Virulence Properties of GI-23 Infectious Bronchitis Virus Isolated in Poland and Efficacy of Different Vaccination strategies

Lessons learnt on infectious bronchitis virus lineage GI-23

Infectious bronchitis virus (IBV) is the first coronavirus discovered in the world in the early 1930s and despite decades of extensive immunoprophylaxis efforts, it remains a major health concern to poultry producers worldwide. Rapid evolution due to large poultry population sizes coupled with high mutation and recombination events and the reliance of the antiviral immune response on specific antibodies against the epitopes of the S1 glycoprotein, render the control of IBV extremely challenging. The numerous and rapidly evolving genetic and antigenic IBV types are currently classified based on the whole S1 gene sequence, into 36 lineages clustered in eight genotypes. Most lineages (29) are grouped in genotype I (GI). "Variant 2" (Israel/Variant 2/1998) is the prototype strain of lineage GI-23 and, since this lineage emerged during the mid-1990s in the Middle East, it has evolved into numerous genetically related strains and disseminated to five continents. The hallmarks of IBV Variant 2-like strain infections are high virulence and remarkable nephrotropism and nephropathogenicity; however, the molecular mechanisms of these traits remain to be elucidated. Limited protection from previously utilized vaccine strains and accumulated losses to poultry producers have urged the development and implementation of homologous Variant 2-like vaccine strains. The latest avian coronavirus biology with specific emphasis on the cumulative knowledge about IBV "Variant 2" and emergence of related strains, characteristics and control are reviewed.

Detection and Molecular Characterization of GI-1 and GI-23 Avian Infectious Bronchitis Virus in Broilers Indicate the Emergence of New Genotypes in Bolivia

Infectious Bronchitis Virus (IBV) is a major threat to the poultry industry worldwide, causing significant economic losses. While the virus's genetic structure is well understood, the specific strains circulating in Bolivia have remained uncharacterized until now. This study aimed to identify and characterize new IBV strains in Bolivia. Tissue samples from broilers exhibiting clinical signs of Infectious Bronchitis were screened to detect IBV using real-time RT-PCR (RT-qPCR). Positive samples with low cycle threshold (Ct) values were selected for sequencing the full S1 gene. Of the 12 samples analyzed, 10 were determined to be positive for IBV. However, only four samples yielded sufficient genetic material for sequencing and subsequent phylogenetic analysis. The results revealed the presence of GI-1 and GI-23 lineages, both belonging to genotype I (GI). The GI-1 lineage showed >99% sequence identity to the H120 and Massachusetts vaccine strains, suggesting a close relationship. In contrast, the GI-23 lineage clustered with other IBV strains, showing a distinct subclade that is genetically distant from Brazilian strains. No evidence of recombination was found. Furthermore, amino acid substitution analysis identified specific mutations in the S1 subunit, particularly in the hypervariable regions 1, 2, and 3. These mutations could potentially alter the virus's antigenicity, leading to reduced vaccine efficacy. The findings of this study highlight the importance of continued and broad genomic surveillance of circulating IBV strains and the need to improve vaccination strategies in Bolivia.

Evaluation of different heterologous-homologous vaccine regimens against challenge with GI-23 lineage infectious bronchitis virus

This study assesses different IBV vaccination regimens in broiler chickens using commercially available live attenuated GI-23 (Egyptian-VAR2) and GI-1 (H120) vaccines. Vaccines were administered at 1, 14 days of age, or both. The ciliostasis test, following wild-type VAR2 challenge at 28 days of age, indicated that classic H120+VAR2 at one day old followed by the VAR2 vaccine at 14 days of age provided the highest level of protection (89.58%). Similarly, administering VAR2 at 1 day of age and classic H120 at 14 days of age demonstrated substantial protection (85.42%). Conversely, administering only classic H120 and VAR2 at one day old resulted in the lowest protection level (54.17%). Tracheal virus shedding quantification and assessment of trachea and kidney degenerative changes were significantly lower in vaccinated groups compared to the unvaccinated-challenged group. In conclusion, a carefully planned vaccination regimen based on homologous vaccination offers the most effective clinical protection in broiler chickens.

