences in the spike glycoprotein gene. The assays successfully detected all the assessed strains belonging to both genotypes, showing high specificity and absence of cross-reactivity. Using serial dilutions of in vitro-transcribed RNA we obtained acceptable determination coefficients, PCR efficiencies and relatively small intra- and inter-assay variability. The assays demonstrated a wide dynamic range between 10(1)-10(7) and 10(2)-10(7) RNA copies/reaction for SAI and A/SAII strains, respectively. The possibility to characterize a large number of samples in a rapid, sensitive and reproducible way makes these techniques suitable tools for routine testing, IBV control, and epidemiological research in poultry.
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Affiliation(s)
- Ana Marandino
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Martín Hernández
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Yanina Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - María Isabel Craig
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25 (1712) Castelar, Buenos Aires, Argentina
| | - Ariel Vagnozzi
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25 (1712) Castelar, Buenos Aires, Argentina
| | - Federico Vera
- Laboratorio Sanidad Aviar, INTA- E.E.A, Concepción del Uruguay, Entre Ríos, Argentina
| | - Claudia Techera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Sofía Grecco
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Alejandro Banda
- Poultry Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, Pearl, MS 39288, USA
| | - Diego Hernández
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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Fellahi S, Harrak ME, Kuhn JH, Sebbar G, Bouaiti EA, Khataby K, Fihri OF, Houadfi ME, Ennaji MM. Comparison of SYBR green I real-time RT-PCR with conventional agarose gel-based RT-PCR for the diagnosis of infectious bronchitis virus infection in chickens in Morocco. BMC Res Notes 2016; 9:231. [PMID: 27106608 PMCID: PMC4841946 DOI: 10.1186/s13104-016-2037-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/11/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND A rapid, sensitive, and specific molecular method for the diagnosis of infectious bronchitis virus (IBV) infection is important in curbing infectious bronchitis outbreaks in Morocco and other countries. METHODS In this study, an easy-to-perform SYBR green I real-time reverse transcriptase polymerase chain reaction (RT-PCR) targeting the nucleocapsid gene of IBV was developed and compared with conventional agarose gel-based RT-PCR for the detection of IBV infection. RESULTS We found that the SYBR green I real-time RT-PCR was at least 10 times more sensitive than the agarose gel electrophoresis detection method. The assay exhibited high specificity for IBV infection. All negative controls, such as Newcastle disease virus, infectious bursal disease virus, and avian influenza virus, were not detected. CONCLUSION The SYBR green I real-time RT-PCR test described herein can be used to rapidly distinguish IBV from other respiratory pathogens, which is important for diagnosis and control of infectious bronchitis outbreaks in Morocco. The test is a valuable and useful method as a routine assay for diagnosis of clinical IBV infection in commercial chickens.
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Affiliation(s)
- Siham Fellahi
- />Unit of Avian Pathology, Agronomic and Veterinary Institute Hassan II, B.P. 6202, Rabat, Morocco
- />Laboratory of Virology, Microbiology and Quality/Ecotoxicology & Biodiversity, Faculty of Sciences and Techniques-University Hassan II Mohammedia, PO Box 146, Quartier Yasmina-Mohammedia, 20650 Casablanca, Morocco
| | - Mehdi El Harrak
- />Laboratory of Molecular Biology-Society of Biological Products and Veterinary Pharmaceuticals (Biopharma), B.P. 4569, Km 2, Route de Casa, Rabat, Morocco
| | - Jens H. Kuhn
- />Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702 USA
| | - Ghizlane Sebbar
- />Laboratory of Molecular Biology-Society of Biological Products and Veterinary Pharmaceuticals (Biopharma), B.P. 4569, Km 2, Route de Casa, Rabat, Morocco
| | - El Arbi Bouaiti
- />Laboratory of Epidemiology and Clinical Research. Faculty of Medicine, B.P. 1014, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Khadija Khataby
- />Laboratory of Virology, Microbiology and Quality/Ecotoxicology & Biodiversity, Faculty of Sciences and Techniques-University Hassan II Mohammedia, PO Box 146, Quartier Yasmina-Mohammedia, 20650 Casablanca, Morocco
| | - Ouafae Fassi Fihri
- />Unit of Avian Pathology, Agronomic and Veterinary Institute Hassan II, B.P. 6202, Rabat, Morocco
| | - Mohammed El Houadfi
- />Unit of Avian Pathology, Agronomic and Veterinary Institute Hassan II, B.P. 6202, Rabat, Morocco
| | - My Mustapha Ennaji
- />Laboratory of Virology, Microbiology and Quality/Ecotoxicology & Biodiversity, Faculty of Sciences and Techniques-University Hassan II Mohammedia, PO Box 146, Quartier Yasmina-Mohammedia, 20650 Casablanca, Morocco
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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: 263] [Impact Index Per Article: 32.9] [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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26
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Chacón JL, Assayag MS, Revolledo L, Astolfi-Ferreira CS, Vejarano MP, Jones RC, Piantino Ferreira AJ. Pathogenicity and molecular characteristics of infectious bronchitis virus (IBV) strains isolated from broilers showing diarrhoea and respiratory disease. Br Poult Sci 2015; 55:271-83. [PMID: 24678626 DOI: 10.1080/00071668.2014.903558] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract 1. The possibility that infectious bronchitis virus (IBV) variants isolated from broilers with enteric and respiratory problems have a different tropism and pathological outcome from those IBV strains causing classical respiratory disease was investigated. 2. IBV variants were isolated from broiler flocks with enteric and respiratory problems in two regions of Brazil. The USP-10 isolate, of enteric origin, was inoculated via the oral oroculonasal routes into IBV-antibody-free broilers and specific pathogen-free (SPF) chickens to determine tissue tropism and pathogenicity and compared with an IBV variant (USP-50) isolated from chickens showing signs of respiratory disease only. 3. Both USP-10 and USP-50 strains caused similar pathological patterns by either route of inoculation. Both variants were detected in respiratory and non-respiratory tissues, including the kidney, intestine and testis. 4. Broilers were more susceptible to infection than SPF chickens, and seroconversion was detected in all of the chicks.
