Molecular Epidemiology of Circulating Human Rhinovirus/Enterovirus in Children and Adults with Acute Respiratory Infections at a Tertiary Hospital in Free State

Abstract

Background: The study focuses on the prevalence and molecular characterization of human rhinoviruses (HRV) and/enteroviruses (EV), describing circulating HRV genotypes in children and adults with acute respiratory infections managed in the Free State province public sector hospitals between January – October 2024. Methods: This descriptive, cross-sectional study analysed nasopharyngeal samples from patients with acute respiratory infections (ARI). RNA from stored samples was extracted, reverse transcribed into cDNA and amplified using nested PCR targeting the VP4/VP2 region. Sequencing was performed on the ONT platform, followed by phylogenetic analysis using iqtree2. Data on patient demographics, clinical details, and Ct values were obtained from the NHLS database, and statistical analysis was conducted to identify significant findings (p < 0.05). Results: The detection rate for circulating respiratory viruses in the Free State province over the study period (10 months) was 59.5% (329/553). Of the 329 samples, 82 (24.9%) were adults and 247 (75.1%) children - with a predominance of infants (n=137; 55.5%). The median age (interquartile range [IQR] of the adult study participants was 26.5 years [32 -58.5] and that of children 1.89 years [0.11 - 2 years]. Human rhinovirus was positive in 35.3% (116/329) of the samples, however only 30 samples were appropriate for genotyping. The majority of viruses occurred as single detections (n=79; 69.1%) however, 37(31.9%) positive for HRV were also positive for another pathogen. RSV was the most common pathogen (n=16; 43 %) found in viral co-detections. Twenty-one samples were successfully genotyped into HRV genotype A, B and C. The majority (n=15, 71.4%) yielded genotype C. HRV genotypes A and B were detected at a frequency of 5 (23.8%) and 1 (4.8%) respectively. Association of HRV genotype C with severity of disease was not undertaken. Conclusion: All three genotypes of HRV were identified in our study cohort, although HRV-C was the commonest, followed by HRV-A and only one HRV-B. HRV genotype association with severity of ARI should be conducted in future studies.