Comparative genomics of Korean infectious bronchitis viruses (IBVs) and an animal model to evaluate pathogenicity of IBVs to the reproductive organs

Receptor binding motif surrounding sites in the spike 1 protein of infectious bronchitis virus have high susceptibility to mutation related to selective pressure

BACKGROUND

To date, various genotypes of infectious bronchitis virus (IBV) have co-circulated and in Korea, GI-15 and GI-19 lineages were prevailing. The spike protein, particularly S1 subunit, is responsible for receptor binding, contains hypervariable regions and is also responsible for the emerging of novel variants.

OBJECTIVE

This study aims to investigate the putative major amino acid substitutions for the variants in GI-19.

METHODS

The S1 sequence data of IBV isolated from 1986 to 2021 in Korea (n = 188) were analyzed. Sequence alignments were carried out using Multiple alignment using Fast Fourier Transform of Geneious prime. The phylogenetic tree was generated using MEGA-11 (ver. 11.0.10) and Bayesian analysis was performed by BEAST v1.10.4. Selective pressure was analyzed via online server Datamonkey. Highlights and visualization of putative critical amino acid were conducted by using PyMol software (version 2.3).

RESULTS

Most (93.5%) belonged to the GI-19 lineage in Korea, and the GI-19 lineage was further divided into seven subgroups: KM91-like (Clade A and B), K40/09-like, QX-like (I-IV). Positive selection was identified at nine and six residues in S1 for KM91-like and QX-like IBVs, respectively. In addition, several positive selection sites of S1-NTD were indicated to have mutations at common locations even when new clades were generated. They were all located on the lateral surface of the quaternary structure of the S1 subunits in close proximity to the receptor-binding motif (RBM), putative RBM motif and neutralizing antigenic sites in S1.

CONCLUSIONS

Our results suggest RBM surrounding sites in the S1 subunit of IBV are highly susceptible to mutation by selective pressure during evolution.

Pathogenicity evaluation of GVI-1 lineage infectious bronchitis virus and its long-term effects on reproductive system development in SPF hens

Infectious bronchitis virus (IBV) has gained increasing attention in the poultry industry due to its ability to cause tissue injuries not only in the respiratory system and kidney but also in the reproductive system of layers. Recently, the GVI-1 lineage IBVs have spread widely in China, whereas their pathogenicity in egg-laying chickens has rarely been studied, especially its long-term influence in egg production upon the early infection in chicks. In this study, 10-day-old SPF chicks were infected with the GVI-1 lineage JX181 strain and monitored over a 170-day period after infection. The pathogenicity evaluation of the JX181 strain included clinical observations, immunohistochemical assay, viral load, viral shedding, gross autopsy, and laying rate. The results showed that JX181 has a high pathogenicity, causing severe system lesions, and the decrease in egg production. In summary, this study describes the long-term damages caused by the early infection with the IBV GVI-1 lineage on the reproductive system of hens, providing a comprehensive understanding of the pathogenicity of the IBV GVI-1 lineage and emphasizing the importance of its early prevention.

The relation between avian coronaviruses and SARS-CoV-2 coronavirus

The coronaviruses (CoVs) are a family of ribonucleic acid viruses that are present in both mammals and birds. SARS-CoV and MERS-CoV originated in bats, and there is a possibility that this could be the case for SARS-CoV-2 as well. There is already evidence that a probable intermediary host is responsible for the emergence of viruses in humans as was the case for SARS-CoVs and MERS-CoV. As the SARS-CoV-2 originated from a live animal market, there is always the question if domestic animals are susceptible to these viruses and the possible risk of zoonotic transmission with mammals, including humans. This uncertainty of the transmission of the COVID-19 virus between humans and animals is of great significance worldwide. Hence, this paper focuses on the avian CoVs and their possible relation and interaction with SARS-CoV-2.