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Affiliation(s)
- J L Chacón
- a Department of Pathology , School of Veterinary Medicine - University of São Paulo , Av. Prof. Dr. Orlando M. Paiva, 87, CEP 05508-900 , São Paulo , SP , Brazil
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27
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Marandino A, Pereda A, Tomás G, Hernández M, Iraola G, Craig MI, Hernández D, Banda A, Villegas P, Panzera Y, Pérez R. Phylodynamic analysis of avian infectious bronchitis virus in South America. J Gen Virol 2015; 96:1340-1346. [PMID: 25667323 PMCID: PMC7081071 DOI: 10.1099/vir.0.000077] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/31/2015] [Indexed: 11/18/2022] Open
Abstract
Infectious bronchitis virus (IBV) is a coronavirus of chickens that causes great economic losses to the global poultry industry. The present study focuses on South American IBVs and their genetic relationships with global strains. We obtained full-length sequences of the S1 coding region and N gene of IBV field isolates from Uruguay and Argentina, and performed Phylodynamic analysis to characterize the strains and estimate the time of the most recent common ancestor. We identified two major South American genotypes, which were here denoted South America I (SAI) and Asia/South America II (A/SAII). The SAI genotype is an exclusive South American lineage that emerged in the 1960s. The A/SAII genotype may have emerged in Asia in approximately 1995 before being introduced into South America. Both SAI and A/SAII genotype strains clearly differ from the Massachusetts strains that are included in the vaccine formulations being used in most South American countries.
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Affiliation(s)
- Ana Marandino
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ariel Pereda
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25 (1712) Castelar, Buenos Aires, Argentina
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Martín Hernández
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Gregorio Iraola
- Unidad de Bioinformática, Instituto Pasteur de Montevideo, 11400 Montevideo, Uruguay.,Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - María Isabel Craig
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25 (1712) Castelar, Buenos Aires, Argentina
| | - Diego Hernández
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Alejandro Banda
- Poultry Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, PO Box 97813, Pearl, MS 39288, USA
| | - Pedro Villegas
- College of Veterinary Medicine, Poultry Diagnostic and Research Center, University of Georgia, 953 College Station Road, Athens, GA 30602-4875, USA
| | - Yanina Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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Day JM, Oakley BB, Seal BS, Zsak L. Comparative analysis of the intestinal bacterial and RNA viral communities from sentinel birds placed on selected broiler chicken farms. PLoS One 2015; 10:e0117210. [PMID: 25635690 PMCID: PMC4311960 DOI: 10.1371/journal.pone.0117210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/21/2014] [Indexed: 12/28/2022] Open
Abstract
There is a great deal of interest in characterizing the complex microbial communities in the poultry gut, and in understanding the effects of these dynamic communities on poultry performance, disease status, animal welfare, and microbes with human health significance. Investigations characterizing the poultry enteric virome have identified novel poultry viruses, but the roles these viruses play in disease and performance problems have yet to be fully characterized. The complex bacterial community present in the poultry gut influences gut development, immune status, and animal health, each of which can be an indicator of overall performance. The present metagenomic investigation was undertaken to provide insight into the colonization of specific pathogen free chickens by enteric microorganisms under field conditions and to compare the pre-contact intestinal microbiome with the altered microbiome following contact with poultry raised in the field. Analysis of the intestinal virome from contact birds ("sentinels") placed on farms revealed colonization by members of the Picornaviridae, Picobirnaviridae, Reoviridae, and Astroviridae that were not present in pre-contact birds or present in proportionally lower numbers. Analysis of the sentinel gut bacterial community revealed an altered community in the post-contact birds, notably by members of the Lachnospiracea/Clostridium and Lactobacillus families and genera. Members of the avian enteric Reoviridae and Astroviridae have been well-characterized and have historically been implicated in poultry enteric disease; members of the Picobirnaviridae and Picornaviridae have only relatively recently been described in the poultry and avian gut, and their roles in the recognized disease syndromes and in poultry performance in general have not been determined. This metagenomic analysis has provided insight into the colonization of the poultry gut by enteric microbes circulating in commercial broiler flocks, and has identified enteric viruses and virus communities that warrant further study in order to understand their role(s) in avian gut health and disease.
