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

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.

Pathological, Immunohistochemical, and Molecular Study of Avian Infectious Bronchitis Virus in Egypt

“…One of the main pathogens affecting poultry that causes severe financial losses is the infectious bronchitis virus. IBV is well-known for its ability to generate many different types of strains that making vaccinations control is difficult to fully manage the disease [1,22]. IBV pathogenesis and diagnosis have been investigated using a variety of methods [23,24].…”

“…Avian infectious bronchitis is a serious and extremely contagious upper respiratory viral infection that affects the world poultry industry. IBV has high virulence, quick distribution, and presence of several serotypes with little cross-protection across types [1]. It belongs to family Corona viridae and subfamily Corona virinae of gamma corona viruses.…”

The Effect of Global Spread, Epidemiology, and Control Strategies on the Evolution of the GI-19 Lineage of Infectious Bronchitis Virus

“…In contrast to the remarkable local dispersal, rare long-distance or intercontinental introduction events were inferred. This distribution pattern may be explained by the requirement for relatively direct contact, unlikely to occur between countries lacking strong commercial or cultural ties [ 38 ]. However, a small Asian clade stemming from the European one was present ( Supplementary Figure S1 ).…”

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

“…More complete IBV GI-23 nucleotide sequences datasets (with the S1 gene and partial HVR1/2 regions) were then constructed to obtain trustable phylogenetic and evolutionary analyses. Although S1 complete gene sequencing has been proposed for robust phylogenetic evaluations, partial HVR1/2 has already been demonstrated to be useful for IBV GI-23 evolutionary analyses [ 11 ]. Additionally, an additional procedure was performed to detect recombinant IBV GI-23 sequences.…”

“…IBV GI-23 S1 complete gene and HVR1/2 partial sequences with the collection date and country available in GenBank were downloaded and compared with two previously constructed reference datasets [ 7 , 11 ]. HVR1/2 sequences were extracted from nucleotide positions 112 to 423 of the S1 subunit complete gene, respectively, according to the sequence M21883 [ 2 ].…”