Efficacy of Commercial Infectious Bronchitis Vaccines against Canadian Delmarva (DMV/1639) Infectious Bronchitis Virus Infection in Layers

Vaccination is the most important way to control infectious bronchitis (IB) in chickens. Since the end of 2015, the Delmarva (DMV)/1639 strain of infectious bronchitis virus (IBV) has caused significant damage to the layer flocks in Eastern Canada. The efficacy of a combination of existing IB vaccines licensed in Canada was assessed against experimental challenge with this IBV strain. The layer pullets were vaccinated during the rearing phase with live attenuated IB vaccines of Massachusetts (Mass) + Connecticut (Conn) types followed by an inactivated IB vaccine of Mass + Arkansas (Ark) types and then challenged with the Canadian IBV DMV/1639 strain at 30 weeks of age. Protection was evaluated based on the egg laying performance, immune responses, viral shedding, and viral genome loads and lesions in IBV target organs. The vaccinated challenged hens were protected from the drop in egg production observed in the non-vaccinated challenged hens. Early (5 dpi) anamnestic serum antibody response was measured in the vaccinated challenged hens as well as a significant level of antibodies was detected in the oviduct washes (14 dpi). In contrast, hens in the non-vaccinated challenged group showed delayed (12 dpi) and significantly lower serum antibody response. Viral RNA loads were reduced in the respiratory, alimentary, and reproductive tissues of the vaccinated challenged hens compared to the non-vaccinated challenged hens. Compared to the control groups, the vaccinated challenged hens had less marked microscopic lesions in the trachea, kidney, magnum, and uterus. Our experimental model demonstrated inconclusive results for cell-mediated immune responses and viral shedding. Overall, the vaccination program used in this study minimized viral replication and histopathological changes in most IBV target organs and protected challenged hens against drop in egg production.

Novel vaccine design based on genomics data analysis: A review

Modification of pathogenic strains with the passage of time is responsible for evolution in the timeline of vaccine development for last 30 years. Recent advancements in computational vaccinology on the one hand and genome sequencing approaches on the other have generated new hopes in vaccine development. The aim of this review was to discuss the evolution of vaccines, their characteristics and limitations. In this review, we highlighted the evolution of vaccines, from first generation to the current status, pointing out how different vaccines have emerged and different approaches that are being followed up in the development of more rational vaccines against a wide range of diseases. Data were collected using Google Scholar, Web of Science, Science Direct, Web of Knowledge, Scopus and Science Hub, whereas computational tools such as NCBI, GeneMANIA and STRING were used to analyse the pathways of vaccine action. Innovative tools, such as computational tools, recombinant technologies and intra-dermal devices, are currently being investigated in order to improve the immunological response. New technologies enlightened the interactions of host proteins with pathogenic proteins for vaccine candidate development, but still there is a need of integrating transcriptomic and proteomic approaches. Although immunization with genomics data is a successful approach, its advantages must be assessed case by case and its applicability depends on the nature of the agent to be immunized, the nature of the antigen and the type of immune response required to achieve effective protection.

Emerging lethal infectious bronchitis coronavirus variants with multiorgan tropism

Infectious bronchitis virus (IBV) causes respiratory diseases in chickens and poses an economic threat to the poultry industry worldwide. Despite vaccine use, there have been field outbreaks of IBV in Taiwan. This study aimed to characterize the emerging IBV variants circulating in Taiwan. The analysis of the structural protein genes showed that these variants emerged through frequent recombination events among Taiwan strains, China strains, Japan strains and vaccine strains. Cross‐neutralization tests revealed that two of the variants exhibited novel serotypes. Clinicopathological assessment showed that two of the variants caused high fatality rates of 67% and 20% in one‐day‐old SPF chicks, and all the variants possessed multiorgan tropisms, including trachea, proventriculus and urogenital tissues. Furthermore, the commercial live‐attenuated Mass‐type vaccine conferred poor protection against these variants. This study identified novel genotypes, serotypes and pathotypes of emerging IBV variants circulating in Taiwan. There is an urgent need for effective countermeasures against these variant strains.