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Affiliation(s)
- J. Michael Day
- United States Department of Agriculture, Agricultural Research Service, Southeast Poultry Research Laboratory, Athens, GA, United States of America
| | - Brian B. Oakley
- United States Department of Agriculture, Agricultural Research Service, Poultry Microbiological Safety Research Unit, Athens, GA, United States of America
| | - Bruce S. Seal
- United States Department of Agriculture, Agricultural Research Service, Poultry Microbiological Safety Research Unit, Athens, GA, United States of America
| | - Laszlo Zsak
- United States Department of Agriculture, Agricultural Research Service, Southeast Poultry Research Laboratory, Athens, GA, United States of America
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29
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Balestrin E, Fraga AP, Ikuta N, Canal CW, Fonseca ASK, Lunge VR. Infectious bronchitis virus in different avian physiological systems-a field study in Brazilian poultry flocks. Poult Sci 2014; 93:1922-9. [PMID: 24894532 PMCID: PMC7107171 DOI: 10.3382/ps.2014-03875] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Avian infectious bronchitis is a highly contagious viral disease with economic effects on poultry agribusiness. The disease presents multi-systemic clinical signs (respiratory, renal, enteric, and reproductive) and is caused by one coronavirus (infectious bronchitis virus, IBV). Infectious bronchitis virus is classified into different serotypes and genotypes (vaccine strains and field variants). This study aimed to evaluate the occurrence of IBV in commercial poultry flocks from 3 important producing regions in Brazil and to determine the tropism of the main circulating genotypes to 3 different avian physiological systems (respiratory, digestive, urinary/reproductive). Clinical samples with suggestive signs of IBV infection were collected from 432 different poultry commercial flocks (198 from broilers and 234 from breeders). The total number of biological samples consisted of organ pools from the 3 above physiological systems obtained of farms from 3 important producing regions: midwest, northeast, and south. Infectious bronchitis virus was detected by reverse-transcription, real-time PCR of the 5′ untranslated region. The results showed 179 IBV-positive flocks (41.4% of the flocks), with 107 (24.8%) from broilers and 72 (16.8%) from breeders. There were similar frequencies of IBV-positive flocks in farms from different regions of the country, most often in broilers (average 54%) compared with breeders (average 30.8%). reverse-transcription was more frequently detected in the digestive system of breeders (40%), and in the digestive (43.5%) and respiratory (37.7%) systems of broilers. Infectious bronchitis virus genotyping was performed by a reverse-transcription nested PCR and sequencing of the S1 gene from a selection of 79 IBV-positive flocks (45 from broilers and 34 from breeders). The majority of the flocks were infected with Brazilian variant genotype than with Massachusetts vaccine genotype. These results demonstrate the predominance of the Brazilian variant (mainly in the enteric tract) in commercial poultry flocks from 3 important producing regions in Brazil.
