ABSTRACT
Avian infectious bronchitis (IB), a Gammacoronavirus, is a highly contagious upper respiratory disease, affecting chickens of all ages with a significant economic threat to the poultry industry. In February 2020, a specimen of imported chicken meat product was received and requested for coronavirus testing. The result was positive for the avian coronavirus, the IB virus (IBV) by molecular detection in the pre-screening test. Thus, this study aimed to isolate and characterize the IBV from the specimen. Virus isolation via egg inoculation was attempted and IBV was successfully isolated. The S1 subunit of the spike (S) gene of the IBV was amplified, sequenced, and the Basic Local Alignment Search Tool (BLAST) analysis showed that the IBV has 99% and 98% nucleotide similarity with the Malaysian and China IBVs, respectively. The phylogenetic analysis indicated that the virus belongs to the GI-19 lineage (also known as the QX strain) and is grouped with other IBVs from Malaysia and China. The GI-19 lineage is one of the primary IB strains that circulate in Malaysia. The recovery of the virus may be due to the persistence characteristic of the virus on meat; and the cold chain practices in the imported food product prolong the survival of this coronavirus. Though IBV is not identified as a hazard in chicken meat or meat products, raw food should be cooked thoroughly before being consumed. With the increase in international trade in poultry and poultry products, disease screening at the entry point and import risk analysis is crucial to ensure food safety and prevent the introduction of new viruses into Malaysia.
Subject(s)
Chickens , Infectious bronchitis virus , Phylogeny , Animals , Infectious bronchitis virus/genetics , Infectious bronchitis virus/isolation & purification , Infectious bronchitis virus/classification , Malaysia , Poultry Diseases/virology , Coronavirus Infections/veterinary , Coronavirus Infections/virology , Meat Products/virology , Spike Glycoprotein, Coronavirus/geneticsABSTRACT
Gammacoronavirus infectious bronchitis virus (IBV) causes a highly contagious disease in chickens and seriously endangers the poultry industry. The emergence and co-circulation of diverse IBV serotypes and genotypes with distinct pathogenicity worldwide pose a serious challenge to the development of effective intervention measures. In this study, we report the epidemic trends of IBV in China from 2019 to 2023 and a comparative analysis on the antigenic characteristics and pathogenicity of isolates among major prevalent lineages. Phylogenetic and recombination analyses based on the nucleotide sequences of the spike (S) 1 gene clustered a total of 205 isolates into twelve distinct lineages, with GI-19 as a predominant lineage (61.77 ± 4.56%) exhibiting an overall increasing trend over the past five years, and demonstrated that a majority of the variants were derived from gene recombination events. Further characterization of the growth and pathogenic properties of six representative isolates from different lineages classified four out of the six isolates as nephropathogenic types with mortality rates in one-day-old SPF chickens varying from 20-60%, one as a respiratory type with weak virulence, and one as a naturally occurring avirulent strain. Taken together, our findings illuminate the epidemic trends, prevalence, recombination, and pathogenicity of current IBV strains in China, providing key information for further strengthening the surveillance and pathogenicity studies of IBV.
Subject(s)
Chickens , Coronavirus Infections , Genetic Variation , Genotype , Infectious bronchitis virus , Phylogeny , Poultry Diseases , Animals , Infectious bronchitis virus/genetics , Infectious bronchitis virus/pathogenicity , Infectious bronchitis virus/classification , Infectious bronchitis virus/isolation & purification , China/epidemiology , Poultry Diseases/virology , Poultry Diseases/epidemiology , Coronavirus Infections/veterinary , Coronavirus Infections/virology , Coronavirus Infections/epidemiology , Prevalence , Virulence , Recombination, Genetic , SerogroupABSTRACT
Infectious bronchitis virus (IBV) is a highly contagious avian Gammacoronavirus that affects mainly chickens (Gallus gallus) but can circulate in other avian species. IBV constitutes a significant threat to the poultry industry, causing reduced egg yield, growth and mortality levels that can vary in impact. The virus can be transmitted horizontally by inhalation or direct/indirect contact with infected birds or contaminated fomites, vehicles, farm personnel and litter (Figure 1). The error-prone viral polymerase and recombination mechanisms mean diverse viral population results, with multiple genotypes, serotypes, pathotypes and protectotypes. This significantly complicates control and mitigation strategies based on vigilance in biosecurity and the deployment of vaccination.
