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Infectious bursal disease virus (IBDV) is a ubiquitous immunosuppressive pathogen which is a severe burden to the poultry industry. Due to frequent mutation and reassortment events, its double-stranded, bi-segmented RNA genome displays a considerable heterogeneity, which in turn produces profound differences in antigenicity and pathogenicity. In recent years, the investigation of IBDV epidemiology has greatly benefited from the proposal of multiple phylogenetic classification systems which prompted the execution of molecular surveys all over the world, producing a wealth of standardized and easily sharable data. The present epidemiological survey was conducted in six Near East and Persian Gulf countries to characterize the field IBDVs circulating in the region. Ninety-three broiler flocks, immunized with different vaccination protocols, were investigated over a one-year period by collecting eight individual bursal samples at a time. Using molecular assays targeting both genome segments, field IBDVs belonging to four genotypes were detected from 42 flocks across all investigated countries. While traditional very virulent IBDVs (genotype A3B2) represented a minority, multiple atypical IBDV genotypes (A3B1, A4B1 and A6B1) were found to circulate in most of the region. Many of the detected strains were related to sequences from other continents, supporting the involvement of the Near and Middle East in complex networks of viral spreading. The obtained results, combined with the available literature, allowed us to update the epidemiological picture, hopefully favouring the identification of epidemiological threats and the planning of effective monitoring and control strategies. Different field IBDVs were found to circulate in the Near and Middle East. Multiple atypical genotypes (A3B1, A4B1, A6B1) were found to circulate extensively. Traditional very virulent IBDVs (A3B2) were a minority of the detected strains. Viral exchanges can be hypothesized between the region and different continents. [ABSTRACT FROM AUTHOR]

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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. 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. [ABSTRACT FROM AUTHOR]