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Affiliation(s)
- Eder Balestrin
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, Prédio 22, Sala 312, Bairro São José, CEP 92425-900, Canoas, RS, Brazil
| | - Aline P Fraga
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, Prédio 22, Sala 312, Bairro São José, CEP 92425-900, Canoas, RS, Brazil
| | - Nilo Ikuta
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, Prédio 22, Sala 312, Bairro São José, CEP 92425-900, Canoas, RS, Brazil Simbios Biotecnologia, Rua Cai, 541, Vila Princesa Izabel, CEP 94940-030, Cachoeirinha, RS, Brazil
| | - Cláudio W Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9090, Bairro Agronomia, CEP 90540-000, Porto Alegre, RS, Brazil
| | - André S K Fonseca
- Simbios Biotecnologia, Rua Cai, 541, Vila Princesa Izabel, CEP 94940-030, Cachoeirinha, RS, Brazil
| | - Vagner R Lunge
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, Prédio 22, Sala 312, Bairro São José, CEP 92425-900, Canoas, RS, Brazil Simbios Biotecnologia, Rua Cai, 541, Vila Princesa Izabel, CEP 94940-030, Cachoeirinha, RS, Brazil
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30
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Torres CA, Villarreal LYB, Ayres GRR, Richtzenhain LJ, Brandão PE. An Avian coronavirus in quail with respiratory and reproductive signs. Avian Dis 2014; 57:295-9. [PMID: 24689189 DOI: 10.1637/10412-100412-reg.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
An Avian coronavirus was detected in pools of lungs, tracheas, female reproductive tracts, kidneys, and enteric contents from quail (Coturnix coturnix japonica) and laying hen flocks, with and without infectious bronchitis (IB)-like signs, cohoused in farms located in two states of southeastern Brazil during 2009-2010. Although Avian metapneumovirus subtype B was found in two layers samples, Newcastle disease virus was not found in quail or in hens. Based on DNA sequences for the 3'-untranslated region and the gene encoding the RNA-dependent RNA polymerase, this avian coronaviruses in quail is an IB virus-like gammacoronavirus.
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31
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Fraga AP, Balestrin E, Ikuta N, Fonseca ASK, Spilki FR, Canal CW, Lunge VR. Emergence of a new genotype of avian infectious bronchitis virus in Brazil. Avian Dis 2014; 57:225-32. [PMID: 24689178 DOI: 10.1637/10346-090412-reg.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Infectious bronchitis virus (IBV) is the agent of a highly contagious disease that affects domestic fowl (Gallus gallus). Recent reports showed a high prevalence of one main IBV genotype (Brazil or BR-I) with low genetic diversity in commercial poultry flocks from Brazil. This research analyzed IBV positive poultry flocks from different rearing regions to verify the S1 gene variability and geographic distribution of variant IBV strains in recent years (2010 and 2011). Samples of IBV-positive flocks were obtained from 60 different farms. Forty-nine partial S1 gene sequences were determined and aligned for phylogenetic and amino acid similarity analyses. Eleven samples (22.4%) were similar to Massachusetts vaccine strains (Mass genotype) and 34 samples (69.4%) to the previously characterized Brazilian BR-I genotype. Interestingly, the remaining four samples (8.2%) clustered into a new IBV variant genotype (Brazil-II or BR-II), divergent from the BR-I. A unique nucleotide sequence insertion coding for five amino acid residues was observed in all the Brazilian variant viruses (BR-I and BR-II genotypes). These results show a higher genetic diversity in Brazilian IBV variants than previously described.
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32
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Emergence of enteric viruses in production chickens is a concern for avian health. ScientificWorldJournal 2014; 2014:450423. [PMID: 24578633 PMCID: PMC3919086 DOI: 10.1155/2014/450423] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/31/2013] [Indexed: 11/17/2022] Open
Abstract
Several viruses have been identified in recent years in the intestinal contents of chickens and turkeys with enteric problems, which have been observed in commercial farms worldwide, including Brazil. Molecular detection of these viruses in Brazil can transform to a big threat for poultry production due to risk for intestinal integrity. This disease is characterized by severely delayed growth, low uniformity, lethargy, watery diarrhea, delayed feed consumption, and a decreased conversion rate. Chicken astrovirus (CAstV), rotavirus, reovirus, chicken parvovirus (ChPV), fowl adenovirus of subgroup I (FAdV-1), and avian nephritis virus (ANV) were investigated using the conventional polymerase chain reaction (PCR) and the reverse transcription polymerase chain reaction (RT-PCR). In addition, the infectious bronchitis virus (IBV), which may play a role in enteric disease, was included. The viruses most frequently detected, either alone or in concomitance with other viruses, were IBV, ANV, rotavirus, and CAstV followed by parvovirus, reovirus, and adenovirus. This study demonstrates the diversity of viruses in Brazilian chicken flocks presenting enteric problems characterized by diarrhea, growth retard, loss weight, and mortality, which reflects the multicausal etiology of this disease.
