Phylogeny of antigenic variants of avian coronavirus IBV

The coronavirus recombination pathway

Recombination is thought to be a mechanism that facilitates cross-species transmission in coronaviruses, thus acting as a driver of coronavirus spillover and emergence. Despite its significance, the mechanism of recombination is poorly understood, limiting our potential to estimate the risk of novel recombinant coronaviruses emerging in the future. As a tool for understanding recombination, here, we outline a framework of the recombination pathway for coronaviruses. We review existing literature on coronavirus recombination, including comparisons of naturally observed recombinant genomes as well as in vitro experiments, and place the findings into the recombination pathway framework. We highlight gaps in our understanding of coronavirus recombination illustrated by the framework and outline how further experimental research is critical for disentangling the molecular mechanism of recombination from external environmental pressures. Finally, we describe how an increased understanding of the mechanism of recombination can inform pandemic predictive intelligence, with a retrospective emphasis on SARS-CoV-2.

Analysis of chicken macrophage functions and gene expressions following infectious bronchitis virus M41 infection

Infectious bronchitis virus (IBV) is a pathogenic coronavirus with high morbidity and mortality in chicken breeding. Macrophages with normal biofunctions are essential for host immune responses. In this study, the HD11 chicken macrophage cell line and chicken peripheral blood mononuclear cell-derived macrophages (PBMCs-Mφ) were infected with IBV at multiplicity of infection (MOI) of 10. The dynamic changes of their biofunctions, including cell viability, pathogen elimination function, phagocytic ability, and gene expressions of related proteins/mediators in innate and acquired immunity, inflammation, autophagy and apoptosis were analyzed. Results showed that IBV infection decreased chicken macrophage viability and phagocytic ability, and increased pathogen elimination function. Moreover, IBV augmented the gene expressions of most related proteins in macrophages involved in multiple host bioprocesses, and the dynamic changes of gene expressions had a close relationship with virus replication. Among them, MHCII, Fc receptor, TLR3, IFN-α, CCL4, MIF, IL-1β, IL-6, and iNOS showed significantly higher expressions in IBV-infected cells. However, TLR7, MyD88, MDA5, IFN-γ, MHCII, Fc receptor, MARCO, CD36, MIF, XCL1, CXCL12, TNF-α, iNOS, and IL-10 showed early decreased expressions. Overall, chicken macrophages play an important role in host innate and acquired immune responses to resist IBV infection, despite early damage or suppression. Moreover, the IBV-induced autophagy and apoptosis might participate in the virus-host cell interaction which is attributed to the biological process.

Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation

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.

Emergence of variant avian infectious bronchitis virus in India

BACKGROUND

Infectious bronchitis virus (IBV) is the etiological agent of an acute and highly contagious disease. Infectious bronchitis (IB) affects chicken of all ages and poses major economic loses to the poultry industry worldwide. The continuous evolution of the spike protein (S1) of IBV is responsible for the prevalence of many serotypes/genotypes around the world. Multiple lineages of IBV strains have been detected in chicken flocks in India since 2003.

AIMS

To detect IBV genotypes prevalent in India.

METHODS

Organ samples from 20 IBV-positive flocks with variable clinical signs were used for the amplification of the S1 gene of IBV by reverse transcriptase-polymerase chain reaction (RT-PCR).

RESULTS

Positive PCR amplicons were sequenced. Sequence analysis showed that 14 field isolates belonged to the GI-1 genetic lineage (Mass 41 serotype), two field isolates belonged to the GI-13 (UK 4/91 variant IBV strain), one field isolate grouped with GIII, GV, and GVI genetic lineage and three belonged to a variant genotype unique to India (GI-24). Phylogenetic analysis also showed a similar type of grouping within the field isolates. Among the fourteen GI-1 isolates, 12 were isolated between 2003 and 2006 and only two were isolated between 2009 and 2011. The two field isolates belonging to GI-13 were isolated in 2007, another one belonging to GIII, GV, and GVI was isolated in 2010 and three field isolates were not close to any reference IBV sequences isolated in 2006 (IND-TN-168-06), 2010 (IND-TN-280-10) and 2011 (IND-TN-290-11).

CONCLUSION

A unique variant of IBV is emerging in India (GI-24). Our findings will have important implications for future vaccine intervention.

Genetic, antigenic and pathogenic characterization of avian coronaviruses isolated from pheasants (Phasianus colchicus) in China

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Two pheasant coronaviruses (PhCoVs) were isolated in 2017 in China.

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The two PhCoVs were genetically similar to IBV.

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Pathogenicity, replication, and shedding of PhCoV were obvious different when infected chickens and pheasants.

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PhCoVs isolated from different outbreaks may have evolved independently from IBVs by adaption in pheasants.

Two viruses were isolated in 2017 from commercial pheasants with severe clinical signs and mortality in Shandong and Anhui provinces, China, respectively. We examined the pathogenic effects of the viruses in chicken embryos and the size and morphology of the virus particles, performed phylogenetic analysis based on the S1 gene and complete genomic sequences, and examined the antibody responses against infectious bronchitis virus (IBV). The results suggested that the viruses I0623/17 and I0710/17 were avian coronaviruses and were identified as pheasant coronaviruses (PhCoV), with greatest similarity to IBV. Further investigations of the antigenicity, complete genome organization, substitutions in multiple genes, and viral pathogenicity, replication, and shedding in chickens and pheasants showed obvious differences between PhCoV and IBV in terms of antigenicity, and viral pathogenicity, replication, and shedding in chickens and pheasants. The close genetic relationship, but obvious differences between PhCoVs and IBVs suggested the IBVs could be the ancestors of PhCoVs, and that PhCoVs isolated from different outbreaks may have evolved independently from IBVs circulating in the specific region by adaption in pheasants. This hypothesis was supported by analysis of the S1 gene fragments of the two PhCoVs isolated in the current study, as well as PhCoVs isolated in the UK and selected IBV strains. Such analyses indicated different evolution patterns and different tissue tropisms between PhCoVs isolated in different outbreaks. Further studies are needed to confirm this hypothesis by studying the complete genomic sequences of PhCoVs from different outbreaks and the pathogenicity of IBVs in pheasants to compare and clarify the relationships between PhCoVs and IBVs.

Genetic and biological characteristics of four novel recombinant avian infectious bronchitis viruses isolated in China

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Two IBV strains were proved to be originated from multiple recombination events.

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Viruses with very similar S1 gene sequences showed varying biological features.

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Point mutations were observed in the RBD and HVRs of the recombinant viruses.

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Point mutations likely have an effect on these differences in biological characteristics.

Infectious bronchitis viruses (IBVs) of GI-13 (793/B) and GI-19 (QX/LX4) lineages have been frequently detected in China in recent years. Naturally recombinant IBVs originating from the GI-13 and GI-19 lineages have also been isolated from chicken flocks with respiratory and renal problems in China. Thorough genetic and biological investigations of these recombinant viruses have led to speculation regarding their origin, evolution, and control. In order to confirm the previous results and further extend our understanding about the characteristics of the four recombinant IBV strains we had previously identified (I0718/17, I0722/17, I0724/17, and I0737/17), we conducted phylogenetic analysis by comparing their complete S1 gene sequences with those of 71 reference strains of different genotypes and lineages. We identified a close relationship between the S1 sequences of the four strains and those of GI-13 strains. The results of complete genome sequence analysis confirmed the previously identified recombination events in the four IBV strains and revealed additional recombination events in different genomic regions of strains I0718/17 and I0724/17, suggesting that the two strains originated from multiple recombination events between 4/91-like and YX10-like viruses. We comparatively evaluated the antigenicity, pathogenicity, and affinity of the four recombinant viruses and their deduced parental strains in the trachea and kidneys. Some of the strains showed comparable antigenic relatedness, pathogenicity, and affinity for the trachea and kidneys among each other and with their parental viruses; however, some of them showed varying biological characteristics. Point mutations observed in the receptor-binding domain and hypervariable region of the S1 subunit of the spike protein likely have an effect on these differences in biological characteristics, although the influence of other factors—such as host innate-immune responses and changes in genomic regions beyond the S1 protein—might also be responsible for such changes.

