Evolution of infectious bronchitis virus in the field after homologous vaccination introduction

International audienceAbstractDespite the fact that vaccine resistance has been typically considered a rare phenomenon, some episodes of vaccine failure have been reported with increasing frequency in intensively-raised livestock. Infectious bronchitis virus (IBV) is a widespread avian coronavirus, whose control relies mainly on extensive vaccine administration. Unfortunately, the continuous emergence of new vaccine-immunity escaping variants prompts the development of new vaccines. In the present work, a molecular epidemiology study was performed to evaluate the potential role of homologous vaccination in driving IBV evolution. This was undertaken by assessing IBV viral RNA sequences from the ORF encoding the S1 portion of viral surface glycoprotein (S) before and after the introduction of a new live vaccine on broiler farms in northern-Italy. The results of several biostatistics analyses consistently demonstrate the presence of a higher pressure in the post-vaccination period. Natural selection was detected essentially on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. This evidence strongly supports the action of vaccine-induced immunity in conditioning viral evolution, potentially leading to the emergence of new vaccine-escape variants. The great plasticity of rapidly-evolving RNA-viruses in response to human intervention, which extends beyond the poultry industry, is demonstrated, claiming further attention due to their relevance for animal and especially human health

A shift in Porcine circovirus 3 (PCV‐3) history paradigm: Phylodynamic analyses reveal an ancient origin and prolonged undetected circulation in the worldwide swine population

The identification of a new circovirus (Porcine circovirus 3, PCV-3) has raised a remarkable concern because of some analogies with Porcine circovirus 2 (PCV-2). Preliminary results suggest an extremely recent PCV-3 emergence and high mutation rate. Retrospective studies prove its circulation at least since the early 1990s, revealing that PCV-3 could have been infecting pigs for an even longer period. Therefore, a new evaluation, based on an updated collection of PCV-3 sequences spanning more than 20 years, is performed using a phylodynamic approach. The obtained results overrule the previous PCV-3 history concept, indicating an ancient origin. These evidences are associated with an evolutionary rate far lower (10 −5 –10 −6 substitution/site/ year) than the PCV-2 one. Accordingly, the action of selective pressures on PCV-3 open reading frames (ORFs) seems to be remarkably lower compared to those acting on PCV-2, suggesting either a reduced PCV-3 plasticity or a less efficient host-induced natural selection. A complex and not-directional viral flow network is evidenced through phylogeographic analysis, indicating a long lasting circulation rather than a recent emergence followed by spreading. Being recent emergence has been ruled out, efforts should be devoted to understand whether its recent discovery is simply due to improved detection capabilities or to the breaking of a previous equilibrium.info:eu-repo/semantics/publishedVersio

Effect of changes of vaccination strategies on IBV epidemiology, diagnosis and control: an Italian retrospective study

Infectious bronchitis virus (IBV) is among the most impactful poultry pathogens, whose control, based on biosecurity and routine vaccination, is hampered by the existence of countless genetic variants sharing poor cross‑protection. A retrospective study was conducted on IBV positive samples collected in Italian broiler farms from 2012 to 2019. In 2015, the adopted vaccination protocol shifted from a Mass and 793B‑based vaccines to the administration of Mass and QX vaccines, allowing to study how changes in vaccination strategies may affect IBV epidemiology, control and diagnosis in the field. The most frequently detected lineages were QX (70.3%), 793B (15.8%) and Mass (11.9%). The relative frequencies of QX and 793B detections remained stable throughout the study, while Mass detections significantly increased after the vaccination change. Rather than to an actual growth of Mass population size, this finding may be attributable to different vaccine interactions, with Mass strains being more frequently concealed by 793B vaccines than by QX ones. Based on the obtained results, the two vaccination protocols appear to be similarly effective in fighting IB outbreaks, which in the last decade have been caused primarily by QX field strains in Italy. These results indicate that vaccination strategies may significantly affect IBV epidemiology and diagnosis, and should therefore be considered when choosing and interpreting diagnostic assays and planning control measures

Detection and Molecular Characterization of a Novel Species of Circovirus in a Tawny Owl ( Strix aluco) in Southern Italy

Thanks to recent developments in molecular methods, many new species have been discovered within the genus Circovirus, which comprises viruses of veterinary relevance found in a broad range of hosts. In particular, several circoviruses are known to infect birds, often causing immunosuppression and feathering disorders. Nonetheless, nothing is known about their circulation in birds of prey. In this study, samples from 61 birds of prey representing ten different species, recovered by a wildlife rescue centre in Southern Italy, were taken at necropsy and analysed by PCR with pan-Circovirus primers. Only one sample, collected from a tawny owl (Strix aluco), tested positive. Its genome, sequenced by primer walking, displays the typical features of circoviruses. Based on demarcation criteria, the detected strain qualifies as a novel species, which was named "tawny owl-associated circovirus" (ToCV). Phylogenetically, ToCV clustered with mammalian rather than avian circoviruses, and its closeness to a rodent circovirus suggests that its host may have been a micromammal eaten by the tawny owl. On the other hand, its detection in the spleen fits with the tropism of other avian circoviruses. Little can be therefore said on its biology and pathogenicity, and further efforts are needed to better characterize its epidemiology