Subject(s)
Chickens , Coronavirus Infections , Infectious bronchitis virus , Poultry Diseases , Infectious bronchitis virus/genetics , Infectious bronchitis virus/classification , Infectious bronchitis virus/physiology , Animals , Chickens/virology , Poultry Diseases/virology , Coronavirus Infections/virology , Coronavirus Infections/veterinaryABSTRACT
Infectious bronchitis virus (IBV) causes a highly contagious respiratory disease in chickens, leading to significant economic losses in the poultry industry worldwide. IBV exhibits a high mutation rate, resulting in the continuous emergence of new variants and strains. A complete genome analysis of IBV is crucial for understanding its characteristics. However, it is challenging to obtain whole-genome sequences from IBV-infected clinical samples due to the low abundance of IBV relative to the host genome. Here, we present a novel approach employing next-generation sequencing (NGS) to directly sequence the complete genome of IBV. Through in silico analysis, six primer pairs were designed to match various genotypes, including the GI-19 lineage of IBV. The primer sets successfully amplified six overlapping fragments by long-range PCR and the size of the amplicons ranged from 3.7 to 6.4 kb, resulting in full coverage of the IBV genome. Furthermore, utilizing Illumina sequencing, we obtained the complete genome sequences of two strains belonging to the GI-19 lineage (QX genotype) from clinical samples, with 100% coverage rates, over 1000 × mean depth coverage, and a high percentage of mapped reads to the reference genomes (96.63% and 97.66%). The reported method significantly improves the whole-genome sequencing of IBVs from clinical samples; thus, it can improve understanding of the epidemiology and evolution of IBVs.
Subject(s)
Chickens , Coronavirus Infections , Genome, Viral , Genotype , High-Throughput Nucleotide Sequencing , Infectious bronchitis virus , Phylogeny , Poultry Diseases , Whole Genome Sequencing , Infectious bronchitis virus/genetics , Infectious bronchitis virus/isolation & purification , Infectious bronchitis virus/classification , Animals , Whole Genome Sequencing/methods , Chickens/virology , Poultry Diseases/virology , Poultry Diseases/epidemiology , Coronavirus Infections/veterinary , Coronavirus Infections/virology , Coronavirus Infections/epidemiology , RNA, Viral/geneticsABSTRACT
Infectious bronchitis is an acute and highly contagious disease in chickens caused by the infectious bronchitis virus (IBV), which has caused significant economic losses to the poultry industry worldwide. The antigenic variant, the QX-like genotype (GI-19 lineage), has been currently reported in epidemics in East Asia, Southeast Asia, the Middle East, Europe, and Africa. We first reported an epidemic of Japanese QX-like IBVs genetically related to Chinese and South Korean strains in the Kyushu region of Japan in 2020. However, because their nationwide prevalence was unknown, we performed a nationwide survey. The testing of 419 reverse transcription (RT)-PCR-positive samples (376 layers and 43 broilers) of IBV field strains between April 2016 and March 2022 detected two QX-like IBVs in 2019 and 2021 broiler samples from one region. A survey of fecal samples collected from 122-layer farms nationwide between November 2022 and January 2023 detected QX-like IBV genes from seven farms in various regions. Phylogenetic tree analysis on the basis of the S1 gene showed that all QX-like IBVs detected in Japan were genetically related to recent Chinese and South Korean strains. A new RT-PCR assay was developed to distinguish between QX-like IBV and other IBV variants prevalent in Japan, whose results were consistent with those of previously reported identification methods. These results suggest that QX-like IBV is rapidly spreading in Japan and that countermeasures are necessary.
Estudio de la prevalencia molecular del virus de la bronquitis infecciosa similar a la cepa QX en Japón entre los años 2016 al 2023. La bronquitis infecciosa es una enfermedad aguda y altamente contagiosa del pollo causada por el virus de la bronquitis infecciosa (IBV), que ha causado importantes pérdidas económicas a la industria avícola en todo el mundo. Actualmente se ha reportado la variante antigénica, el genotipo similar a la cepa QX (cepa GI-19), en brotes en el este de Asia, el sudeste de Asia, el Medio Oriente, Europa y África. Primeramente, se reportó un brote con virus japoneses similares a QX que eran genéticamente relacionados con cepas chinas y surcoreanas en la región de Kyushu en Japón en el 2020. Sin embargo, debido a que se desconocía su prevalencia a nivel nacional, se realizó una encuesta a nivel nacional. Mediante el análisis de 419 muestras positivas a la presencia de cepas de campo por transcripción reversa (RT) y PCR (376 de ponedoras y 43 de pollos de engorde) entre abril del 2016 y marzo del 2022 se detectaron dos virus de bronquitis infecciosa similares a la cepa QX en el 2019 y en el 2021 en muestras de pollos de engorde de una región. Una encuesta de muestras fecales recolectadas de granjas de 122 ponedoras en todo el país entre noviembre del 2022 y enero del 2023 detectó genes de bronquitis infecciosa similares a la cepa QX de siete granjas en varias regiones. El análisis del árbol filogenético basado en el gene S1 mostró que todos los virus similares a la cepa QX detectados en Japón estaban relacionados genéticamente con cepas recientes de China y Corea del Sur. Se desarrolló un nuevo ensayo de RT-PCR para distinguir entre los virus de bronquitis infecciosa similares a la cepa QX y otras variantes del IBV prevalentes en Japón, cuyos resultados fueron consistentes con los de los métodos de identificación reportados anteriormente. Estos resultados sugieren que virus de bronquitis infecciosa similares a la cepa QX se están extendiendo rápidamente en Japón y que se necesitan medidas de control.