The first evidence of a new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and unvaccinated broiler flocks in Algeria

Background and Aim

Avian infectious bronchitis virus (IBV) frequently infects broilers and is responsible for severe economic losses to the poultry industry worldwide. It has also been associated with kidney damage in the broiler flocks. The aim of the present study is to determine the presence of IBV and its possible involvement in kidney damage of broiler chicks.

Materials and Methods

14 clinically diseased broiler flocks from Western and Central Algeria were sampled and analyzed by hemagglutination inhibition (HI) test and reverse transcriptase-polymerase chain reaction (RT-PCR) followed by phylogenic analysis.

Results

The QX (100%) and 4/91 (60%) IBV serotypes were the most prevalent in the kidney damaged broilers regardless of vaccination status. The molecular detection of avian IBV by RT-PCR identified six samples as positive, of which only two isolates were typable by sequencing. We identified a novel IBDZ13a genotype which showed 93% sequence homology to the partial-S1 gene sequence of the IB 4/91 commercial vaccine strain. Sequencing analysis characterized this virus as a novel and divergent IB 4/91 field virus with eight amino acid substitutions that might have resulted in altered immunogenicity.

Conclusion

The isolation of a new IBV strain (IBDZ13a) from vaccinated broiler flocks may explain the failure of the vaccination programs against IBV field strains. Combination of the HI test and RT-PCR indicated that the nephropathogenic IB outbreaks in broilers are related to this novel strain.

Infectious Bronchitis Virus S2 of 4/91 Expressed from Recombinant Virus Does Not Protect Against Ark-Type Challenge

We previously demonstrated that chickens primed with a recombinant Newcastle disease virus LaSota (rLS) expressing the S2 gene of infectious bronchitis virus (IBV) and boosted with an attenuated IBV Massachusetts (Mass)-type vaccine were protected against IBV Arkansas (Ark)-type virulent challenge. A possible basis for the reported ability of IBV 4/91 (serotype 793/B) vaccine to protect against divergent IBV strains (e.g., QX, Q1, and D1466) in a prime-boost approach with an IBV Mass vaccine is that an immune response against the S2 protein of IBV 4/91 is cross-protective. Therefore, we evaluated the protective capabilities of the S2 protein of IBV 4/91 expressed from rLS. The level of S2 amino acid sequence identity between 4/91 and the Ark challenge strain used in this study (90.7%) is within the range of S2 amino acid sequence identities between 4/91 and Q1 (91%-94%) and QX (89%-94%) strains. Chickens primed with attenuated Mass IBV at 1 day of age and boosted with rLS/IBV.S2-4/91 at 14 days of age were challenged with a virulent Ark IBV strain at 28 days of age. Protection (reduction of clinical signs and viral loads) assessed 5 days postchallenge showed nonsignificant differences between chickens primed with Mass vaccine and boosted with rLS/IBV.S2-4/91 and chickens vaccinated with Mass only. Thus, the observed level of protection is attributable only to the effect of the Mass vaccine, indicating that the S2 of IBV 4/91 does not induce broad cross-protective immunity.

Characterization of the complete genome, antigenicity, pathogenicity, tissue tropism, and shedding of a recombinant avian infectious bronchitis virus with a ck/CH/LJL/140901-like backbone and an S2 fragment from a 4/91-like virus

In this study, we isolated an infectious bronchitis virus, designated I1101/16, from broiler breeders in China. Analysis of the S1 gene showed that isolate I1101/16 was genetically close to strain ck/CH/LJL/140901, which belongs to the TW I genotype (also known as lineage GI-7 based on the recent IBV classification), however the S2 gene showed genetic diversity comparing to that of S1 gene. Comparison of the genomic sequences showed that the genome of isolate I1101/16 was similar to that of strain ck/CH/LJL/140901 from the 5' end of the genome to the 5' end of the S2 gene and from the 5' end of the 3a gene to the end of the genome, whereas the remaining parts of the genome sequences were more closely related to those of strain 4/91 than those of ck/CH/LJL/140901, thereby suggesting that recombination might have occurred during the origin of the virus. SimPlot and Bootscan analysis of the complete genomic sequence confirmed this hypothesis, where it showed that isolate I1101/16 arose through recombination events between ck/CH/LJL/140901- and 4/91-like viruses. Isolate I1101/16 and strain ck/CH/LJL/140901 shared identical amino acids in almost all five of their B cell epitopes, but the two viruses had a serotype relatedness value of 65, which is well below 80, i.e., the lower cutoff value for viruses of the same serotype. In addition, pathogenicity tests demonstrated that isolate I1101/16 was more pathogenic to 1-day-old specific-pathogen-free chickens than strain ck/CH/LJL/140901, according to analysis of the clinical signs, whereas strain ck/CH/LJL/140901 exhibited prolonged replication and shedding after challenge compared with isolate I1101/16. This study did not provide evidence that recombination can directly alter the antigenicity, virulence, replication, shedding, and tissue tropism of a virus, but it did show that recombination events are likely to be major determinants of viral evolution.

Protection against infectious bronchitis virus by spike ectodomain subunit vaccine

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Strep-tagged trimeric recombinant IBV S1 and S-ectodomain proteins were produced.

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Recombinant S-ectodomain has improved binding to tissues compared to S1 protein.

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Immunization with S-ectodomain confers effective protection against IBV challenge.

The avian coronavirus infectious bronchitis virus (IBV) S1 subunit of the spike (S) glycoprotein mediates viral attachment to host cells and the S2 subunit is responsible for membrane fusion. Using IBV Arkansas-type (Ark) S protein histochemistry, we show that extension of S1 with the S2 ectodomain improves binding to chicken tissues. Although the S1 subunit is the major inducer of neutralizing antibodies, vaccination with S1 protein has been shown to confer inadequate protection against challenge. The demonstrated contribution of S2 ectodomain to binding to chicken tissues suggests that vaccination with the ectodomain might improve protection compared to vaccination with S1 alone. Therefore, we immunized chickens with recombinant trimeric soluble IBV Ark-type S1 or S-ectodomain protein produced from codon-optimized constructs in mammalian cells. Chickens were primed at 12 days of age with water-in-oil emulsified S1 or S-ectodomain proteins, and then boosted 21 days later. Challenge was performed with virulent Ark IBV 21 days after boost. Chickens immunized with recombinant S-ectodomain protein showed statistically significantly (P < 0.05) reduced viral loads 5 days post-challenge in both tears and tracheas compared to chickens immunized with recombinant S1 protein. Consistent with viral loads, significantly reduced (P < 0.05) tracheal mucosal thickness and tracheal lesion scores revealed that recombinant S-ectodomain protein provided improved protection of tracheal integrity compared to S1 protein. These results indicate that the S2 domain has an important role in inducing protective immunity. Thus, including the S2 domain with S1 might be promising for better viral vectored and/or subunit vaccine strategies.