Development and validation of direct PCR and quantitative PCR assays for the rapid, sensitive, and economical detection of porcine circovirus 3

Since the identification of species Porcine circovirus 2, the relevance of genus Circovirus has increased given its impact on the swine industry. A new species (Porcine circovirus 3, PCV-3) has been detected in association with various clinical conditions. Consequently, there is an urgent need for reliable and widely accessible tests for both routine diagnostic and research purposes. We developed a direct PCR (requiring no DNA extraction) and a quantitative (q)PCR targeting the conserved rep gene to detect the PCV-3 genome. Test performance was assessed by testing 120 field samples within different matrices. Both methods were sensitive (detection of 10 viral genome/µL), specific, and repeatable. The substantially perfect agreement between the 2 assays strongly supports their high sensitivity and specificity. The low cost and short processing time of the direct PCR protocol, together with the reliable quantitative results provided by qPCR, support the establishment of common testing guidelines.info:eu-repo/semantics/acceptedVersio

Wilder than intense: higher frequency, variability, and viral flows of porcine circovirus 3 in wild boars and rural farms compared to intensive ones in northern Italy

IntroductionPorcine circovirus 3 (PCV-3) was firstly reported in 2017. Although evidence of its pathogenic role has been provided, its clinical relevance seems lower than Porcine circovirus 2 (PCV-2), as well as its evolutionary rate. Different studies have reported a high PCV-3 prevalence in wild boars, sometimes higher than the one observed in commercial pigs. Nevertheless, to date, few studies have objectively investigated the relationships between these populations when inhabiting the same area. Moreover, the role of small-scale, backyard pig production in PCV-3 epidemiology is still obscure.MethodsThe present study investigated PCV-3 occurrence in 216 samples collected from the same area of Northern Italy from commercial and rural pigs, and wild boars. PCV-3 presence was tested by qPCR and complete genome or ORF2 sequences were obtained when possible and analysed using a combination of statistical, phylogenetic and phylodynamic approaches.ResultsA higher infection risk in wild boars and rural pigs compared to the commercial ones was demonstrated. The phylodynamic analysis confirmed a larger viral population size in wild and rural populations and estimated a preferential viral flow from these populations to commercial pigs. A significant flow from wild to rural animals was also proven. The analysis of the Italian sequences and the comparison with a broader international reference dataset highlighted the circulation of a highly divergent clade in Italian rural pigs and wild boars only.DiscussionOverall, the present study results demonstrate the role of non-commercial pig populations in PCV-3 maintenance, epidemiology and evolution, which could represent a threat to intensive farming

D for dominant: porcine circovirus 2d (PCV-2d) prevalence over other genotypes in wild boars and higher viral flows from domestic pigs in Italy

IntroductionPorcine circovirus 2 (PCV-2) is a key pathogen for the swine industry at a global level. Nine genotypes, differing in epidemiology and potentially virulence, emerged over time, with PCV-2a, -2b, and -2d being the most widespread and clinically relevant. Conversely, the distribution of minor genotypes appears geographically and temporally restricted, suggesting lower virulence and different epidemiological drivers. In 2022, PCV-2e, the most genetically and phenotypically divergent genotype, was identified in multiple rural farms in North-eastern Italy. Since rural pigs often have access to outdoor environment, the introduction from wild boars was investigated.MethodsThrough a molecular and spatial approach, this study investigated the epidemiology and genetic diversity of PCV-2 in 122 wild boars across different provinces of North-eastern Italy.ResultsMolecular analysis revealed a high PCV-2 frequency (81.1%, 99/122), and classified the majority of strains as PCV-2d (96.3%, 78/81), with sporadic occurrences of PCV-2a (1.2%, 1/81) and PCV-2b (2.5%, 2/81) genotypes. A viral flow directed primarily from domestic pigs to wild boars was estimated by phylogenetic and phylodynamic analyses.DiscussionThese findings attested that the genotype replacement so far described only in the Italian domestic swine sector occurred also in wild boars. and suggested that the current heterogeneity of PCV-2d strains in Italian wild boars likely depends more on different introduction events from the domestic population rather than the presence of independent evolutionary pressures. While this might suggest PCV-2 circulation in wild boars having a marginal impact in the industrial sector, the sharing of PCV-2d strains across distinct wild populations, in absence of a consistent geographical pattern, suggests a complex interplay between domestic and wild pig populations, emphasizing the importance of improved biosecurity measures to mitigate the risk of pathogen transmission

Evolution of infectious bronchitis virus in the field after homologous vaccination introduction