Subject(s)
Chickens , Coronavirus Infections , Infectious bronchitis virus , Phylogeny , Poultry Diseases , Infectious bronchitis virus/genetics , Infectious bronchitis virus/isolation & purification , Infectious bronchitis virus/classification , Animals , Poultry Diseases/virology , Poultry Diseases/epidemiology , Coronavirus Infections/veterinary , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Japan/epidemiology , Prevalence , GenotypeABSTRACT
Infectious bronchitis is an acute and highly contagious disease caused by avian infectious bronchitis virus (IBV). As well as the typical clinical respiratory signs, such as dyspnoea and tracheal rales, QX genotype strains can also cause damage to the urinary system and reproductive system. Our previous studies found that chickens infected with QX-type IBV also displayed damage to the bursa of Fabricius. To investigate the effects of different genotypes of IBV on the bursa of Fabricius, we challenged one-week-old SPF chickens with Mass, QX and TW genotype IBV strains and compared the clinical signs, gross lesions, histopathological damage, viral loads, and expression levels of inflammatory cytokines (IL-6, IL-8, IL-1ß, IFN-α,ß, γ and TNF-α). The results showed that all three strains caused tissue damage, while significant temporal variations in the viral loads of the different infected groups were detected. IBV infection seriously interfered with the natural immune response mediated by inflammatory cytokines (IFN-α, IFN-ß, IL-6 and IFN-γ) in chickens. Our results suggested that IBV has potential immunological implications for chickens that may lead to poor production efficiency. RESEARCH HIGHLIGHTSAvian coronavirus IBV is an important pathogen of chickens.IBV has potential immunological implications in chickens.The bursal viral load of different IBV strains varies significantly.
Subject(s)
Bursa of Fabricius , Coronavirus Infections , Infectious bronchitis virus , Poultry Diseases , Animals , Bursa of Fabricius/pathology , Bursa of Fabricius/virology , Chickens , Coronavirus Infections/pathology , Coronavirus Infections/veterinary , Coronavirus Infections/virology , Cytokines/metabolism , Infectious bronchitis virus/classification , Infectious bronchitis virus/genetics , Infectious bronchitis virus/pathogenicity , Interleukin-6 , Poultry Diseases/pathology , Poultry Diseases/virologyABSTRACT
Infectious bronchitis virus (IBV, genus Gammacoronavirus) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity.
Subject(s)
Chickens/virology , Genomics , Infectious bronchitis virus/classification , Infectious bronchitis virus/genetics , Virome/genetics , Animals , Infectious bronchitis virus/pathogenicity , Poultry Diseases/virologyABSTRACT
Infectious bronchitis virus (IBV) causes significant losses in the poultry industry throughout the world. Here we characterize the lesions of infectious bronchitis (IB) and IBV prevalence and identify the circulating strains in small flocks in California. Backyard chickens (BYCs) submitted to the Davis (Northern California; NorCal) and San Bernardino (Southern California; SoCal) branches of the California Animal Health and Food Safety Laboratory System from January through March 2019 were included in the study. Trachea, kidney, and cecal tonsils were collected for real-time reverse transcriptase (qRT)-PCR, histology, immunohistochemistry (IHC), and sequence analysis. A total of 50 chickens out of 169 submissions tested positive for IBV by qRT-PCR. Of these, 16% (20/123) were from NorCal and 65% (30/46) from SoCal laboratory. The cecal tonsil was the most frequently positive tissue by qRT-PCR and IHC. Lymphoplasmacytic tracheitis was the most frequent histopathologic finding in 24 of 39 birds, while the kidney showed interstitial nephritis, tubular necrosis, tubular dilation, and/or gout in 14 of 43 chickens. Infectious bronchitis virus played a primary role or a synergistic effect in the mortality of chickens that succumbed to other infectious diseases. The sequences of IBV detected in 22 birds were analyzed, and 14 strains were most similar to CA1737. One strain each matched Conn46, Cal99, and ArkDPI, and the remaining five did not have a substantial match to any available reference strains. The findings in this study indicate that small flocks can be reservoirs of IBV and might facilitate evolution of new variants as well as reversion of attenuated strains to virulence.