Genetic and Pathologic Characterization of a Novel Recombinant TC07-2-Type Avian Infectious Bronchitis Virus

Avian infectious bronchitis viruses (IBVs) with the TC07-2 genotype have spread rapidly in East Asia since they were first reported in China in 2007. In 2015, an IBV with the TC07-2 genotype (designated KrD1515) was isolated from layer chickens with severe respiratory symptoms in Korea. In the present study, the full-length open reading frames of the spike (S) and nucleocapsid (N) genes of the virus were sequenced and analyzed. S1 gene phylogenetic analysis revealed that the KrD1515 virus clustered with viruses with the TC07-2 genotype, whereas N gene phylogenetic analysis revealed that the KrD1515 virus clustered with Korean IBVs, but not with Chinese TC07-2 IBV. When 7-day-old specific-pathogen-free chickens were inoculated with the KrD1515 virus, they developed severe respiratory symptoms and tracheal lesions. However, there were no other clinical symptoms or pathologic lesions in other tissues. The virus was shed from the trachea for at least a week and from the cloaca for only a day. Our findings suggest that the KrD1515 virus is a recombinant virus between a Chinese TC07-2 IBV and a non-TC07-2 Korean IBV and engages in respiratory tropism in chickens.

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.

Gonadal pathogenicity of an infectious bronchitis virus strain from the Massachusetts genotype

An outbreak of infectious bronchitis caused by the IBVPR03 strain of the Massachusetts genotype affected H-120 vaccinated laying hens in South Brazil. We investigated the cross protection of the vaccine by assessing the traqueal ciliostasis, virus recovery, and histopathological changes typically observed in the respiratory tract. Although the IBVPR03 strain is S1-genotyped as Massachusetts with a high genomic similarity to the H-120 vaccine strains, surprisingly, we found no tropism or pathogenicity to the trachea in birds infected with this strain. On the other hand, we observed ovarian and testicle lesions. Here, we show that, despite belonging in the Massachusetts genotype, the IBVPR03 pathotype differs from the expected respiratory pattern, causing instead marked histopathological changes in the gonads, so far not associated with this group.

Comparative features of infections of two Massachusetts (Mass) infectious bronchitis virus (IBV) variants isolated from Western Canadian layer flocks

BACKGROUND

Infectious bronchitis virus (IBV) is one of the leading causes of mortality and morbidity in chickens. There are numerous serotypes and variants, which do not confer cross protection resulting in failure of currently used IBV vaccines. Although variant IBV isolates with major genetic differences have been subjected to comparative studies, it is unknown whether minor genetic differences in IBV variants within a serotype are different in terms of pathogenesis and eliciting host responses. Two Massachusetts (Mass) variant IBV isolates recovered from commercial layer flocks in the Western Canadian provinces of Alberta (AB) and Saskatchewan (SK) were compared genetically and evaluated for their pathogenicity, tissue distribution and ability to recruit and replicate in macrophages.

RESULTS

Although whole genome sequencing of these two Mass IBV isolates showed low similarity with the M41 vaccinal strain, they had an identical nucleotide sequence at open reading frames (ORFs) 3a, 3b, envelop (E), matrix (M), 5a and 5b. The rest of the ORFs of these 2 IBV isolates showed 99.9% nucleotide similarity. However, upon experimental infection, we found that the IBV isolate originating from AB was different to the one that originated in SK due to higher tracheal lesion scores and lower lung viral replication and lower genome loads in cecal tonsils. Nevertheless, both IBV isolates elicited host responses characterized by significant macrophage recruitment to the respiratory tract and there was evidence that both IBV isolates replicated within tracheal and lung macrophages.

CONCLUSIONS

Overall, this study shows that Mass variant IBV isolates, although possessing minor genetic variations, can lead to significant differences in pathogenicity in young chickens. Further studies are required to investigate the pathogenicity of these two Mass variant IBV isolates in laying hens.