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Fernando FS, da Silva M MDF, Rodrigues K, Okino CH, de Oliveir ES, Fernandes CC, Bandarra MDB, Mello Gonc MC, Monezi Bor M, dos Santos RM, Vasconcelo RDO, Alessi AC, Montassier HJ. Nephritis Associated with a S1 Variant Brazilian Isolate of Infectious Bronchitis Virus and Vaccine Protection Test in Experimentally Infected Chickens. ACTA ACUST UNITED AC 2013. [DOI: 10.3923/ijps.2013.639.646] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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34
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Sjaak de Wit JJ, Cook JKA, van der Heijden HMJF. Infectious bronchitis virus variants: a review of the history, current situation and control measures. Avian Pathol 2012; 40:223-35. [PMID: 21711181 PMCID: PMC7154306 DOI: 10.1080/03079457.2011.566260] [Citation(s) in RCA: 275] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The history, current situation and control measures for infectious bronchitis virus (IBV) variants are reviewed. A large number of IBV variants exist worldwide; some being unique to a particular area, others having a more general distribution. The possible reasons why some strains spread readily over major parts of the world, whereas other strains stay more localized are discussed. The advantages and disadvantages of strain classification by protectotyping, serotyping and genotyping are discussed in relation to in vivo protection. The different vaccination strategies are also considered.
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Affiliation(s)
- J J Sjaak de Wit
- GD (Animal Health Service), P.O.B. 9, 7400 AA, Deventer, The Netherlands.
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35
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Sjaak de Wit JJ, Cook JKA, van der Heijden HMJF. Infectious bronchitis virus variants: a review of the history, current situation and control measures. Avian Pathol 2012. [PMID: 21711181 DOI: 10.1080/03079457.2011.56626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The history, current situation and control measures for infectious bronchitis virus (IBV) variants are reviewed. A large number of IBV variants exist worldwide; some being unique to a particular area, others having a more general distribution. The possible reasons why some strains spread readily over major parts of the world, whereas other strains stay more localized are discussed. The advantages and disadvantages of strain classification by protectotyping, serotyping and genotyping are discussed in relation to in vivo protection. The different vaccination strategies are also considered.
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Affiliation(s)
- J J Sjaak de Wit
- GD (Animal Health Service), P.O.B. 9, 7400 AA, Deventer, The Netherlands.
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Chacon JL, Rodrigues JN, Assayag Junior MS, Peloso C, Pedroso AC, Ferreira AJP. Epidemiological survey and molecular characterization of avian infectious bronchitis virus in Brazil between 2003 and 2009. Avian Pathol 2011; 40:153-62. [PMID: 21500035 DOI: 10.1080/03079457.2010.544641] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
As part of an epidemiological study of infectious bronchitis virus (IBV) in Brazil, 252 samples from IBV-suspect flocks were tested and the IBV-positive samples were analysed by sequencing of hypervariable regions 1 and 2 of the S1 gene. A high prevalence of IBV variants was found and the sequence analysis of 41 samples revealed a high molecular similarity among the Brazilian isolates (from 90.2 to 100% and from 85.3 to 100% nucleotide and amino acid identity, respectively). The Brazilian isolates showed low genetic relationship with Massachusetts (63.4 to 70.7%), European (45.9 to 75.6%), American (49.3 to 76.4%) and other reference serotypes (67.5 to 78.8%). The Brazilian isolates branched into one unique cluster, separate from the reference serotypes used for infectious bronchitis control in other countries. The variants analysed in this work had a high similarity with all previously published Brazilian IBV isolates, suggesting the presence and high prevalence of a unique or predominant genotype circulating in Brazil. In addition, the virus neutralization test showed that the three Brazilian isolates analysed in the present study are antigenically related to one another but are different from the Massachusetts serotype. The present study shows that IBVs of a unique genotype can be associated with different clinical diseases, and that low genetic variation was detected in this genotype over a long period of time. The molecular characterization of the Brazilian variants isolated from 2003 to 2009 from different geographic regions of the country shows that only one predominant genotype is widespread in the Brazilian territory, denominated in this study as BR-I genotype.