Potential Transcriptional Enhancers in Coronaviruses: From Infectious Bronchitis Virus to SARS-CoV-2

Coronaviruses constitute a global threat to human and animal health. It is essential to investigate the long-distance RNA-RNA interactions that approximate remote regulatory elements in strategies, including genome circularization, discontinuous transcription, and transcriptional enhancers, aimed at the rapid replication of their large genomes, pathogenicity, and immune evasion. Based on the primary sequences and modeled RNA-RNA interactions of two experimentally defined coronaviral enhancers, we detected via an in silico primary and secondary structural analysis potential enhancers in various coronaviruses, from the phylogenetically ancient avian infectious bronchitis virus (IBV) to the recently emerged SARS-CoV-2. These potential enhancers possess a core duplex-forming region that could transition between closed and open states, as molecular switches directed by viral or host factors. The duplex open state would pair with remote sequences in the viral genome and modulate the expression of downstream crucial genes involved in viral replication and host immune evasion. Consistently, variations in the predicted IBV enhancer region or its distant targets coincide with cases of viral attenuation, possibly driven by decreased open reading frame (ORF)3a immune evasion protein expression. If validated experimentally, the annotated enhancer sequences could inform structural prediction tools and antiviral interventions.

The spike protein of the apathogenic Beaudette strain of avian coronavirus can elicit a protective immune response against a virulent M41 challenge

The avian Gammacoronavirus infectious bronchitis virus (IBV) causes major economic losses in the poultry industry as the aetiological agent of infectious bronchitis, a highly contagious respiratory disease in chickens. IBV causes major economic losses to poultry industries across the globe and is a concern for global food security. IBV vaccines are currently produced by serial passage, typically 80 to 100 times in chicken embryonated eggs (CEE) to achieve attenuation by unknown molecular mechanisms. Vaccines produced in this manner present a risk of reversion as often few consensus level changes are acquired. The process of serial passage is cumbersome, time consuming, solely dependent on the supply of CEE and does not allow for rapid vaccine development in response to newly emerging IBV strains. Both alternative rational attenuation and cell culture-based propagation methods would therefore be highly beneficial. The majority of IBV strains are however unable to be propagated in cell culture proving a significant barrier to the development of cell-based vaccines. In this study we demonstrate the incorporation of a heterologous Spike (S) gene derived from the apathogenic Beaudette strain of IBV into a pathogenic M41 genomic backbone generated a recombinant IBV denoted M41K-Beau(S) that exhibits Beaudette's unique ability to replicate in Vero cells, a cell line licenced for vaccine production. The rIBV M41K-Beau(S) additionally exhibited an attenuated in vivo phenotype which was not the consequence of the presence of a large heterologous gene demonstrating that the Beaudette S not only offers a method for virus propagation in cell culture but also a mechanism for rational attenuation. Although historical research suggested that Beaudette, and by extension the Beaudette S protein was poorly immunogenic, vaccination of chickens with M41K-Beau(S) induced a complete cross protective immune response in terms of clinical disease and tracheal ciliary activity against challenge with a virulent IBV, M41-CK, belonging to the same serogroup as Beaudette. This implies that the amino acid sequence differences between the Beaudette and M41 S proteins have not distorted important protective epitopes. The Beaudette S protein therefore offers a significant avenue for vaccine development, with the advantage of a propagation platform less reliant on CEE.

Study of coinfection with local strains of infectious bursal disease virus and infectious bronchitis virus in specific pathogen-free chickens

Immunosuppressive diseases cause great losses in the poultry industry, increasing the susceptibility to infections by other pathogens and promoting a suboptimal response to vaccination. Among them, infectious bursal disease virus (IBDV) arises as one of the most important around the world. IBDV infects immature B lymphocytes, affecting the immune status of birds and facilitating infections by other pathogens such as avian infectious bronchitis virus (IBV). Although it has been reported that the interaction between these viruses increases IBV clinical signs, there are no actual studies about the interaction between regional circulating isolates that validate this statement. In this context, the objective of our work was to evaluate the effect of the interaction between local isolates of IBDV (belonging to genogroup 4) and IBV (lineage GI-16) in chickens. Thus, specific pathogen-free chickens were orally inoculated with IBDV genogroup (G) 4 or with PBS at 5 d of age. At 14-days postinoculation (dpi) the animals were intratracheally inoculated with a GI-16 IBV or with PBS. At multiple time points, groups of birds were euthanized and different parameters such as histological damage, viral load, lymphocyte populations and specific antibodies were evaluated. The success of IBDV infection was confirmed by the severity of bursal atrophy, viral detection, and presence of anti-IBDV antibodies. In IBV-infected animals, the presence of viral genome was detected in both kidney and bursa. The coinfected animals showed higher degree of lymphocyte infiltration in kidney, higher rate of animals with IBV viral genome in bursa at 28 dpi, and a clear decrease in antibody response against IBV at 28, 35, and 40 dpi. The results indicate that the infection with the local isolate of IBDV affects the immune status of the chickens, causing major severe damage, in response to IBV infection, which could consequently severely affect the local poultry industry.