Pathobiological and Genomic Characterization of a Cold-Adapted Infectious Bronchitis Virus (BP-caKII)

We established a cold-adapted infectious bronchitis virus (BP-caKII) by passaging a field virus through specific pathogen-free embryonated eggs 20 times at 32 °C. We characterized its growth kinetics and pathogenicity in embryonated eggs, and its tropism and persistence in different tissues from chickens; then, we evaluated pathogenicity by using a new premature reproductive tract pathogenicity model. Furthermore, we determined the complete genomic sequence of BP-caKII to understand the genetic changes related to cold adaptation. According to our results, BP-caKII clustered with the KII genotype viruses K2 and KM91, and showed less pathogenicity than K2, a live attenuated vaccine strain. BP-caKII showed delayed viremia, resulting in its delayed dissemination to the kidneys and cecal tonsils compared to K2 and KM91, the latter of which is a pathogenic field strain. A comparative genomics study revealed similar nucleotide sequences between BP-caKII, K2 and KM91 but clearly showed different mutations among them. BP-caKII shared several mutations with K2 (nsp13, 14, 15 and 16) following embryo adaptation but acquired multiple additional mutations in nonstructural proteins (nsp3, 4 and 12), spike proteins and nucleocapsid proteins following cold adaptation. Thus, the establishment of BP-caKII and the identified mutations in this study may provide insight into the genetic background of embryo and cold adaptations, and the attenuation of coronaviruses.

Comparative transcriptome analysis reveals induction of apoptosis in chicken kidney cells associated with the virulence of nephropathogenic infectious bronchitis virus

Avian infectious bronchitis virus (IBV) that causes respiratory and nephritic diseases in chicken is a major poultry pathogen leading to serious economic loss worldwide. The nephropathogenic IBV strains cause nephritis and kidney lesions intrinsically and the pathogenic mechanism is still unclear. In the present study, SPF chicks were infected with three nephropathogenic IBVs of different virulence and their gene expression profiles in chicken kidney were compared at transcriptome level. As a result, 1279 differentially expressed (DE) genes were found in very virulent SCDY2 inoculated group, 145 in virulent SCK2 group and 74 in non-virulent LDT3-A group when compared to mock infected group. Gene Ontology (GO) and KEGG pathway enrichment analysis on SCDY2 group displayed that the up-regulated DE genes were mainly involved in cell apoptosis, and the down-regulated genes were involved in metabolic processes and DNA replication. Protein-Protein Interaction (PPI) analysis showed that DE genes in SCDY2 group formed a network, and the core of the network was composed by cell apoptosis and immune response proteins. The clustering of gene expression profile among the three virus inoculated groups indicated that the majority of up-regulated DE genes on apoptosis in very virulent SCDY2 group were up-regulated more or less in virulent SCK2 group and those down-regulated on innate immune response in SCDY2 group were also down-regulated differently in SCK2 group. In addition, the number of apoptotic cells detected experimentally in kidney tissue were very different among the three virus inoculated groups and were positively accordant with the viral titer, kidney lesions and viral virulence of each group. Taken all together, the present study revealed that virulent nephropathogenic IBV infection modified a number of gene expression and induction of apoptosis in kidney cells may be a major pathogenic determinant for virulent nephropathogenic IBV.

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Genes expression in chicken kidney cells post inoculation of three nephro IBVs was studied by transcriptome analysis.

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DE genes post challenge mainly involved in the pathways of apoptosis, immune response, metabolic and DNA replication.

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Activation of apoptosis and suppression of innate immune response were accordant with the virulence of inoculated IBVs.

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Induction of apoptosis is triggered by suppression of immune response and productive replication of virus post infection.

Infectious Bronchitis Virus Variants: Molecular Analysis and Pathogenicity Investigation

Infectious bronchitis virus (IBV) variants constantly emerge and pose economic threats to poultry farms worldwide. Numerous studies on the molecular and pathogenic characterization of IBV variants have been performed between 2007 and 2017, which we have reviewed herein. We noted that viral genetic mutations and recombination events commonly gave rise to distinct IBV genotypes, serotypes and pathotypes. In addition to characterizing the S1 genes, full viral genomic sequencing, comprehensive antigenicity, and pathogenicity studies on emerging variants have advanced our understanding of IBV infections, which is valuable for developing countermeasures against IBV field outbreaks. This review of IBV variants provides practical value for understanding their phylogenetic relationships and epidemiology from both regional and worldwide viewpoints.

