Infectious bronchitis virus (IBV) commonly produces a range of genetic sequences during replication, particularly in the spike 1 (S1)-coding portion of the S gene, leading to distinct subpopulations within the broader viral population. It has been shown that certain microenvironments exert selective pressure on the S1-coding sequences and their encoded proteins, influencing the selection of viral subpopulations in these environments. In this study, high-throughput next-generation sequencing (NGS) was used to analyze the S1-coding sequences from tissues of the respiratory, digestive, renal, and reproductive systems of specific pathogen-free (SPF) laying hens. These tissues were collected nine days after infection with the California 1737/04 (CA1737/04) IBV strain, which is known to cause varying degrees of pathology in these tissues. Using a specific bioinformatics pipeline, 27 single nucleotide variants (SNVs) were detected in the S1-coding sequences derived from different tissues. These SNVs shaped multiple subpopulations (SP1–SP15), with SP1 being the core subpopulation present in all tissues, while others were tissue-specific. The IBV RNA loads in the tissues were negatively correlated with the number of SNVs or the Shannon entropy values, and phylogenetic analysis revealed a genetic divergence in the S1-coding sequences from certain tissues with lower viral RNA loads, particularly those from the trachea and ovary. Furthermore, the SNVs were associated with nonsynonymous mutations, primarily located in hypervariable region 2 (HVR 2) within the N-terminal domain of S1 (S1-NTD), except for those in SP7, which was exclusive to the trachea and contained changes in HVR 3 in the C-terminal domain of S1 (S1-CTD). Overall, this study adds to the existing knowledge about IBV evolution by highlighting the role of tissue-specific environments in shaping viral genetic diversity.

This study investigated the impact of poor drinking water quality on infectious bronchitis virus (IBV) pathogenesis. Drinking water samples from Alberta layer farms were assessed based on physical, chemical, and microbiological properties. The highest-scoring field water (FW), which is suboptimal with higher pH, hardness and bicarbonate concentration was selected, transported in clean containers, and used in this control experiment. Forty-eight specific pathogen free White Leghorn chicks were divided into four groups: Tap water non-infected (TW-control), field water non-infected (FW-control), tap water infected (TW-infected), and field water infected (FW-infected). They were maintained on their respective water types for 7 weeks. The IBV genome load was significantly higher in the lungs of the FW-infected when compared to TW-infected group at 4 days post-infection (dpi). The histopathological lesion scores in the trachea and lungs were higher in the FW-infected birds when compared to the uninfected controls at observed time points. However, the histopathological lesion scores in the trachea and lungs of the TW-infected birds were not different when compared to that of FW-infected group. In the lungs, the CD4 + and CD8 + T cell populations were significantly higher in the TW-infected group at observed time points when compared to uninfected controls. However, the CD4 + and CD8 + T cell populations in lungs of the FW-infected birds were not different when compared to that of TW-infected group. In the spleen, CD4 + and CD8 + T cell populations were significantly higher in TW-infected and FW-infected birds when compared to uninfected controls depending on the observed time point and we did not observe differences in CD4 + and CD8 + T cell populations in spleen between TW-infected and FW-infected birds. These findings suggest that sub-optimal drinking water can exacerbate IBV infection by weakening immune responses and increasing disease severity. Further studies are necessary to observe the effect of suboptimal water quality on the development of vaccine-mediated immune response. Understanding these interactions is key for improving water management strategies for maintaining poultry health and productivity.