Variability Assessment of California Infectious Bronchitis Virus Variants

On the basis of the data from the California Animal Health and Food Safety Laboratory System, 1444 infectious bronchitis (IB) cases were diagnosed between 1997 and 2012. Epidemiologic analyses demonstrated two major IB virus (IBV) outbreak peaks, affecting mainly 35-to-49-day-old broiler chickens. California variant 1737 (CA1737) and California variant 1999 (Cal 99) IBV types were the most prevalent genotypes during the analyzed period. To further understand the increased prevalence of these genotypes, we assessed and compared the variability of the S1 gene hypervariable region of CA1737 and Cal 99 with the variability of IBV strains belonging to the Massachusetts 41 (M41) and Arkansas (Ark) types during serial passages in embryonated chicken eggs. On the basis of the S1 nonsynonymous changes, seven different subpopulations were detected in M41. However, the predominant population of the field strain M41 before passages continued to be predominant throughout the experiment. In contrast, Ark passaging resulted in the detection of 13 different subpopulations, and the field sequence became extinct after the first passage. In IBV Cal 99, eight different subpopulations were detected; one of these became predominant after the second passage. In CA1737, 10 different subpopulations were detected. The field strain major sequence was not detected after the first passage but reappeared after the second passage and remained at low levels throughout the experiment. Compared with M41 and Ark, Cal 99 and CA1737 showed intermediate variability.

New oligonucleotide microarray for rapid diagnosis of avian viral diseases

BACKGROUND

We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in single- and mixed-virus infections. The objective of the study was to develop an oligonucleotide microarray for rapid diagnosis of avian diseases that would be used in the course of mass analysis for routine epidemiological surveillance owing to its ability to test one specimen for several infections.

METHODS AND RESULTS

The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. Sensitivity and specificity of the developed microarray was evaluated with use of 122 specimens of biological material: 44 cloacal swabs from sick birds and 78 tissue specimens from dead wild and domestic birds, as well as with use of 15 AIV, NDV, IBV and IBDV strains, different in their origin, epidemiological and biological characteristics (RIBSP Microbial Collection). This microarray demonstrates high diagnostic sensitivity (99.16% within 95% CI limits 97.36-100%) and specificity (100%). Specificity of the developed technique was confirmed by direct sequencing of NP and M (AIV), VP2 (IBDV), S1 (IBV), NP (NDV) gene fragments.

CONCLUSION

Diagnostic effectiveness of the developed DNA microarray is 99.18% and therefore it can be used in mass survey for specific detection of AIV, NDV, IBV and IBDV circulating in the region in the course of epidemiological surveillance. Rather simple method for rapid diagnosis of avian viral diseases that several times shortens duration of assay versus classical diagnostic methods is proposed.

Recombinant Newcastle disease virus expressing the infectious bronchitis virus S1 gene protects chickens against Newcastle disease virus and infectious bronchitis virus challenge

The recombinant LaSota strain expressing a chimeric IBV S1 gene (rLaSota-S1) was constructed with the S1 gene of the LX4 type IBV ck/CH/LDL/091022. The expression of the S1 protein was detected by an indirect immunofluorescence assay and Western blotting. The rLaSota-S1 strain was slightly attenuated, and its growth dynamics were similar to that of the parental LaSota strain. Vaccination of specific pathogen-free chickens with the rLaSota-S1 strain induced NDV hemagglutination inhibition antibodies, and it protected chickens from challenge with virulent NDV. In addition, vaccination with the rLaSota-S1 strain induced IBV-specific IgG antibodies and cellular immunity; however, a single vaccination provided partial protection with reduced virus shedding. Better protection efficiency was observed after a booster vaccination, which resulted in higher antibody titers, significantly fewer disease symptoms, and reduced virus replication and shedding. Our results suggest that the rLaSota-S1 strain is a bivalent vaccine candidate against both NDV and IBV.

Evolutionary and bioinformatic analysis of the spike glycoprotein gene of H120 vaccine strain protectotype of infectious bronchitis virus from India

The infectious bronchitis virus is a causative agent of avian infectious bronchitis (AIB), and is is an important disease that produces severe economic losses to the poultry industry worldwide. Recent AIB outbreaks in India have been associated with poor growth in broilers, drop in egg production, and thin egg shells in layers. The complete spike gene of Indian AIB vaccine strain was amplified and sequenced using a conventional reverse transcription polymerase chain reaction and is submitted to the GenBank (accession no KF188436). Phylogenetic analysis revealed that the vaccine strain currently used belongs to H120 genotype, an attenuated strain of Massachusetts (Mass) serotype. Nucleotide and amino acid sequence comparisons have shown that the reported spike gene from Indian isolates have 71.8%-99% and 71.4%-96.9% genetic similarity with the sequenced H120 strain. The study identifies live attenuated IBV vaccine strain, which is routinely used for vaccination, for the first time. Based on nucleotide and amino acid relatedness studies of the vaccine strain with reported IBV sequences from India, it is shown that the current vaccine strain is efficient in controlling the IBV infection. Continuous monitoring of IBV outbreaks by sequencing for genotyping and in vivo cross protection studies for serotyping is not only important for epidemiological investigation but also for evaluation of efficacy of the current vaccine.

Distribution of infectious bronchitis virus strains in different organs and evidence of vertical transmission in natural infection

On the basis of partial sequencing of the infectious bronchitis virus (IBV) S1 gene, this study investigated the molecular diversity of the virus in two life periods of a batch of breeding hens at the field level. The chicks were vaccinated against IBV on the second day of life with the vaccine Ma5, but at the age of 18 days, they exhibited clinical signs and macroscopic lesions compatible with avian infectious bronchitis (IB). In the clinical disease stage, the Ma5 vaccine strain was detected in the trachea, lungs, and small intestine of the chicks, while IBV variants were detected in the bursa of Fabricius and kidneys. Subsequently, new samples were collected from the same batch at the end of the production cycle. In this phase, the Ma5 vaccine strain was detected in the kidneys, small intestine, and oviduct of the hens. However, a previously unidentified IBV variant was found in the cecal tonsils. Additionally, a fragment of viral RNA with that was completely identical to the corresponding region of the Ma5 vaccine was detected in the allantoic fluid of viable embryos from the hens under study after 18 days of incubation. These findings suggest that, in addition to the Ma5 vaccine, other strains of IBV variants can coexist, seeming to establish a chronic infection in the chickens, and that they can potentially be transmitted vertically. These results may assist in immunoprophylaxis control programs against IBV.

Recombinant duck enteritis viruses expressing major structural proteins of the infectious bronchitis virus provide protection against infectious bronchitis in chickens

To design an alternative vaccine for control of infectious bronchitis in chickens, three recombinant duck enteritis viruses (rDEVs) expressing the N, S, or S1 protein of infectious bronchitis virus (IBV) were constructed using conventional homologous recombination methods, and were designated as rDEV-N, rDEV-S, and rDEV-S1, respectively. Chickens were divided into five vaccinated groups, which were each immunized with one of the rDEVs, covalent vaccination with rDEV-N & rDEV-S, or covalent vaccination with rDEV-N & rDEV-S1, and a control group. An antibody response against IBV was detectable and the ratio of CD4⁺/CD8⁺ T-lymphocytes decreased at 7 days post-vaccination in each vaccinated group, suggesting that humoral and cellular responses were elicited in each group as early as 7 days post-immunization. After challenge with a homologous virulent IBV strain at 21 days post-immunization, vaccinated groups showed significant differences in the percentage of birds with clinical signs, as compared to the control group (p < 0.01), as the two covalent-vaccination groups and the rDEV-S group provided better protection than the rDEV-N- or rDEV-S1-vaccinated group. There was less viral shedding in the rDEV-N & rDEV-S- (2/10) and rDEV-N & rDEV-S1- (2/10) vaccinated groups than the other three vaccinated groups. Based on the clinical signs, viral shedding, and mortality rates, rDEV-N & rDEV-S1 covalent vaccination conferred better protection than use of any of the single rDEVs.