Pathological assessment and tissue tropism of two different Egyptian infectious bronchitis strains

Avian infectious bronchitis is one of the most common viral infections in chickens affecting all ages. The tropism of infectious bronchitis virus (IBV) strains became broader and more variable posing major implications for the effective control of IBV infection. In this study, two IBV viruses representing classic and variant strains were inoculated intranasally into day-old SPF chicks (105 EID50/0.2 ml/bird). Clinical signs were observed for 15 days post-infection (DPI). Five chicks from each group were euthanized at 2, 4, 6, 8, 10, 12, and 15 DPI for histopathology and virus antigen detection by IHC and quantitative rRT-PCR. Results revealed that both classic and variant IBV strains induced mild clinical signs with no mortalities and fewer various histopathological lesions in infected SPF chickens. Although the viruses were detected by rRT-PCR up to 12 DPI, the affected tissues showed regeneration after 10 DPI with IHC revealing no IBV antigen. In summary, no differences were found in the behaviour of both IBV isolates in chickens. The broad tissue tropism for both IBV strains as indicated by viral antigen detection in various organs with no clinical or gross lesion suggest that the main cause of death in IBV infection under field conditions occurs as a result of complication with secondary infections rather single IBV infection. Due to positive immunostaining in the bursa, it is thought that IBV infection has immunosuppressive consequences, hence further study is required to validate this impact.

Evolution and Epidemic Spread of the Avian Infectious Bronchitis Virus (IBV) GI-23 in Brazil

Infectious bronchitis virus (IBV) is a pathogen affecting poultry flocks worldwide. GI-23 is an IBV lineage with a rapid spread into different continents of the world, and it was reported for the first time in South American/Brazilian broiler farms last year. This study aimed to investigate the recent introduction and epidemic spread of IBV GI-23 in Brazil. Ninety-four broiler flocks infected with this lineage were evaluated from October 2021 to January 2023. IBV GI-23 was detected using real-time RT-qPCR, and the S1 gene hypervariable regions 1 and 2 (HVR1/2) were sequenced. S1 complete and HVR1/2 nucleotide sequence datasets were used to carry out phylogenetic and phylodynamic analyses. Brazilian IBV GI-23 strains clustered into two specific subclades (SA.1 and SA.2), both in tree branches with IBV GI-23 from Eastern European poultry-producing countries, suggesting two independent and recent introductions (around 2018). Viral phylodynamic analysis showed that the IBV GI-23 population increased from 2020 to 2021, remaining constant for one year and declining in 2022. S1 amino acid sequences from Brazilian IBV GI-23 presented specific and characteristic substitutions in the HVR1/2 for subclades IBV GI-23 SA.1 and SA.2. This study brings new insights into the introduction and recent epidemiology of IBV GI-23 in Brazil.

Pathogenicity of GI-23 Avian Infectious Bronchitis Virus Strain Isolated in Brazil

IBV variants belonging to the GI-23 lineage have circulated since 1998 in the Middle East and have spread to several countries over time. In Brazil, the first report of GI-23 occurred in 2022. The study aimed to evaluate the in vivo pathogenicity of exotic variant GI-23 isolates. Biological samples were screening by real-time RT-PCR and classified in to GI-1 or G1-11 lineages. Interestingly, 47.77% were not classified in these lineages. Nine of the unclassified strains were sequenced and showed a high similarity to the GI-23 strain. All nine were isolated and three, were studied for pathogenicity. At necropsy, the main observations were the presence of mucus in the trachea and congestion in the tracheal mucosa. In addition, lesions on the tracheas showed marked ciliostasis, and the ciliary activity confirmed the high pathogenicity of isolates. This variant is highly pathogenic to the upper respiratory tract and can cause severe kidney lesions. This study confirm a circulation of GI-23 strain in the country and report, to first time, the isolation of an exotic variant of IBV in Brazil.