Artículo regularPrevalencia, caracterización e identificación de cepas del virus de la bronquitis infecciosa en pollos de traspatio de California. El virus de la bronquitis infecciosa (con las siglas en inglés IBV) causa pérdidas significativas en la industria avícola en todo el mundo. En este estudio se caracterizaron las lesiones de la bronquitis infecciosa (IB), la prevalencia del virus y se identificó a las cepas circulantes en pequeñas parvadas en California. Se incluyeron en el estudio pollos de traspatio (BYC) remitidos a las sedes en Davis (norte de California; NorCal) y San Bernardino (sur de California; SoCal) del Sistema de Laboratorios de Salud Animal y Seguridad Alimentaria de California de enero a marzo del 2019. Se recolectaron tráquea, riñón y tonsilas cecales para análisis cuantitativo en tiempo real (qRT)-PCR, histología, inmunohistoquímica (IHC) y análisis de secuencias. Un total de 50 pollos de 169 casos dieron positivo para la presencia del virus de bronquitis infecciosa por qRT-PCR. De estos, el 16% (20/123) provenían del norte de California y el 65% (30/46) del laboratorio del sur de California. Las tonsilas cecales fueron las muestras de tejidos positivos con mayor frecuencia por qRT-PCR e IHC. La traqueítis linfoplasmocítica fue el hallazgo histopatológico más frecuente en 24 de 39 aves, mientras que el riñón mostró nefritis intersticial, necrosis tubular, dilatación tubular y/o gota en 14 de 43 pollos. El virus de la bronquitis infecciosa jugó un papel principal o un efecto sinérgico en la mortalidad de los pollos que murieron por otras enfermedades infecciosas. Se analizaron las secuencias del virus de bronquitis detectadas en 22 aves y 14 cepas fueron muy similares al virus de bronquitis infecciosa CA1737. Tres virus coincidieron con Conn46, Cal99 y ArkDPI, y las cinco restantes no tenían una coincidencia sustancial con ninguna cepa de referencia disponible. Los hallazgos de este estudio indican que las pequeñas parvadas pueden ser reservorios del virus de la bronquitis infecciosa y podrían facilitar la evolución de nuevas variantes, así como la reversión de cepas atenuadas a formas virulentas.
Subject(s)
Chickens , Coronavirus Infections/veterinary , Infectious bronchitis virus/isolation & purification , Poultry Diseases/virology , Animals , California/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Infectious bronchitis virus/classification , Poultry Diseases/epidemiologyABSTRACT
Infectious bronchitis viruses (IBVs) are evolving continuously via genetic drift and genetic recombination, making disease prevention and control difficult. In this study, we undertook genetic and pathogenic characterization of recombinant IBVs isolated from chickens in South Korea between 2003 and 2019. Phylogenetic analysis showed that 46 IBV isolates belonged to GI-19, which includes nephropathogenic IBVs. Ten isolates formed a new cluster, the genomic sequences of which were different from those of reference sequences. Recombination events in the S1 gene were identified, with putative parental strains identified as QX-like, KM91-like, and GI-15. Recombination detection methods identified three patterns (rGI-19-I, rGI-19-II, and rGI-19-III). To better understand the pathogenicity of recombinant IBVs, we compared the pathogenicity of GI-19 with that of the rGI-19s. The results suggest that rGI-19s may be more likely to cause trachea infections than GI-19, whereas rGI-19s were less pathogenic in the kidney. Additionally, the pathogenicity of rGI-19s varied according to the genotype of the major parent. These results indicate that genetic recombination between heterologous strains belonging to different genotypes has occurred, resulting in the emergence of new recombinant IBVs in South Korea.
Subject(s)
Chickens/virology , Genotype , Infectious bronchitis virus/genetics , Infectious bronchitis virus/pathogenicity , Phylogeny , Recombination, Genetic , Animals , Genomics , Infectious bronchitis virus/classification , Poultry Diseases/epidemiology , Poultry Diseases/virology , Republic of Korea/epidemiology , Sequence Analysis, RNA , VirulenceABSTRACT
Infectious bronchitis virus (IBV) was first identified in the 1930s and it imposes a major economic burden on the poultry industry. In particular, GI-19 lineage has spread globally and has evolved constantly since it was first detected in China. In this study, we analyzed S1 gene sequences from 60 IBVs isolated in South Korea. Two IBV lineages, GI-15 and GI-19, were identified in South Korea. Phylogenetic analysis suggested that there were six distinct subgroups (KM91-like, K40/09-like, and QX-like I to IV) of the South Korean GI-19 IBVs. Among them, QX-type III and IV subgroups, which are phylogenetically different from those reported in South Korea in the past, accounted for more than half of the total. Moreover, the phylogeographic analysis of the QX-like subgroups indicated at least four distinct introductions of GI-19 IBVs into South Korea during 2001-2020. The efficacy of commercialized vaccines against the recently introduced QX-like subgroups should be verified, and continuous international surveillance efforts and quarantine procedures should be enhanced to prevent the incursion of viruses.