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Infectious bronchitis virus (IBV) causes a respiratory disease in domestic chickens worldwide.

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Duck enteritis virus (DEV) was used as viral vaccine vector in chickens.

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Recombinant DEV (rDEV) expressing IBV N, S, or S1 conferred protection against IBV.

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Covalent vaccination with rDEV-N & rDEV-S1 conferred higher level of protection against IBV.

S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification

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.

Phylogenetic analysis of avian infectious bronchitis virus S1 glycoprotein regions reveals emergence of a new genotype in Moroccan broiler chicken flocks

BACKGROUND

Infectious bronchitis virus (IBV), a major pathogen of commercial poultry flocks, circulates in the form of several serotypes/genotypes. Only a few amino-acid changes in the S1 subunit of wild-type IBVS proteins may result in mutants unaffected by current vaccines.

METHODS

Partial S1 gene sequences of 3 IBV isolates of the Moroccan Italy 02 genotype from vaccinated and unvaccinated broiler chicken flocks, located in southern and central regions of Morocco, were amplified by RT-PCR, sequenced, and aligned for phylogenetic and amino-acid similarity analyses.

RESULTS

The three isolates were found genetically highly distant from known avian IBV based on partial sequences of their S1 genes: gammaCoV/chicken/Morocco/I01/2011(IBV/Morocco/01), gammaCoV/chicken/Morocco/I30/2010 (IBV/Morocco/30), and gammaCoV/chicken/Morocco/I38/2013 (IBV/Morocco/38), nucleotide sequence identities reached 89.5 % to 90.9 % among the three isolates. The deduced protein sequence identities ranged from 29.7 % (between IBV/Morocco/38 and Egypt SCU-14/2013-1) to 78.2 % (between IBV/Morocco/01 and Spain/05/866). Amino acid sequence comparison and phylogenetic analysis indicated the emergence of a new Moroccan genotype, clustering with regionally related isolates from Spain (Spain/05/866) and belonging to a new sub-genotype.

CONCLUSION

Our sequencing results demonstrate a co-circulation of wild-type infectious bronchitis viruses in broiler chickens. These results justify permanent monitoring of circulating strains in order to rationally modify vaccination strategies to make them appropriate to the evolving field situation.

Serotype shift of a 793/B genotype infectious bronchitis coronavirus by natural recombination

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Infectious bronchitis virus causes a respiratory disease in domestic chickens worldwide.

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Recombination is thought to contribute to the emergence of IBV variants.

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Strain ck/CH/LHLJ/140906 is originated from recombination events between 4/91- and H120-like strains.

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Recombination of the S1 domain resulted in the emergence of a novel serotype of IBV.

An infectious bronchitis coronavirus, designated as ck/CH/LHLJ/140906, was isolated from an infectious bronchitis virus (IBV) strain H120-vaccinated chicken flock, which presented with a suspected infectious bronchitis virus (IBV) infection. A phylogenetic analysis based on the S1 gene clustered ck/CH/LHLJ/140906 with the 793/B group; however, a pairwise comparison showed that the 5′ terminal of the S1 gene (containing hypervariable regions I and II) had high sequence identity with the H120 strain, while the 3′ terminal sequence was very similar to that of IBV 4/91 strain. A SimPlot analysis of the complete genomic sequence, which was confirmed by a phylogenetic analysis and nucleotide similarities using the corresponding gene fragments, suggested that isolate ck/CH/LHLJ/140906 emerged from multiple recombination events between parental IBV strains 4/91 and H120. Although the isolate ck/CH/LHLJ/140906 had slightly higher S1 amino acid sequence identity to strain 4/91 (88.2%) than to strain H120 (86%), the serotype of the virus was more closely related to that of the H120 strain (32% antigenic relatedness) than to the 4/91 strain (15% antigenic relatedness). Whereas, vaccination of specific pathogen-free chickens with the 4/91 vaccine provided better protection against challenge with ck/CH/LHLJ/140906 than did vaccination with the H120 strain according to the result of virus re-isolation. As the spike protein, especially in the hypervariable regions of the S1 domain, of IBVs contains viral neutralizing epitopes, the results of this study showed that recombination of the S1 domain resulted in the emergence of a new serotype.

Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS

Although sequencing of the 3' end of the genome of Australian infectious bronchitis viruses (IBVs) has shown that their structural genes are distinct from those of IBVs found in other countries, their replicase genes have not been analysed. To examine this, the complete genomic sequences of the two subpopulations of the VicS vaccine, VicS-v and VicS-del, were determined. Compared with VicS-v, the more attenuated VicS-del strain had two non-synonymous changes in the non-structural protein 6 (nsp6), a transmembrane (TM) domain that may participate in autocatalytic release of the 3-chymotrypsin-like protease, a polymorphic difference at the end of the S2 gene, which coincided with the body transcription-regulating sequence (B-TRS) of mRNA 3 and a truncated open reading frame for a peptide encoded by gene 4 (4b). These genetic differences could be responsible for the differences between these variants in pathogenicity in vivo, and replication in vitro. Phylogenetic analysis of the whole genome showed that VicS-v and VicS-del did not cluster with strains from other countries, supporting the hypothesis that Australian IBV strains have been evolving independently for some time, and analyses of individual polymerase peptide and S glycoprotein genes suggested a distant common ancestor with no recent recombination. This study suggests the potential role of the TM domain in nsp6, the integrity of the S2 protein and the B-TRS 3, and the putative accessory protein 4b, as well as the 3' untranslated region, in the virulence and replication of IBV and has provided a better understanding of relationships between the Australian vaccine strain of IBV and those used elsewhere.

The avian coronavirus spike protein

Avian coronaviruses of the genus Gammacoronavirus are represented by infectious bronchitis virus (IBV), the coronavirus of chicken. IBV causes a highly contagious disease affecting the respiratory tract and, depending on the strain, other tissues including the reproductive and urogenital tract. The control of IBV in the field is hampered by the many different strains circulating worldwide and the limited protection across strains due to serotype diversity. This diversity is believed to be due to the amino acid variation in the S1 domain of the major viral attachment protein spike. In the last years, much effort has been undertaken to address the role of the avian coronavirus spike protein in the various steps of the virus' live cycle. Various models have successfully been developed to elucidate the contribution of the spike in binding of the virus to cells, entry of cell culture cells and organ explants, and the in vivo tropism and pathogenesis. This review will give an overview of the literature on avian coronavirus spike proteins with particular focus on our recent studies on binding of recombinant soluble spike protein to chicken tissues. With this, we aim to summarize the current understanding on the avian coronavirus spike's contribution to host and tissue predilections, pathogenesis, as well as its role in therapeutic and protective interventions.

