Phylogenetic Reconstruction and Homology Modeling Reveal Genotypic Diversity and Immune Dysregulation in Children with Rhinovirus- Associated Pneumonia

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Background Rhinoviruses (RVs) are the most frequent cause of community acquired pneumonia in children and the major cause of exacerbations of chronic obstructive pulmonary disease, leading to substantial morbidity, mortality and hospital admission. The spectrum of RV serotypes in circulation, their genetic variability and immune responses could be implicated in the etiology of disease severity. During rhinovirus infection, both antiviral immunity and pro-inflammatory responses play a critical role in the clearance of the virus. A variation in these responses leads to deficient clearing of the virus and sustained inflammation. Materials and methods The study specimens were obtained from pediatric pneumonia patients (n = 374) attending the outpatient department (OPD) or admitted to the intensive care unit (ICU) at King Fahad Medical City. All patient’ samples testing positive for rhinovirus (n = 102) by conventional nested reverse transcription PCR (RT-PCR) assay were used for genetic sequencing by Sanger sequencing and phylogenetic analyses. The clinical datasets used and analyzed during the current study are available from the corresponding author on request. Results We investigated 374 children with pneumonia and RV was detected in 27% with radiological evidence of consolidation and ground glass opacities in the lung. Genetic sequencing and homology 3D modeling revealed changes at amino terminal of conserved Viral Protein 4 (VP4) epitope in RV-A101 serotype especially serine at several positions that is important for interactive binding with the host immune cells. We found dysregulation of pulmonary gene expression of Th1- and Th2 cytokines and chemokines in RV-A 101 and RV-C 8 associated pneumonia patients, and found that 29 genes were overexpressed. IFN-γ (Interferon gamma) and IL-18 (Interleukin or interferon-gamma-inducing factor) mRNA expression levels were significantly upregulated in the RV-A101-associated pneumonia patients. Conclusion This study provided evidence of mutations at the amino terminal of the conserved VP4 epitope that could shape the immune response as well as affect the cross neutralizing capacity of the conserved epitopes, thus helping RVs escape the immune responses. Further functional studies are needed to determine any changes in the cross serotype virus neutralization ability for vaccine development.