Genomic alterations of the Infectious Bronchitis Virus (IBV) strain of the GI-23 lineage induced by passages in chickens and quails

Abstract

Infectious bronchitis virus (IBV) of the GI-23 lineage, which first emerged in theMiddle 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 stillunclear. This study aimed to trace the genome evolution of GI-23 IBV in chickens and itsadaptability to quails, which are susceptible to both gamma- and deltacoronaviruses. Thirtyspecific-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 thethird 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 ninemore times during consecutive IBV passages (P-I–P-X), and eventually, virus sequencingwas performed using Next-Generation Sequencing (NGS). The obtained results showedthat quails were not susceptible to the IBV GI-23 lineage, as the virus RNA was detected inlow amounts only during the first passage (QP-I) with no further detections in later roundsof 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 whichcaused amino acid changes, twenty-eight were synonymous, and one SNV introduced astop codon. Three SNVs were found in untranslated regions. However, none of these SNVslasted beyond seven passages, with forty-four being unique SNVs. The Shannon entropyvalues measured during passages varied for pol1a, pol1b, S, 5a, 5b, and N genes, with overallgenome complexity peaking at CP-VI and CP-X. The highest complexity was observed inthe pol1a (CP-X) and S genes (CP-IV, CP-VI, CP-VIII, and CP-X). Along with the S genethat was under positive selection, eight codons in pol1a were also positively selected. Thesefindings suggest that even in an adapted host, IBV variability does not stabilize withoutimmune pressure, indicating continuous molecular changes within its genome.