Viral subpopulation variability in different batches of Infectious bronchitis virus (IBV) vaccines based on GI-23 lineage: Implications for the field

Genomic Alterations of the Infectious Bronchitis Virus (IBV) Strain of the GI-23 Lineage Induced by Passages in Chickens and Quails

Infectious bronchitis virus (IBV) of the GI-23 lineage, which first emerged in the Middle East in the late 1990s, has since spread worldwide. The factors driving its expansion, whether human involvement, wild bird migration, or the virus's biological traits, are still unclear. This study aimed to trace the genome evolution of GI-23 IBV in chickens and its adaptability to quails, which are susceptible to both gamma- and deltacoronaviruses. Thirty specific-pathogen-free (SPF) birds, aged between two and three weeks, were used. Initially, three birds were inoculated with the G052/2016 IBV via the oculo-nasal route. On the third day post-infection (dpi), oropharyngeal swabs were collected from the whole group, pooled, and subsequently used to infect three next birds. This process was repeated nine more times during consecutive IBV passages (P-I-P-X), and eventually, virus sequencing was performed using Next-Generation Sequencing (NGS). The obtained results showed that quails were not susceptible to the IBV GI-23 lineage, as the virus RNA was detected in low amounts only during the first passage (QP-I) with no further detections in later rounds of IBV passaging. In chickens, only mild diarrhea symptoms appeared in a few individuals. The NGS analysis identified sixty-two single nucleotide variants (SNVs), thirty of which caused amino acid changes, twenty-eight were synonymous, and one SNV introduced a stop codon. Three SNVs were found in untranslated regions. However, none of these SNVs lasted beyond seven passages, with forty-four being unique SNVs. The Shannon entropy values measured during passages varied for pol1a, pol1b, S, 5a, 5b, and N genes, with overall genome complexity peaking at CP-VI and CP-X. The highest complexity was observed in the pol1a (CP-X) and S genes (CP-IV, CP-VI, CP-VIII, and CP-X). Along with the S gene that was under positive selection, eight codons in pol1a were also positively selected. These findings suggest that even in an adapted host, IBV variability does not stabilize without immune pressure, indicating continuous molecular changes within its genome.

Laboratory safety and immunogenicity evaluation of live attenuated avian infectious bronchitis GI-23 virus vaccine

Avian infectious bronchitis virus (IBV) is responsible for a highly contagious disease that poses a significant threat to the poultry industry due to its high rates of evolution. The occurrence of vaccination failure can frequently be attributed to the emergence of novel strains that exhibit antigenic divergence from conventional vaccine strains. This study aims to evaluate the safety and efficacy of the Eg/1212B-based live attenuated virus vaccine indicated for immunization of chickens against nephropathogenic GI-23 variant strains reported globally. Studies were designed in compliance with European Pharmacopeia Ph. Eur. 0442. The attenuated vaccine virus did not exhibit any tendency to revert or increase in virulence after five back-passages in SPF chickens. Ciliostasis scores and kidney lesions (histology) were comparable between vaccinated and control birds. No chicken showed clinical signs of an infection with IBV or died from causes attributable to the vaccine after receiving a 10× overdose. A single vaccination was able to protect the birds in a challenge model with a recent European wild-type IBV strain. The study demonstrated an onset of immunity of 21 days and a duration of immunity lasting up to 56 days. Vaccination administered individually through the ocular route resulted in a protection rate of 100 % to 85 %, whereas mass application by spraying offered a protection rate of 85 % to 80 %. In conclusion, the safety and efficacy data confirm a positive benefit/risk balance, and the investigated product can be considered a suitable vaccine candidate for controlling avian infectious bronchitis nephropathogenic variant strains related to GI-23.

Genome stability assessment of PRRS vaccine strain with new ARTIC-style sequencing protocol

A tiling amplicon sequencing protocol was developed to analyse the genome sequence stability of the modified live PRRSV vaccine strain, Porcilis MLV. The backbone of the ARTIC-style protocol was formed by 34 individual primer pairs, which were divided into two primer pools. Primer pairs were designed to amplify 532 to 588 bp fragments of the corresponding genomic region. The amplicons are suitable for sequencing on Illumina DNA sequencers with available 600-cycle sequencing kits. The concentration of primer pairs in the pools was optimized to obtain a balanced sequencing depth along the genome. Deep sequencing data of three vaccine batches were also analysed. All three vaccine batches were very similar to each other, although they also showed single nucleotide variations (SNVs) affecting less than 1 % of the genome. In the three vaccine strains, 113 to 122 SNV sites were identified; at these sites, the minority variants represented a frequency range of 1 to 48.7 percent. Additionally, the strains within the batches contained well-known length polymorphisms; the genomes of these minority deletion mutants were 135 to 222 bp shorter than the variant with the complete genome. Our results show the usefulness of ARTIC-style protocols in the evaluation of the genomic stability of PRRS MLV strains.