Infectious bronchitis virus S2 expressed from recombinant virus confers broad protection against challenge

We developed a recombinant Newcastle disease virus (NDV) LaSota (rLS) expressing the infectious bronchitis virus (IBV) S2 gene (rLS/IBV.S2). The recombinant virus showed somewhat-reduced pathogenicity compared to the parental lentogenic LaSota strain but effectively elicited hemagglutination inhibition antibodies against NDV and protected chickens against lethal challenge with virulent NDV/CA02. IBV heterotypic protection was assessed using a prime-boost approach with a commercially available attenuated IBV Massachusetts (Mass)-type vaccine. Specific-pathogen-free chickens primed ocularly with rLS/IBV.S2 at 4 days of age and boosted with Mass at 18 days of age were completely protected against challenge at 41 days of age with a virulent Ark-type strain. In a second experiment, we compared protection conferred by priming with rLS/IBV.S2 and boosting with Mass (rLS/IBV.S2+Mass) versus priming and boosting with Mass (Mass+Mass). We also modified the timing of vaccination to prime at 1 day of age and boost at 12 days of age. Challenge with virulent Ark was performed at 21 days of age. Based on clinical signs, both vaccinated groups appeared equally protected against challenge compared to unvaccinated challenged chickens. Viral loads in lachrymal fluids of birds receiving rLS/IBV.S2+Mass showed a clear tendency of improved protection compared to Mass+Mass; however, the difference did not achieve statistical significance. A significant difference (P < 0.05) was determined between these groups regarding incidence of detection of challenge IBV RNA in the trachea; viral RNA was detected in 50% of rLS/IBV.S2+Mass-vaccinated chickens while chickens vaccinated with Mass+Mass and unvaccinated challenged controls showed 84 and 90% incidence of IBV RNA detection in the trachea, respectively. These results demonstrate that overexposing the IBV S2 to the chicken immune system by means of a vectored vaccine, followed by boost with whole virus, protects chickens against IBV showing dissimilar S1.

Simultaneous detection of five major serotypes of Avian coronavirus by a multiplex microsphere-based assay

Avian coronavirus (commonly known as Infectious bronchitis virus [IBV]) is of major economic importance to commercial chicken producers worldwide. Due to the existence of multiple serotypes and variants of the virus that do not cross-protect, it is important to diagnose circulating serotypes and choose the right vaccine type for successful protection. In an effort to improve conventional diagnostic tests, a microsphere-based assay was developed and evaluated for simultaneous detection of the most common IBV vaccine serotypes in the United States: Arkansas (Ark), Connecticut (Conn), Massachusetts (Mass), Delaware (DE072), and Georgia 98 (GA98). The analytical specificity and sensitivity, and diagnostic specificity and sensitivity, were evaluated. The microsphere-based assay was highly specific to designated serotypes and generated reproducible data. Comparing the microsphere-based assay to nucleotide sequencing, the 2 methods agreed more than 93% (kappa value > .77). In addition, the microsphere-based assay could detect coinfections in clinical samples. The results demonstrate the utility of the microsphere-based assay as a rapid and accurate diagnostic tool with the potential for high throughput diagnosis.

Genetic diversity and selection regulates evolution of infectious bronchitis virus

Conventional and molecular epidemiologic studies have confirmed the ability of infectious bronchitis virus (IBV) to rapidly evolve and successfully circumvent extensive vaccination programs implemented since the early 1950s. IBV evolution has often been explained as variation in gene frequencies as if evolution were driven by genetic drift alone. However, the mechanisms regulating the evolution of IBV include both the generation of genetic diversity and the selection process. IBV's generation of genetic diversity has been extensively investigated and ultimately involves mutations and recombination events occurring during viral replication. The relevance of the selection process has been further understood more recently by identifying genetic and phenotypic differences between IBV populations prior to, and during, replication in the natural host. Accumulating evidence suggests that multiple environmental forces within the host, including immune responses (or lack thereof) and affinity for cell receptors, as well as physical and biochemical conditions, are responsible for the selection process. Some scientists have used or adopted the related quasispecies frame to explain IBV evolution. The quasispecies frame, while providing a distinct explanation of the dynamics of populations in which mutation is a frequent event, exhibits relevant limitations which are discussed herein. Instead, it seems that IBV populations evolving by the generation of genetic variability and selection on replicons follow the evolutionary mechanisms originally proposed by Darwin. Understanding the mechanisms underlying the evolution of IBV is of basic relevance and, without doubt, essential to appropriately control and prevent the disease.

Epidemiology of infectious bronchitis virus in Belgian broilers: a retrospective study, 1986 to 1995

Infectious bronchitis virus (IBV) was isolated from each of 236 broiler flocks that had respiratory infection (86%), impaired growth, enteritis and/or nephritis (14%), over a 10-year period from 1986 to 1995 in Belgium. Among them, 65% of the investigated flocks had not been vaccinated against infectious bronchitis. Type-specific reverse transcriptase polymerase chain reactions (RT-PCRs) were used after propagation of the isolates in embryonated eggs in order to detect and differentiate Massachusetts, D274, B1648 and 793/B types. The incidence of these types was approximately 50, 38, 11 and 1%, respectively. In 16% of cases, two or three types of IBV were detected, representing mostly combinations of Massachusetts and D274. The majority of the Massachusetts and D274 isolates (68 and 69%, respectively) were recovered from non-vaccinated flocks, confirming that such flocks are at greatest risk of infection by these types of IBV. Interestingly, the B1648 type was isolated from more vaccinated flocks (14%) than non-vaccinated flocks (7.6%). Most surprising was the very low incidence (1%) of the 793/B type, which was the dominant type in some neighbouring countries, during the period of investigation. The DNA derived by RT-PCR from 24 of the Massachusetts-type isolates from 12 vaccinated and 12 non-vaccinated flocks was sequenced and compared with the sequence of Massachusetts vaccines used in Belgium. This revealed that the sequence of four of the isolates (two from vaccinated and two from non-vaccinated flocks) was identical to that of a Massachusetts vaccine strain. Similar results were obtained for D274 isolates when compared with the sequence of D274 vaccines. These sequencing results demonstrate a co-circulation of vaccine and wild-type infectious bronchitis viruses in broilers, and are further justification for permanent monitoring of circulating strains in order to rationally modify vaccination strategies to make them appropriate to the field situation.

Molecular analysis of the 793/B serotype of infectious bronchitis virus in Great Britain

Since the winter of 1990/91 respiratory disease of poultry in Great Britain has commonly been associated with the 793/B (or 4/91) serotype of infectious bronchitis virus (IBV). We have sequenced a variable part of the S1 region of the spike protein (5) gene. Comparison of up to 270 nucleotides of 12 British 793/B isolates, obtained in 1991 and 1993, revealed 94 to 100% nucleotide identity with each other. Eleven of them fell into one of two subgroups, A and B, one isolate forming subgroup C. Identity within subgroups A and B was > 98%. The whole S1 gene sequence (1617 nucleotides) was determined for five 793/B isolates, two from each of subgroups A and B and one from subgroup C; nucleotide identity between any two isolates was > 97%. A large proportion of the nucleotide differences corresponded to amino acid changes. The whole S1 amino acid sequence differed by 21 to 25% or more from that of all other published IBV sequences. This extensive difference has probably contributed to the persistence of the 793/B serotype in Britain even though het-erologous vaccines have been used. The finding that the 793/B isolates could be placed into three subgroups suggests that either (a) they had diverged from a common progenitor present, but undetected, in Britain prior to 1990/91 or (b) at least three different strains of the 793/B serotype had entered Britain in or prior to 1990/91.