Comparative genomics of QX-like infectious bronchitis viruses in Korea

To minimize the spread of infectious bronchitis virus (IBV), domestic fowl have been extensively vaccinated with the KM91 strain. However, various IBV QX-like virus strains have become increasingly prevalent in Korea. We conducted comparative genomic analyses of seven QX-like viruses: early viruses (n = 2), new cluster 1 (NC1; recombinants of KM91 and the early QX-like viruses, n = 3) and recurrent viruses (n = 2), to understand their genomic backgrounds. The early and NC1 viruses had KM91-like backgrounds, but the recurrent viruses had QX-like genomic backgrounds. The absence of pure QX-like viruses before the appearance of the early viruses suggests that the viruses were introduced from other countries after recombination, but the NC1 viruses originated in Korea. The recent prevalence of recurrent viruses with different genomic backgrounds and spike genes from the early and the NC1 viruses may indicate the repeated introduction of different infectious bronchitis viruses from other countries and their successful evasion of vaccine immunity in the field. Furthermore, a 1ab gene-based phylogenetic analysis revealed three distinct lineages: North America-Europe, China/Taiwan, and China. KM91 and the early and NC1 viruses were included in the North America-Europe lineage, and the recurrent QX-like viruses were included in the China lineage. The phylogenetic positions of KM91-like 1ab and QX-like spike suggest frequent recombination between the North America-Europe and China lineages. Additional studies on the patterns of recombination, including donor-acceptor relationships, geographical sites, and non-poultry hosts, may be valuable for understanding the evolution of IBVs.

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.

Pathogenicity of virulent infectious bronchitis virus isolate YN on hen ovary and oviduct

Avian infectious bronchitis is an economically important poultry disease caused by avian infectious bronchitis virus (IBV). IBV isolate YN is a virulent strain, which is genetically similar to most of the prevalent strains in China. In this study, 21-day-old commercial laying hens were infected with IBV strain YN. The damaging effects of the virus on the reproductive organs were evaluated with clinical observations, gross autopsy and histopathological examinations during the 100-day monitoring period post infection. IBV strain YN infection caused a death rate of 40.5%. Microscopic lesions were observed on the ovary post-infection, but were restricted to the acute infection period. The pathological damage to the cystic oviducts were observed throughout the surveillance period. This study provides detailed information on the pathological changes in the hen ovary and oviduct after challenge with IBV strain YN, which could provide a better understanding about the pathogenicity of 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.

Emergence of Avian Infectious Bronchitis Virus and its variants need better diagnosis, prevention and control strategies: a global perspective

Growth in poultry sector is being challenged due to increased incidence and re-emergence of diseases caused due to evolution of several viral pathogens and use of live vaccines. Piles of economic losses are encountered due to these diseases. Avian Infectious Bronchitis (IB), caused by Corona virus, is OIE-listed disease and characterized by respiratory, renal and urogenital involvements, causing high mortality. Economic losses are encountered due to loss of productive performance of both egg and meat-type chickens. Variant viruses evolve due to spontaneous mutations and recombinations, causing disease in vaccinated flocks of all ages. Serotyping and genotyping are the common methods of classification of IBV strains. The virus has 4 clusters, grouped into 7 serotypes and the most important strains are Massachusetts, Connecticut, Arkansas, Gray, Holte and Florida along with numerous others, distributed round the globe. Several conventional and molecular diagnostic methods have been described for the diagnosis of IB in chickens. 'All-in/all-out' operations of rearing along with good biosafety measures forms the basis of prevention, whereas vaccination forms the backbone of IB control programme. Both live and inactivated (oil emulsified) conventional vaccines are available. The new generation vaccines (recombinant and vector-based) developed against locally prevailing IBV strains may be more helpful and avoid the reversion of virulence in live vaccine viruses. The present review deals with all these perspectives of this important emerging poultry pathogen.