Subject(s)
Coronavirus Infections/veterinary , Infectious bronchitis virus/genetics , Poultry Diseases/virology , Animals , Chickens , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Genomics , Genotype , Infectious bronchitis virus/classification , Infectious bronchitis virus/isolation & purification , Phylogeny , Poultry Diseases/epidemiology , Republic of Korea/epidemiology , Sequence Analysis, RNA , Sequence Homology , Spike Glycoprotein, Coronavirus/geneticsABSTRACT
Infectious bronchitis virus (IBV), an avian coronavirus, is highly contagious. Chickens with IBV infection develop acute pathogenesis in multiple organs, including the respiratory and urogenital tracts. Frequent recombination in the spike (S) glycoprotein gene has made vaccine strategies ineffective. To understand IBV pathogenesis, we analyzed the genetic distance between Korean IBV isolates and other coronaviruses, including SARS-CoV-2. To obtain comprehensive information about early immune responses such as innate cytokine production and associated immune regulation during IBV infection, we infected primary chicken embryonic kidney cells and performed transcriptome analysis. We observed that the functional pathways of innate immunity are regulated and confirmed expression of genes that coordinate early immune responses. Understanding the immune profile of the host cell may assist in vaccine development.
Subject(s)
Infectious bronchitis virus/physiology , Animals , Cells, Cultured , Chickens , Coronavirus Infections/virology , Cytokines/genetics , Gene Expression Profiling , Host-Pathogen Interactions , Immunity, Innate/genetics , Infectious bronchitis virus/classification , Infectious bronchitis virus/genetics , Infectious bronchitis virus/isolation & purification , Kidney/cytology , Phylogeny , Republic of Korea , Spike Glycoprotein, Coronavirus/geneticsABSTRACT
Infectious bronchitis virus (IBV) was first isolated in Australia in 1962. Ongoing surveillance and characterization of Australian IBVs have shown that they have evolved separately from strains found throughout the rest of the world, resulting in the evolution of a range of unique strains and changes in the dominant wild-type strains, affecting tissue tropism, pathogenicity, antigenicity, and gene arrangement. Between 1961 and 1976 highly nephropathogenic genotype GI-5 and GI-6 strains, causing mortalities of 40% to 100%, predominated, while strains causing mainly respiratory disease, with lower mortality rates, have predominated since then. Since 1988, viruses belonging to two distinct and novel genotypes, GIII and GV, have been detected. The genome organization of the GIII strains has not been seen in any other gammacoronavirus. Mutations that emerged soon after the introduction of vaccination, incursion of strains with a novel lineage from unknown sources, recombination between IBVs from different genetic lineages, and gene translocations and deletions have contributed to an increasingly complex IBV population. These processes and the consequences of this variation for the biology of these viruses provide an insight into the evolution of endemic coronaviruses during their control by vaccination and may provide a better understanding of the potential for evolution of other coronaviruses, including SARS-CoV-2. Furthermore, the continuing capacity of attenuated IBV vaccines developed over 40 years ago to provide protection against viruses in the same genetic lineage provides some assurance that coronavirus vaccines developed to control other coronaviruses may continue to be effective for an extended period.
Subject(s)
Biological Evolution , Chickens , Coronaviridae Infections/veterinary , Infectious bronchitis virus/physiology , Poultry Diseases/virology , Animals , Antigenic Variation , Australia/epidemiology , Coronaviridae Infections/epidemiology , Coronaviridae Infections/prevention & control , Coronaviridae Infections/virology , Evolution, Molecular , Genetic Variation , Infectious bronchitis virus/classification , Infectious bronchitis virus/genetics , Infectious bronchitis virus/immunology , Phenotype , Phylogeny , Poultry Diseases/epidemiology , Poultry Diseases/prevention & control , Viral VaccinesABSTRACT
Infectious bronchitis of chicken is a high morbidity and mortality viral disease affecting the poultry industry worldwide; therefore, a better understanding of this pathogen is of utmost importance. The primary aim of this study was to obtain a deeper insight into the genomic diversity of field infectious bronchitis virus (IBV) strains using phylogenetic and recombination analysis. We sequenced the genome of 20 randomly selected strains from seven European countries. After sequencing, we created a genome sequence data set that contained 36 European origin field isolates and 33 vaccine strains. When analyzing these 69 IBV genome sequences, we identified 215 recombination events highlighting that some strains had multiple recombination breaking points. Recombination hot spots were identified mostly in the regions coding for non-structural proteins, and multiple recombination hot spots were identified in the nsp2, nsp3, nsp8, and nsp12 coding regions. Recombination occurred among different IBV genotypes and involved both field and vaccine IBV strains. Ninety percent of field strains and nearly half of vaccine strains showed evidence of recombination. Despite the low number and the scattered geographical and temporal origin of whole-genome sequence data collected from European Gammacoronaviruses, this study underlines the importance of recombination as a major evolutionary mechanism of IBVs.