Relationship between sequence variation in the S1 spike protein of infectious bronchitis virus and the extent of cross-protection in vivo

The notion that the S1 subunit of the spike glycoprotein (S) of infectious bronchitis virus (IBV) is the major inducer of protective immunity has been examined. Groups of 10 1-day-old chicks were vaccinated with isolate UK/6/82 and challenged in-tranasally 3 or 6 weeks later with strains whose S1 protein differed from that of UK/6/82 to different extents: NL/D207/79, UK/142/86 and UK/167/84 (2%), UK/123/82 (4%), UK/918/67 (19%), USA/M41/41 and Portugal/322/82 (20%; both of the Massachusetts serotype), and NL/D1466/79 (49%). Four days after challenge tracheas were removed and observed for ciliary activity. Overall, the degree of cross-protection induced by UK/6/82 diminished as the similarity of the S1 proteins diminished, although in only two cases was the protection induced statistically less (P< 0.10) against the heterologous isolates than against the homologous strain. Even when a group as a whole was poorly protected against heterologous challenge, some individual chicks, including some challenged with D1466, exhibited high protection of the trachea. Conversely, in groups where protection was high overall, a few individuals were poorly protected. The results broadly support the view that differences in the sequence of the S1 protein do contribute to the ability of an IBV strain to break through the immunity induced by another strain. However, they also indicate that some conserved sequences in S1 and/or epitopes in the other, less variable, proteins also contribute to immunity. Moreover, individual chicks can differ greatly in their response to vaccination with IBV, a factor which should not be overlooked.

A long-term study of Australian infectious bronchitis viruses indicates a major antigenic change in recently isolated strains

The antigenic relationship among 36 IBV strains isolated between 1961 and 1994 from vaccinated and non-vaccinated chicken flocks was determined. Based on the reaction with nine monoclonal antibodies (MAbs) in ELISA and polyclonal chicken sera in western blotting, IBV strains clearly fell into two distinct antigenic groups. Nineteen IBV strains isolated between 1961 and 1994 from various locations were antigenically related, having common cross-reactive epitopes on the peplomer S, the nucleocapsid N and the membrane M proteins. IBV strains within this classical group could be antigenically differentiated further by serotyping and by their reaction with MAbs. Seventeen IBV strains isolated between 1988 and 1994, shared only a minor degree of antigenic similarity with strains in the classical group. Strains in this novel group were antigenically related to each other and shared cross-reactive epitopes particularly on the N and M proteins. The novel IBV strains were not detected before 1988 and their origin is unknown. They appeared suddenly and almost simultaneously at two distant commercial sites, Redland Bay and Appin, and were also isolated at a third location in Victoria 3 years later. The Appin strains persisted on the site for 3 years without changes in antigenicity, including the serotype; however, following introduction of vaccination with novel strains a variant of new serotype was isolated. Variants isolated in Victoria on the other hand showed greater antigenic diversity and tendency for change. Novel strains have not displaced classical strains which continued to be isolated frequently.

Effects of chicken anaemia virus and infectious bursal disease virus-induced immunodeficiency on infectious bronchitis virus replication and genotypic drift

We followed changes in a portion of the S1 gene sequence of the dominant populations of an infectious bronchitis virus (IBV) Arkansas (Ark) vaccine strain during serial passage in chickens infected with the immunosuppressive chicken anaemia virus (CAV) and/or infectious bursal disease virus (IBDV) as well as in immunocompetent chickens. The IBV-Ark vaccine was applied ocularly and tears were collected from infected chickens for subsequent ocular inoculation in later passages. The experiment was performed twice. In both experiments the dominant S1 genotype of the vaccine strain was rapidly and negatively selected in all chicken groups (CAV, IBDV, CAV+IBDV and immunocompetent). Based on the S1 genotype, the same IBV subpopulations previously reported in immunocompetent chickens and named component (C) 1 to C5 emerged both in immunocompetent and immunodeficient chickens. During the first passage different subpopulations emerged, followed by the establishment of one or two predominant populations after further passages. Only when the subpopulation designated C2 became established in either CAV-infected or IBDV-infected chickens was IBV maintained for more than four passages. These results indicate that selection does not cease in immunodeficient chickens and that phenotype C2 may show a distinct adaptation to this environment. Subpopulations C1 or C4 initially became established in immunocompetent birds but became extinct after only a few succeeding passages. A similar result was observed in chickens co-infected with CAV+IBDV. These results suggest that the generation of genetic diversity in IBV is constrained. This finding constitutes further evidence for phenotypic drift occurring mainly as a result of selection.

Application of purified recombinant antigenic spike fragments to the diagnosis of avian infectious bronchitis virus infection

The spike (S) protein, containing two subunits, S1 and S2, is the major immunity-eliciting antigen of avian infectious bronchitis virus (IBV), a highly contagious disease of chickens. Several immunogenic regions, mainly located within the S1 subunit, have been identified. Nonetheless, these immune-dominant regions were defined using selected monoclonal antibodies or using a short peptide approach that involves only certain limited regions of the S protein. In addition, some immune-dominant regions are located in hypervariable regions (HVRs) which are not present in all serotypes. Hence, the aim of this study was to determine a broader range of antigenic regions that have strong antibody eliciting ability; these could then be applied for development of an IBV-diagnostic tool. Initially, the S1 and part of the S2 subunit protein (24-567 amino acids) were expressed as five fragments in prokaryotic system. The antigenicity was confirmed using IBV immunized sera. Performance of the S subfragments was evaluated by ELISA using a panel of field chicken sera with known IBV titres determined by a commercial kit. This indicated that, among the five antigenic recombinant proteins, the region S-E showed the highest specificity and sensitivity, namely 95.38 % and 96.29 %, respectively. The κ value for the in-house ELISA using the S-E fragment compared to a commercial kit was 0.9172, indicating a high agreement between these two methods. As region S-E harbors strong immunogenicity within the spike protein, it has the potential to be exploited as an antigen when developing a cost-effective ELISA-based diagnosis tool.

Genotyping of newly isolated infectious bronchitis virus isolates from northeastern Georgia

Sixteen infectious bronchitis virus (IBV) field isolates obtained from vaccinated commercial broiler chickens showing clinical respiratory disease were characterized by reverse transcriptase-polymerase chain reaction and sequence analysis of the hypervariable region of the S1 spike glycoprotein gene. The genetic relationship among these variants and reference strains was determined by phylogenetic analysis and use of the basic local alignment search tool. All the isolates formed a distinct phylogenetic group with very short branched distances, suggesting that isolates had a similar origin. All the isolates showed 85% amino acid identity with recently described Australian isolates, particularly N1-62. Given that little was known about this new emergent IBV we have characterized five field isolates by sequencing the entire S1 gene. Multiple sequence alignment of deduced amino acid sequences with commonly used vaccine strains revealed that most substitutions occurred in the 53-148 amino acid region. A possible recombination site with N1-62 isolate was identified between amino acid residues 115-121. All the field isolates shared four or five out of seven amino acid residues with N1-62 in this region as opposed to Ark-DPI and Mass 41 reference strains, which shared only two residues. Results indicate that IBV isolates reported here can be considered as new IBV genotype.

Molecular epizootiology of infectious bronchitis virus in Sweden indicating the involvement of a vaccine strain

To improve the detection and molecular identification of infectious bronchitis virus (avian coronavirus), two reverse transcriptase-polymerase chain reaction (PCR) assays were developed. As 'diagnostic#10; PCR', a set of consensus nested primers was selected from highly conserved stretches of the nucleocapsid (N) gene. As 'phylogeny' PCR, a fragment of the spike protein gene (S1) was amplified and the PCR products were directly sequenced. To study the phylogenetic relationships of the viruses from various outbreaks, studies of molecular epizootiology were performed in Sweden, a Nordic region, where the occurrence of natural cases of the disease is relatively low and the occasional use of live vaccine(s) is well recorded and monitored. The disease appeared in the region in 1994, associated with production problems among layers of various ages. During outbreaks in 1995 and 1997, both layers and broilers were affected. To reduce losses, a live attenuated vaccine has been applied since 1997. By examining 12 cases between 1994 and 1998, molecular epizootiology revealed that, before 1997, the viruses had gene sequences very similar to strains of the Massachusetts serotype. However, comparative sequence analysis of the S1 gene revealed that the identity was not 100% to any of the strains of this serotype that we analysed. A virus related to the Dutch-type strain, D274, was also identified on one farm. Surprisingly, from 1997, the year that vaccination commenced with a live Massachusetts serotype vaccine, the majority of viruses detected had S1 sequences identical to the live Massachusetts vaccine strain. This genetic relation to the vaccine virus was also confirmed by N gene sequence analysis. The studies of molecular epizootiology reveal a strong probability that the vaccination had lead to the spread of the vaccine virus, causing various disease manifestations and a confusing epizootiological situation in the poultry population.

Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand

Thirteen field isolates of infectious bronchitis virus (IBV) were isolated from broiler flocks in Thailand between January and June 2008. The 878-bp of the S1 gene covering a hypervariable region was amplified and sequenced. Phylogenetic analysis based on that region revealed that these viruses were separated into two groups (I and II). IBV isolates in group I were not related to other IBV strains published in the GenBank database. Group 1 nucleotide sequence identities were less than 85% and amino acid sequence identities less than 84% in common with IBVs published in the GenBank database. This group likely represents the strains indigenous to Thailand. The isolates in group II showed a close relationship with Chinese IBVs. They had nucleotide sequence identities of 97-98% and amino acid sequence identities 96-98% in common with Chinese IBVs (strain A2, SH and QXIBV). This finding indicated that the recent Thai IBVs evolved separately and at least two groups of viruses are circulating in Thailand.

Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in South China during 2004-2008

Twenty-seven strains of avian infectious bronchitis virus (IBV) were isolated from dead or diseased chickens at different chicken farms in South China during 2004–2008, of which the S1 gene was sequenced. Phylogenetic analysis of the S1 gene sequences of the isolated 27 strains together with 29 strains published in Genbank revealed that all IBV strains except for one isolated and one published were clustered into six distinct genotypes I-VI. 26 isolated strains belong to genotypes I, II, and III, forming a big phylogenetic branch without new predominant strains, whereas all five vaccine strains belong to genotype V that is evolutionarily distant from genotypes I, II, and III. The study of the protease cleavage motif within the S1 protein found 12 different cleavage motifs, of which 3 motifs are shared by both isolated and published strains, 2 motifs unique to isolated strains, and 7 motifs unique to published strains, further bolstering the notion of no new predominant strains. Alignment analysis of the S1 amino acid sequences indicated that the amino acid substitutions, insertions, and deletions are polymorphic and diverse, showing no sign of predominant genetic changes among the isolated strains. Taken together, there was no predominant new strain circulating in South China during 2004–2008. Nonetheless, circulating IBV strains have been continuously evolving with genetic compositions distant from vaccine strains; this explains why there have been constant but infrequent outbreaks in commercial flocks in South China during 2004–2008. Furthermore, in order to safe guard against the sudden emergence of new predominant strains, continuing surveillance of IBV strains circulating in the field is of extreme importance.

Genetic analysis of the S1 gene of 4/91 type infectious bronchitis virus isolated in Japan

S1 gene sequences for infectious bronchitis virus (IBV) strains of the 4/91 genotype (commonly called 793B) isolated from field outbreaks in Japan were analyzed to ascertain the relationship to 4/91 vaccine strain. Three field isolates (JP/Wakayama/2003, JP/Iwate/2005 and JP/Saitama/2006) from flocks not immunized with a 4/91 type live IBV vaccine and one isolate (JP/Wakayama-2/2004) from a flock immunized with a 4/91 type live vaccine were examined. The amino acid identities among JP/Wakayama/2003, JP/Iwate/2005 and JP/Saitama/2006 were about 98%, whereas the identities to the 4/91 vaccine strain and JP/Wakayama-2/2004 were about 90%. Three of the field isolates, JP/Wakayama/2003, JP/Iwate/2005 and JP/Saitama/2006, were classified into a cluster closely related to French and Spanish isolates, but different from the cluster including the vaccine and JP/Wakayama-2/2004. These results indicate that JP/Wakayama/2003, JP/Iwate/2005 and JP/Saitama/2006 were derived from foreign field isolates, but not from the vaccine strain. On the other hand, the S1 gene of JP/Wakayama-2/2004 revealed high sequence similarity with that of the 4/91 vaccine strain and appeared to be a vaccine-like virus derived from a vaccine. The field isolates of 4/91 genotype IBV could be distinguished from other genotypes by using the BalI and Pst I enzymes in addition to the polymerase chain reaction (PCR) -restriction fragment length polymorphism (RFLP) methods of Mase et al. [16] using Hae II and EcoR I enzymes. Furthermore, the 4/91 vaccine strain and vaccine-like isolate (JP/Wakayama-2/2004) could be differentiated from the other field isolates by Bgl II digestion. This method, therefore, would assist in identification of field isolates of the 4/91 genotype as outbreaks of IBV in vaccinated flocks.

Existence of avian infectious bronchitis virus with a European-prevalent 4/91 genotype in Japan

Eight isolates of infectious bronchitis virus (IBV) were obtained from various prefectures in Japan during 2003-2007 and were genetically analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR) coupled with direct sequencing. These IBV isolates were classified into three genetic groups, including two that have already been reported (JP-I and JP-III). The remaining group is related to the 4/91 (also known as 793/B) type, prevalent mainly in European countries, and has not been identified in Japan until now.

A reverse transcriptase-polymerase chain reaction survey of infectious bronchitis virus genotypes in Western Europe from 2002 to 2006

A survey of infectious bronchitis virus (IBV) genotypes in poultry flocks in selected countries in Western Europe was carried out between March 2002 and December 2006. Identification of IBV was by reverse transcriptase-polymerase chain reaction of RNA extracted from oropharyngeal swabs taken from poultry flocks exhibiting signs of clinical disease thought to be attributable to IBV. Part of the hypervariable S1 gene of IBV was sequenced to differentiate between the various genotypes. During the survey, 4103 samples were processed, of which 2419 (59%) were positive for IBV. The predominant IBV genotypes detected were 793B and Massachusetts. The third and fourth most common genotypes were two new economically important field types: Italy02, and a virus similar to genotypes originally detected in China called QX. Analysis of the partial S1 sequences of the genotypes detected suggested that approximately 50% of all 793B, Massachusetts types and D274 IBVs were identical to the homologous commercially available live vaccines. Since 2004 the prevalence of Italy02 (present in all countries from which samples were received) has been declining in all countries except Spain, where it appeared to be the predominant genotype. Since 2004 an IBV genotype has been detected in Holland, Germany, Belgium and France similar to QX and the incidence has increased. QX was not detected in the United Kingdom or Spain. When detections thought to be attributable to vaccines were removed, the dominant genotype in France and Europe overall was 793B; in Germany, Holland and Belgium, it was QX-like IBV; and in the United Kingdom and Spain the dominant genotype was Italy02. The present study is the first to identify the prevalence of both Italy02 and QX field-type variants in poultry flocks in Western Europe. Several novel genotypes have also been detected.