Emergence and molecular characterization of the avian infectious bronchitis virus GI-23 in commercial broiler farms from South America

Avian infectious bronchitis virus (IBV) is the etiological agent of a highly contagious disease in the poultry industry. The spike protein (S1 subunit) is responsible for the molecular diversity of the virus and many genetic types, and lineages are described worldwide. IBV genetic type I-strain 23 (GI-23) has spread across different continents (including Asia, Europe and Africa), causing multiple outbreaks and severe economic losses throughout the poultry industry in the last decade. The present study aimed to report the emergence and molecular characterization of GI-23 in South Brazil, being detected for the first time in South America. Eighty-two broiler flocks presenting clinical suspicion of infectious bronchitis were selected for this study. Tracheal, renal and intestinal samples were collected for IBV detection and genotyping. A total of 57 flocks were positive for IBV by generic RT-qPCR targeting 5' untranslated region and 31 also tested positive for GI-11 by a specific RT-qPCR targeting S1 gene for this lineage. The remaining 26 IBV-positive samples were genotyped by partial and one by complete S1 gene/protein sequencing. Phylogenetic analysis demonstrated that all of them clustered into a specific branch of the GI-23. S1 protein sequence analysis evidenced that all Brazilian GI-23 IBVs had the two characteristic amino acid substitutions A93T and S/H118P/L, but other changes were also observed, such as S37F (n = 21; 81%), G117S (n = 17, 65%), P122S (n = 16; 61%) and W71R (n = 9; 35%). This study brings new insights into the epidemiology of the IBV GI-23 in the world, highlighting its emergence and molecular characteristics in Brazil, South America.

Phylodynamic and Recombination Analyses of Avian Infectious Bronchitis GI-23 Reveal a Widespread Recombinant Cluster and New Among-Countries Linkages

Simple Summary

Infectious bronchitis virus (IBV) is one of the main infectious agents affecting the avian industry. The remarkable evolutionary rate of this virus represents an often unsurmountable challenge to its control, leading to the emergence of different lineages featured by different biological properties and limited cross-protection. In the present study, the origin, spreading and evolution of GI-23, one of the most important IBV emerging lineages, has been reconstructed using a phylodynamic approach. To this purpose, the broadest available collection of complete and partial S1 sequences was downloaded from GenBank and merged with specifically sequenced European strains. After a likely ancient origin, GI-23 circulated undetected in the Middle East for a considerable time, thereafter emerging as a threat in parallel with the intensification of the poultry industry and its introduction in other countries. An intensive viral circulation affecting mainly neighbouring countries or those with strong economic and political relationships was demonstrated, even though some nations appear to play a major role as a “bridge” among less related locations. Of note, a big recombinant cluster, likely originating in the Middle East but spreading thereafter, especially to Europe through Turkey, demonstrated a much-marked increase in viral population size, and potentially fitness, compared to previously circulating variants.

Abstract

Infectious bronchitis virus GI-23 lineage, although described approximately two decades ago in the Middle East, has recently drawn remarkable attention and is considered an “emerging” lineage due to its current spread to several other regions, including Europe. Despite the relevance, no comprehensive studies are available investigating its epidemiologic and evolutionary pattern. The present phylodynamic study was designed to fill this gap, benefitting from a collection of freely available GI-23 sequences and ad-hoc generated European ones. After a relatively ancient origin in the Middle East, likely in the first half of the previous century, GI-23 circulated largely undetected or underdiagnosed for a long time in this region, likely causing little damage, potentially because of low virulence coupled with limited development of avian industry in the considered years and regions and insufficient diagnostic activity. The following development of the poultry industry and spread to other countries led to a progressive but slow increase of viral population size between the late ‘90s and 2010. An increase in viral virulence could also be hypothesized. Of note, a big recombinant cluster, likely originating in the Middle East but spreading thereafter, especially to Europe through Turkey, demonstrated a much-marked increase in viral population size compared to previously circulating variants. The extensive available GI-23 sequence datasets allowed to demonstrate several potential epidemiological links among African, Asian, and European countries, not described for other IBV lineages. However, differently from previously investigated IBV lineages, its spread appears to primarily involve neighbouring countries and those with strong economic and political relationships. It could thus be speculated that frequent effective contacts among locations are necessary for efficient strain transmission. Some countries appear to play a major role as a “bridge” among less related locations, being Turkey the most relevant example. The role of vaccination in controlling the viral population was also tentatively evaluated. However, despite some evidence suggesting such an effect, the bias in sequence and data availability and the variability in the applied vaccination protocols prevent robust conclusions and warrant further investigations.