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Affiliation(s)
- Jorge Luis Chacon
- Department of Pathology, College of Veterinary Medicine, University of Sao Paulo, Sao Paulo, Brazil
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Felippe PAN, da Silva LHA, Santos MMAB, Spilki FR, Arns CW. Genetic diversity of avian infectious bronchitis virus isolated from domestic chicken flocks and coronaviruses from feral pigeons in Brazil between 2003 and 2009. Avian Dis 2011; 54:1191-6. [PMID: 21313839 DOI: 10.1637/9371-041510-reg.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
To detect the presence of infectious bronchitis virus or avian coronavirus, a nested reverse transcriptase PCR (RT-PCR) method was developed with the aim of amplifying a fragment of 530 bases, comprising the gene coding S1 protein. In the first step, all samples were submitted to RNA extraction, RT-PCR, and nested PCR. Next, only the positive nested-PCR samples were propagated in specific-pathogen-free (SPF) embryonated chicken eggs for virus isolation. Positive samples were then sequenced and analyzed using a molecular phylogeny approach. Tracheal swab samples were collected from 23 different domestic chickens distributed in three regions of Brazil, in the period between 2003 and 2009. Also analyzed were six swab samples (tracheal and cloacal) from asymptomatic pigeons (Columba livia), caught in an urbanized region in southeastern Brazil. The study revealed two major phylogenetic groups: one clustered with the Massachusetts vaccine serotype and another joined with the D207 strain. Interestingly, samples grouped with the Connecticut and Arkansas serotypes were also found. Pigeon isolates clustered with the Massachusetts serotype showed significant similarity (close to 100%) to those obtained from chickens. Only one pigeon isolate was seen to be grouped with the Connecticut serotype, and no correlation was observed between sample grouping and region origin. Understanding the diversity of genotypes and eco-epizootiology of the disease in different environments is expected to be helpful for vaccine production aimed at the main circulating variants. In this respect, one could also expect benefits in the management of other bird species that may act as avian coronavirus reservoirs.
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Affiliation(s)
- P A N Felippe
- Laboratory of Virology, Institute of Biology, State University of Campinas, São Paulo, Brazil PB 6109
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Abstract
The use of vaccines is the main approach to control of the economically important poultry viral respiratory diseases infectious laryngotracheitis (ILT), avian metapneumovirus (aMPV) infections and infectious bronchitis (IB). This paper appraises the current methods of vaccine control in the light of the nature of each virus and epidemiological factors associated with each disease. Infectious laryngotracheitis virus (ILTV) exists as a single type with a wide range of disease severity. It is a serious disease in certain regions of the world. Recent work has distinguished molecular differences between vaccine and field strains and vaccine virus can be a cause of disease. Vaccines have remained unaltered for many years but new ones are being developed to counter vaccine side effects and reversion and reactivation of latent virus. Avian metapneumoviruses, the cause of turkey rhinotracheitis and respiratory disease in chickens exists as 4 subtypes, A, B, C and D. A and B are widespread and vaccines work well provided that accurate doses are given. Newer vaccine developments are designed to eliminate reversion and possibly counter the appearance of newer field strains which may break through established vaccine coverage. IB presents the biggest problem of the three. Being an unstable RNA virus, part of the viral genome that codes for the S1 spike gene can undergo mutation and recombination so that important antigenic variants can appear irregularly which may evade existing vaccine protection. While conventional vaccines work well against homologous types, new strategies are needed to counter this instability. Molecular approaches involving tailoring viruses to suit field challenges are in progress. However, the simple use of two genetically different vaccines to protect against a wide range of heterologous types is now a widespread practice that is very effective. None of the three diseases described can claim to be satisfactorily controlled and it remains to be seen whether the newer generations of vaccines will be more efficacious and cost effective. The importance of constant surveillance is emphasised and the testing of novel vaccines cannot be achieved without the use of vaccine-challenge experiments in poultry.
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Affiliation(s)
- Richard C Jones
- School of Veterinary Science, University of Liverpool, Neston, South Wirral, England, UK.
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Ferreira A, Astolfi Ferreira C, Chacón J, Revolledo L, Gross R, Cotrim E. In vitro virucidal and bactericidal activities of Aviclor (a formulation of sodium dichloroisocyanurate) against pathogens of poultry origin. J APPL POULTRY RES 2010. [DOI: 10.3382/japr.2009-00030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Montassier HJ. Molecular epidemiology and evolution of avian infectious bronchitis virus. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2010. [DOI: 10.1590/s1516-635x2010000200003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Wit JJ(SD, Cook JKA, van der Heijden HMJF. Infectious bronchitis virus in Asia, Africa, Australia and Latin America: history, current situation and control measures. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2010. [DOI: 10.1590/s1516-635x2010000200004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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