Subject(s)
Coronavirus Infections/veterinary , Evolution, Molecular , Genome, Viral , Infectious bronchitis virus/genetics , RNA, Viral/genetics , Recombination, Genetic , Animals , Chickens/virology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Europe/epidemiology , Genotype , Infectious bronchitis virus/classification , Infectious bronchitis virus/isolation & purification , Whole Genome SequencingABSTRACT
Avian infectious bronchitis virus is one of the most important gammacoronaviruses, which causes a highly contagious disease. In this study, we investigated changes in the proteome of kidney tissue of specific-pathogen-free (SPF) chickens that were infected with an isolate of the nephrotropic variant 2 genotype (IS/1494/06) of avian coronavirus. Twenty 1-day-old SPF White Leghorn chickens were randomly divided into two groups, each comprising 10 chickens, which were kept in separate positive-pressure isolators. Chickens in group A served as a virus-free control group up to the end of the experiment, whereas chickens in group B were inoculated with 0.1 ml of 104.5 EID50 of the IBV/chicken/Iran/UTIVO-C/2014 isolate of IBV, and kidney tissue samples were collected at 2 and 7 days post-inoculation (dpi) from both groups. Sequencing of five protein spots at 2 dpi and 22 spots at 7 dpi that showed differential expression by two-dimensional electrophoresis (2DE) along with fold change greater than 2 was done by MS-MALDI/TOF/TOF. Furthermore, the corresponding protein-protein interaction (PPI) networks at 2 and 7 dpi were identified to develop a detailed understanding of the mechanism of molecular pathogenesis. Topological graph analysis of this undirected PPI network revealed the effect of 10 genes in the 2 dpi PPI network and nine genes in the 7 dpi PPI network during virus pathogenesis. Proteins that were found by 2DE analysis and MS/TOF-TOF mass spectrometry to be down- or upregulated were subjected to PPI network analysis to identify interactions with other cellular components. The results show that cellular metabolism was altered due to viral infection. Additionally, multifunctional heat shock proteins with a significant role in host cell survival may be employed circuitously by the virus to reach its target. The data from this study suggest that the process of pathogenesis that occurs during avian coronavirus infection involves the regulation of vital cellular processes and the gradual disruption of critical cellular functions.
Subject(s)
Coronavirus Infections/pathology , Coronavirus Infections/veterinary , Infectious bronchitis virus/genetics , Kidney/pathology , Proteome/genetics , Animals , Chickens , Coronavirus Infections/virology , Infectious bronchitis virus/classification , Infectious bronchitis virus/isolation & purification , Kidney/virology , Poultry Diseases/virology , Proteomics , Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationABSTRACT
Infectious bronchitis virus (IBV) of GI-19 (QX), GI-7 (TW), GI-13 (4/91) and GI-1 (Mass) lineages have been frequently detected in China in recent years. Here, An IBV strain, referred as GD17/04, was isolated from the dead yellow feather chicken vaccinated with H52 and 4/91 vaccines, whose genome sequence was obtained through high-throughput sequencing. Then it has been confirmed by the RDP and SimPlot analysis that GD17/04 is a recombinant strain deriving from YX10, 4/91, TW 2575/98 and H52 strains. Therein S1 gene of GD17/04 consists of sequences of TW2575/98 and 4/91, the former for the region of 20,371 to 21,072 nt and 21,847 to 21,975 nt, the latter for the sandwiched region of 21,073 to 21,846 nt. Moreover, as a nephropathogenic variant which caused high morbidity of 100 % and mortality of 60 %, unlike most other IBV strains, GD17/04 can cause obvious cell lesion in primary CEK cell, and even in DF-1 cells, without the process of continuous passage. As the few IBV strain can infect avian passage cell line, GD17/04 provides a material basis for further study of the interaction mechanism between IBV and avian host. Collectively, the findings highlight the significance that biological characteristics of novel strain should be studied, in addition to constant epidemiologic and molecular surveillance for IBV.