International audienceAbstractDespite the fact that vaccine resistance has been typically considered a rare phenomenon, some episodes of vaccine failure have been reported with increasing frequency in intensively-raised livestock. Infectious bronchitis virus (IBV) is a widespread avian coronavirus, whose control relies mainly on extensive vaccine administration. Unfortunately, the continuous emergence of new vaccine-immunity escaping variants prompts the development of new vaccines. In the present work, a molecular epidemiology study was performed to evaluate the potential role of homologous vaccination in driving IBV evolution. This was undertaken by assessing IBV viral RNA sequences from the ORF encoding the S1 portion of viral surface glycoprotein (S) before and after the introduction of a new live vaccine on broiler farms in northern-Italy. The results of several biostatistics analyses consistently demonstrate the presence of a higher pressure in the post-vaccination period. Natural selection was detected essentially on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. This evidence strongly supports the action of vaccine-induced immunity in conditioning viral evolution, potentially leading to the emergence of new vaccine-escape variants. The great plasticity of rapidly-evolving RNA-viruses in response to human intervention, which extends beyond the poultry industry, is demonstrated, claiming further attention due to their relevance for animal and especially human health

Epidemiologia molecolare del virus della bronchite infettiva: approfondimenti sulle interazioni tra evoluzione virale, diagnosi e controllo

Il virus della bronchite infettiva (IBV) è responsabile di una sintomatologia respiratoria, renale e riproduttiva in polli di tutte le età e categorie produttive, che ne fa uno dei patogeni dal maggior impatto economico e sanitario sull’avicoltura mondiale. La notevole variabilità genetica di IBV, legata alla sua natura di virus a RNA, esita nell’emergenza e nella cocircolazione di innumerevoli varianti genetiche. Questa eterogeneità ha profonde ripercussioni su questioni pratiche quali il controllo della malattia, perseguito tramite elevati standard di biosicurezza uniti alla vaccinazione di massa, e la sua diagnosi, basata principalmente su metodiche molecolari. Ciononostante, queste interazioni non vanno considerate come unidirezionali, in quanto sia le misure di controllo che le procedure diagnostiche adottate possono avere profondi effetti, diretti o indiretti, sull’evoluzione di IBV, oltre che le une sulle altre. Questo lavoro riporta i risultati di numerosi studi che esplorano diversi aspetti dell’epidemiologia di IBV e permettono di approfondire le interconnessioni tra i tre argomenti sopraccitati. Se alcune di esse, come gli effetti della variabilità genetica sull’efficacia dei protocolli vaccinali, risultano ben caratterizzate, altre sono più oscure e spesso trascurate. Le evidenze di campo e sperimentali qui raccolte, unite a una revisione dello stato dell’arte, sono state usate come base per un approccio olistico allo studio di IBV, la cui adozione avvantaggerebbe non solo la nostra comprensione di questo patogeno, ma anche le attuali possibilità di controllo.Infectious bronchitis virus (IBV) is one of the most impactful pathogens for the worldwide poultry industry, being responsible of respiratory, renal and reproductive symptoms in chickens of every age and productive type. Being an RNA virus, IBV is featured by a remarkable genetic variability, resulting in the emergence and cocirculation of a plethora of genetic variants. This heterogeneity has significant practical repercussions on its control, which is pursued through high standards of biosecurity along with mass vaccination, and diagnosis, mainly achieved with the use of molecular methods. However, this interplay should not be considered as unidirectional. In fact, the adopted control measures and diagnostic procedures may have profound effects, either direct or indirect, on IBV evolution and also on each other. This work reports the results of several studies that explore different aspects of IBV epidemiology and provide novel insights on the interactions between these three subjects. While some of them, like the way in which genetic variability drives the choice of vaccination protocols, are fairly well-known, others are less evident and often overlooked. The collected field and experimental evidence, along with a review of the current literature, served as the basis of a comprehensive approach towards the study of IBV, whose adoption would benefit not only the knowledge of this challenging pathogen, but also our control capabilities

Infectious Bronchitis Virus Evolution, Diagnosis and Control

RNA viruses are characterized by high mutation and recombination rates, which allow a rapid adaptation to new environments. Most of the emerging diseases and host jumps are therefore sustained by these viruses. Rapid evolution may also hinder the understanding of molecular epidemiology, affect the sensitivity of diagnostic assays, limit the vaccine efficacy and favor episodes of immune escape, thus significantly complicating the control of even well-known pathogens. The history of infectious bronchitis virus (IBV) fits well with the above-mentioned scenario. Despite being known since the 1930s, it still represents one of the main causes of disease and economic losses for the poultry industry. A plethora of strategies have been developed and applied over time, with variable success, to limit its impact. However, they have rarely been evaluated objectively and on an adequate scale. Therefore, the actual advantages and disadvantages of IBV detection and control strategies, as well as their implementation, still largely depend on individual sensibility. The present manuscript aims to review the main features of IBV biology and evolution, focusing on their relevance and potential applications in terms of diagnosis and control