Global Emergence of Infectious Bronchitis Virus Variants: Evolution, Immunity, and Vaccination Challenges

Infectious bronchitis is an acute, extremely contagious viral disease affecting chickens of all ages, leading to devastating economic losses in the poultry industry worldwide. Affected chickens show respiratory distress and/or nephritis, in addition to decrease of egg production and quality in layers. The avian coronavirus, infectious bronchitis virus (IBV), is a rapidly evolving virus due to the high frequency of mutations and recombination events that are common in coronaviruses. This leads to the continual emergence of novel genotypes that show variable or poor crossprotection. The immune response against IBV is complex. Passive, innate and adaptive humoral and cellular immunity play distinct roles in protection against IBV. Despite intensive vaccination using the currently available live-attenuated and inactivated IBV vaccines, IBV continues to circulate, evolve, and trigger outbreaks worldwide, indicating the urgent need to update the current vaccines to control the emerging variants. Different approaches for preparation of IBV vaccines, including DNA, subunit, peptides, virus-like particles, vectored and recombinant vaccines, have been tested in many studies to combat the disease. This review focuses on several key aspects related to IBV, including its clinical significance, the functional structure of the virus, the factors that contribute to its evolution and diversity, the types of immune responses against IBV, and the characteristics of both current and emerging IBV vaccines. The goal is to provide a comprehensive understanding of IBV and explore the emergence of variants, their dissemination around the world, and the challenges to define the efficient vaccination strategies.

When Everything Becomes Bigger: Big Data for Big Poultry Production

In future decades, the demand for poultry meat and eggs is predicted to considerably increase in pace with human population growth. Although this expansion clearly represents a remarkable opportunity for the sector, it conceals a multitude of challenges. Pollution and land erosion, competition for limited resources between animal and human nutrition, animal welfare concerns, limitations on the use of growth promoters and antimicrobial agents, and increasing risks and effects of animal infectious diseases and zoonoses are several topics that have received attention from authorities and the public. The increase in poultry production must be achieved mainly through optimization and increased efficiency. The increasing ability to generate large amounts of data ("big data") is pervasive in both modern society and the farming industry. Information accessibility-coupled with the availability of tools and computational power to store, share, integrate, and analyze data with automatic and flexible algorithms-offers an unprecedented opportunity to develop tools to maximize farm profitability, reduce socio-environmental impacts, and increase animal and human health and welfare. A detailed description of all topics and applications of big data analysis in poultry farming would be infeasible. Therefore, the present work briefly reviews the application of sensor technologies, such as optical, acoustic, and wearable sensors, as well as infrared thermal imaging and optical flow, to poultry farming. The principles and benefits of advanced statistical techniques, such as machine learning and deep learning, and their use in developing effective and reliable classification and prediction models to benefit the farming system, are also discussed. Finally, recent progress in pathogen genome sequencing and analysis is discussed, highlighting practical applications in epidemiological tracking, and reconstruction of microorganisms' population dynamics, evolution, and spread. The benefits of the objective evaluation of the effectiveness of applied control strategies are also considered. Although human-artificial intelligence collaborations in the livestock sector can be frightening because they require farmers and employees in the sector to adapt to new roles, challenges, and competencies-and because several unknowns, limitations, and open-ended questions are inevitable-their overall benefits appear to be far greater than their drawbacks. As more farms and companies connect to technology, artificial intelligence (AI) and sensing technologies will begin to play a greater role in identifying patterns and solutions to pressing problems in modern animal farming, thus providing remarkable production-based and commercial advantages. Moreover, the combination of diverse sources and types of data will also become fundamental for the development of predictive models able to anticipate, rather than merely detect, disease occurrence. The increasing availability of sensors, infrastructures, and tools for big data collection, storage, sharing, and analysis-together with the use of open standards and integration with pathogen molecular epidemiology-have the potential to address the major challenge of producing higher-quality, more healthful food on a larger scale in a more sustainable manner, thereby protecting ecosystems, preserving natural resources, and improving animal and human welfare and health.

Longitudinal Survey on aMPV Circulation in French Broiler Flocks following Different Vaccination Strategies

In recent years, the impact of respiratory disease resulting from Avian Metapneumovirus (aMPV) infection has been generally rising in the broiler industry in Europe. In this context, in order to investigate aMPV contribution to the clinical picture and the potential benefits of diversified vaccination strategies compared to nonvaccination policies, a longitudinal monitoring was performed, also evaluating Infectious Bronchitis Virus (IBV) presence. Broiler flocks located in Western France, where aMPV has already proven to be a health and productivity issue, were screened by RT-PCR on rhino-pharyngeal swabs, and the viruses were genetically characterized by sequence analysis. For a more comprehensive picture of aMPV molecular epidemiology and evolution in France, aMPV subtype B strains detected from 1985 to 1998 were sequenced and included in the analysis. The survey confirmed the detection of aMPV subtype B in commercial broiler flocks in France, together with a certain heterogeneity demonstrated by the circulation of more recent and historical French field strains. No IBV field strains were detected. The implementation and evaluation of different management choices and vaccine strategies suggests once again that immunization does not prevent infection but contributes greatly to the containment of the clinical manifestations.