Subject(s)
Coronavirus Infections/veterinary , Infectious bronchitis virus/genetics , Infectious bronchitis virus/pathogenicity , Poultry Diseases/virology , Animals , Cell Line , Chickens , China , Coronavirus Infections/mortality , Coronavirus Infections/virology , Genome, Viral , Infectious bronchitis virus/classification , Infectious bronchitis virus/physiology , Phylogeny , Poultry Diseases/mortality , Recombination, Genetic , VirulenceABSTRACT
BACKGROUND: Avian Infectious Bronchitis Virus (IBV) is a highly contagious disease that imposes a huge economic burden on the global poultry industry. IBV contains numerous serotypes and variants with incomplete tenuous cross immunological protection. The failure of currently used vaccines to protect against diverse, circulating IBV strains that are specific to a given region poses a major problem for the poultry industry. Thus, there is an urgent need to conduct studies aimed at genotyping field IB viruses. In this study, we have determined the molecular characteristics of circulating IBV by sequencing the S1 gene of viral isolates from affected previously vaccinated broiler flocks suffering from the disease. RESULTS: Ten isolates propagated in embryonated eggs showed an ability to induce typical IBV lesions after three successive viral passages. We performed a nested RT-PCR assay that targeted the hypervariable region 3 (HVR-3) of the S1 gene, and identified the isolates as IBV through sequence analysis. The IBV isolates showed sequence similarity between the Syrian isolates that vary from 96.20 to 100%, and those being closer to the Variant-2 strain IS/1494/06 (EU780077.2) with 97.5 to 99.4% similarities. However, less nucleotide identity was found with sequences belonging to the used vaccine strains such as H120, Mass5, and 4/91. CONCLUSIONS: This study showed the presence of the Variant-2 strain circulating in Syrian broiler flocks showing signs of IBV disease. Currently, there is no commercial effective vaccine which protects birds against the Variant-2 strain. Continuous monitoring procedures should be taken to control and limit the spread of the IBV Variant-2 strain. This research emphasizes both the importance of epidemiological monitoring in intensive poultry farming for novel pathogens and the use of local isolates as future vaccine targets.
Subject(s)
Coronavirus Infections/veterinary , Infectious bronchitis virus/genetics , Poultry Diseases/virology , Animals , Chickens , Coronavirus Infections/virology , Infectious bronchitis virus/classification , Real-Time Polymerase Chain Reaction/veterinary , Sequence Analysis, RNA , Syria , Vaccination/veterinaryABSTRACT
Infectious bronchitis virus (IBV), a gamma-coronavirus, causes infectious bronchitis (IB), a major respiratory disease of chicken. Its high mutation rate in conjunction with recombination of the RNA genome constantly creates IBV variants that are difficult to control by currently available vaccines. In this study, we addressed the question whether small-scale holdings might harbor IBV variants that serve as a reservoir for newly emerging variants. Egyptian IBV isolate EGY/NR725/2016 (NR725/16) from a small-scale broiler farm was assigned to genotype I, clade 23 (S1:GI-23), based on partial S1 gene sequences and corroborated by full genome sequencing. Analysis of the S1 gene established three subclades for historical IBV strains (S1:GI-23.1, S1:GI-23.2.1 and S1:GI-23.2.2) and confirmed NR725/16 as being part of a separate fourth subclade (S1:GI-23.3). Samples from the years 2018 and 2019 revealed that the new subclade prevails in Egypt, carrying fixed mutations within the hypervariable regions (HVR) 1-3 of the S1 protein that affect two neutralization sensitive epitopes at sites 294F, 297S and 306Y (48.2) and 329R (62.1). In addition, recombination was recognized in isolate NR 725/16, with intra-subtype mixing for the entire genes 3ab and E and inter-subtype mixing for the entire gene 6b with a close match to QX like viruses of genotype GI-19. Further analysis of gene 3ab detected the homologous gene pool to NR725/16 in samples from 2013 (3ab:C) and closely related 3ab genotypes in IBV Egyptian isolates from 2016, 2018 and 2019. These data prove a flourishing exchange between poultry holdings with a common gene pool. The continued circulation of viruses harboring genes S1:GI-23.3 and 3ab:C indicates an evolutionary advantage of this combination possibly by combining antigenic escape with modulated pathogenicity to facilitate IBV spread in the vaccinated poultry population in Egypt.
Subject(s)
Coronavirus Infections/veterinary , Infectious bronchitis virus/classification , Poultry Diseases/virology , Spike Glycoprotein, Coronavirus/genetics , Whole Genome Sequencing/methods , Animals , Chickens , Egypt , Evolution, Molecular , Infectious bronchitis virus/genetics , Infectious bronchitis virus/isolation & purification , Mutation , Phylogeny , RNA, Viral/genetics , Recombination, Genetic , Sequence Analysis, RNA , Trachea/virologyABSTRACT
Infectious bronchitis (IB) is a highly contagious viral disease of chickens, known to cause severe economic losses. Vaccination against IB virus (IBV) is an important control measure against the disease. The objective of the present study was to test Avishield IB GI-13, the vaccine candidate against IBV, strain V-173/11 (GI-13 genotype), according to European Pharmacopoeia (Ph. Eur.) efficacy requirements. Laboratory study on specific-pathogen-free (SPF) chickens showed 100% protection against challenge 10 days after vaccination of 1-7 day-old chickens by three recommended routes. Duration of immunity was shown to be at least 8 weeks after vaccination. Chickens with maternally derived antibodies (MDA) were 100% protected against challenge 21 and 35 days after vaccination. Testing of the vaccine candidate in field conditions on commercial broiler and layer farms showed 80-90% protection against homologous challenge after spray (broilers and layers) or oral (broilers) vaccine administration. Serum antibodies were monitored during the studies, and although good seroconversion was observed in MDA-positive chickens 34 days after vaccination or later, the data from SPF chickens indicate that non-humoral immunity is important in protection against challenge. Neutralizing antibodies in tears were detected, however, their level could not be fully linked with individual protection scores. A cross-protection study showed that administration of the combination of Avishield IB H120 vaccine and Avishield IB GI-13 vaccine candidate at day 1, confers good protection against heterologous QX-like challenge. Stability of the vaccine after reconstitution in 0.2% skimmed milk solution or distilled water at room temperature was confirmed over the period of 3 h. The vaccine candidate fully complied with Ph. Eur. requirements, with very good protection levels, indicating that it can be administered already at 1 day of age by spray at the hatchery or at 7 days of age by drinking water on the farm.