Pathogenicity of infectious bronchitis virus isolates from Ontario chickens

Infectious bronchitis (IB) is one of the important viral diseases of chickens, and in spite of regular vaccination, IB is a continuous problem in Canadian poultry operations. In an earlier study using sentinel chickens we determined the incidence of infectious bronchitis virus (IBV) in Ontario commercial layer flocks. The objective of this study was to determine the pathogenicity of 5 nonvaccine-related IBV isolates recovered from the sentinel birds. The clinical signs, gross, and histological lesions in specific pathogen-free chickens indicated that all 5 isolates caused mild lesions in the respiratory tract. An important finding of this study was the significantly lower average daily weight gain among virus-inoculated groups of chickens during the acute phase of infection. Based on sequences of part of the S1 gene IBV-ON2, IBV-ON3, and IBV-ON5 formed a cluster and they were closely related to strain CU-82792. IBV-ON4 had 98.7% identity with the strain PA/1220/9, a nephropathogenic variant.

Location of the amino acid differences in the S1 spike glycoprotein subunit of closely related serotypes of infectious bronchitis virus

Four UK strains of three different serotypes were found to differ by only 2-3% of their S1 amino acids. The S1 sequences were also very similar to those of three Dutch isolates (D207, D274 and D3896), the greatest difference between two of the seven isolates being 4.4%. The few amino acid differences between the seven isolates were located largely between residues 19-122 and 251-347 of the mature S1 subunit. The seven isolates could be differentiated using 16 monoclonal antibodies in an enzyme-linked immunosorbent assay. Some virus neutralizing (VN) antibody-inducing epitopes were common to all seven isolates even though the strains had been differentiated into three serotypes by polyclonal sera. The results indicate that the most antigenic of the VN antibody-inducing epitopes are formed by very few amino acids and that these occur in the first and third quarters of the S1 subunit. We suggest that serology-based epizootiological studies of IBV should, therefore, be augmented by the inclusion of nucleic acid sequencing and/or monoclonal antibody analysis.

Sequence analysis of the gene coding for the S1 glycoprotein of infectious bronchitis virus (IBV) strains from New Zealand

Four new infectious bronchitis virus (IBV) strains (T6, K32, K43, and K87) were isolated from clinically infected chickens in New Zealand. These strains were compared with four strains (A, B, C, and D), which had circulated 25 years previously, by sequencing the gene coding for the S1 subunit of the spike glycoprotein. Analysis of the nucleotide and deduced amino acid sequences revealed that the eight strains from New Zealand are genetically related and share greater than 82.8% nucleotide and 79% amino acid homology within the S1 region. Strains T6, K43, and K87 were more than 99% homologous to previously described strains C and D. A fourth new strain (K32) was most closely related to the previously described B strain. Phylogenetic analysis of strains revealed that New Zealand strains were more closely related to Australian than European or North American strains. The New Zealand A strain shared 99.5% nucleotide and 98.7% amino acid homology with the Australian Vic S strain. Deduced amino acid sequence of the S1 glycoprotein indicated differences between strains that were, in general, consistent with virus neutralization patterns.

S1 gene sequence heterogeneity of a pathogenic infectious bronchitis virus strain and its embryo-passaged, attenuated derivatives

Infectious bronchitis virus CK/CH/LDL/97I was attenuated by serial passage in chicken embryos. Virus of passage 115 was attenuated as determined by clinical response to inoculation to 15-day-old specific pathogen free chickens. The vaccination-challenge test showed that the attenuated passage 115 virus could afford protection against the homologous pathogenic virus, passage 5, by the clinical response. Based on the sequence analysis and comparison of the S1 gene, both the pathogenic and attenuated CK/CH/LDL/97I viruses were populations that each included at least two subpopulations. Also, from analysis of the amino acid and nucleotide sequences of S1 gene, we speculate that recombination between the minor and dominant subpopulations plus accumulation of mutations in the S1 region of pathogenic passage 5 might lead to the formation of the embryo-passaged, attenuated passage 115.

Different genotypes of nephropathogenic infectious bronchitis viruses co-circulating in chicken population in China

Chicken nephropathogenic infectious bronchitis (IB) was prevalent in the most chicken farms during recent years, although the IB vaccination program has been widely performed in China. To characterize the S1 protein of infectious bronchitis virus (IBV) from China, five representative nephropathogenic IB viruses isolated from chickens in different provinces were genetically and phylogenetically analyzed. The results showed that the length of the S1 genes of the isolates were quite different (1,617, 1,620, 1,623, 1,629, and 1,632 nucleotides, respectively). The homology of the nucleotides and amino acids among the five isolates were 76.7%-92.1% and 73.9%-89.5%, respectively, indicating a great variation in S1 genes of the isolates. The variation in S1 genes might affect the antigenicity and pathogenicity of the viruses. Genetically, point mutations, insertions, and deletions in the S1 protein can be observed at many positions, especially at the first 150 amino acids in the N-terminal of the S1 protein. Two motif cleavage sites (R-R-X-R-R/S, H-R-R-R-R/S) were observed in the five sequenced strains. Phylogenetic analysis suggested that they belonged to different lineages. These findings indicated that different genotypes of nephropathogenic IB viruses were co-circulating in the chicken population in China.

Molecular analysis of Brazilian infectious bronchitis field isolates by reverse transcription-polymerase chain reaction, restriction fragment length polymorphism, and partial sequencing of the N gene

Molecular analysis of 15 Brazilian infectious bronchitis virus (IBV) isolates, obtained from clinical outbreaks of the disease in chickens (broilers or layers) in the state of Minas Gerais (Brazil) between 1972 and 1989, is reported. Using the N protein gene as target, IBVs were analyzed by reverse transcription-polymerase chain reaction/restriction fragment length polymorphism (RT-PCR/RFLP) with the restriction enzymes AvaII, HphI, Sau96I, and Tsp509I and cDNA sequencing. Results obtained from those isolates were compared to 19 sequences available in GenBank. N gene RFLP profiles, cDNA sequences, and predicted amino acid composition were used for the construction of dendrograms. Brazilian isolates were grouped into one distinct group. Identity of predicted N protein amino acid composition varied from 45% (between isolates G and 208) up to 99% (PM 1 and PM2), and, when compared to the other IBVs, the amino acid identity was from 42% (Q3/88 and G) up to 97% (D41 and PM1). The great genetic diversity was shown to occur before the official use of vaccination in Brazil and has remained thereafter.

S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt

BACKGROUND

Infectious bronchitis is highly contagious and constitutes one of the most common and difficult poultry diseases to control. IBV is endemic in probably all countries that raise chickens. It exists as dozens of serotypes/genotypes. Only a few amino acid differences in the S1 protein of vaccine and challenge strains of IBV may result in poor protection. Tropism of IBV includes the respiratory tract tissues, proventriculus and caecal tonsils of the alimentary tract, the oviduct and the kidney.

RESULTS

Infectious bronchitis virus (IBV) strain closely related to Massachusetts (Mass) serotype was isolated from broiler chickens suffering from severe renal and respiratory distresses. The isolate was serologically identified by Dot-ELISA and further characterized by RT-PCR then genotyped using S1 gene sequence analysis. Alignment of the S1 sequence of the isolate with 16 IBV strains revealed high homology to isolates related to Mass serotype. Inoculation with the strain reproduced the disease in experimental 1-day-old chickens and resulted in 20% mortality, severe renal and moderate respiratory distresses. Marked histopathological changes in both kidney and trachea were observed in experimentally infected chickens. A protection study using the H120 live attenuated vaccine showed low protection rate in spite of high S1 sequence homology (97%). Protection based criteria were: virus re-isolation attempts from trachea, tracheal and renal histopathology as well as IBV antigens detection by immunofluorescent antibody technique in kidney sections.

CONCLUSION

Periodical evaluation of cross-protective capabilities of IBV vaccine(s) versus recently recovered field isolates should be performed to ensure optimum control of IBV.