Subject(s)
Antibodies, Viral/blood , Coronavirus Infections/prevention & control , Coronavirus Infections/veterinary , Cross Protection/immunology , Infectious bronchitis virus/immunology , Poultry Diseases/prevention & control , Viral Vaccines/immunology , Viral Vaccines/standards , Animals , Antibodies, Neutralizing/blood , Chickens/immunology , Coronavirus Infections/immunology , European Union , Genotype , Infectious bronchitis virus/classification , Infectious bronchitis virus/genetics , Poultry Diseases/immunology , Poultry Diseases/virology , Specific Pathogen-Free Organisms , Vaccination , Vaccines, Attenuated/administration & dosage , Vaccines, Attenuated/immunology , Viral Vaccines/administration & dosageABSTRACT
In the present study, an IBV strain I0305/19 was isolated from a diseased commercial broiler flock in 2019 in China with high morbidity and mortality. The isolate I0305/19 was clustered together with viruses in sublineage D of GI-19 lineage on the basis of the complete S1 sequence analysis. Isolate I0305/19 and other GI-19 viruses isolated in China have the amino acid sequence MIA at positions 110-112 in the S protein. Further analysis based on the complete genomic sequence showed that the isolate emerged through at least four recombination events between GI-19 ck/CH/LJS/120848- and GI-13 4/91-like strains, in which the S gene was found to be similar to that of the GI-19 ck/CH/LJS/120848-like strain. Pathological assessment showed the isolate was a nephropathogenic IBV strain that caused high morbidity of 100 % and mortality of 80 % in 1-day-old specific-pathogen-free (SPF) chicks. The isolate I0305/19 exhibited broader tropisms in different tissues, including tracheas, lungs, bursa of Fabricius, spleen, liver, kidneys, proventriculus, small intestines, large intestines, cecum, and cecal tonsils. Furthermore, subpopulations of the virus were found in tissues of infected chickens; this finding is important in understanding how the virulent IBV strains can potentially replicate and evolve to cause disease. This information is also valuable for understanding the mechanisms of replication and evolution of other coronaviruses such as the newly emerged SARS-CoV-2.
Subject(s)
Chickens/virology , Coronavirus Infections/veterinary , Infectious bronchitis virus/genetics , Infectious bronchitis virus/pathogenicity , Poultry Diseases/virology , Recombination, Genetic , Viral Tropism , Animals , China , Coronavirus Infections/virology , Genome, Viral , Infectious bronchitis virus/classification , Infectious bronchitis virus/physiology , Phylogeny , Specific Pathogen-Free Organisms , Spike Glycoprotein, Coronavirus/genetics , Virus ReplicationABSTRACT
Avian infectious bronchitis is a serious and highly contagious disease caused by infectious bronchitis virus (IBV). We isolated a highly virulent IBV strain (CK/CH/JS/TAHY) from kidneys of diseased chickens. Phylogenetic analysis based on the S1 gene revealed that CK/CH/JS/TAHY clustered with the QX-like type. The S1 gene has 1,620 nucleotides and encoded a polypeptide of 540 amino acids with typical coronavirus cleavage recognition sites of HRRR. About 1-day-old specific pathogen-free White Leghorn chickens inoculated with CK/CH/JS/TAHY at 105.5 EID50 exhibited clinical signs including coughing, sneezing, nasal discharge, and tracheal vocalization accompanied by depression with 84% mortality and 100% morbidity. The kidneys of dead birds were swollen and pale and exhibited severe urate deposition. Histopathological examination revealed kidney hemorrhages, multifocal necrosis of the renal tubules and trachea with cilia loss, sloughing of epithelial cells, and edema of the lamina propria. IBV-specific antibodies appeared at 10 D post-infection. Chickens vaccinated with a CK/CH/JS/TAHY oil-emulsion vaccine showed 26.7% morbidity and 3% mortality indicating a protective effect. In conclusion, the IBV strain is a virulent avian IBV and that exhibited severe pathogenicity in chickens and is a vaccine candidate to prevent infection by Chinese QX-like nephropathogenic IBV strains.