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Objective: To investigate the efficacy and optimal timing of prophylactic medication before pollen season for children with seasonal allergic rhinitis (AR) and allergic asthma (AA) in Hohhot. Methods: A prospective, self-controlled study was conducted. Children aged 4-14 years who were diagnosed with AR or AR+AA in Hohhot First Hospital from January to August 2024 were enrolled, with the same patients undergoing self-medication in 2024 pollen season as the controls. Before 2025 pollen season, children were stratified into eight groups based on disease type (AR/AR+AA), severity of disease (mild/moderate-severe), and onset season (spring/autumn). For each group, prophylactic medication was initiated at 5, 10, 15, and 20 days before the season, respectively. Symptom onset time, symptomatic days, visual analogue scale (VAS) score, total medication score (TMS), and childhood asthma control test (C-ACT) score were compared between the two groups. Results: A total of 312 children were included in the study, consisting of 183 males (58.7%) and 129 females (41.3%), with a mean age of (8.6±3.0) years. After initiating medication 5, 10, and 15 days before the season for mild spring, moderate-severe spring and mild autumn, and moderate-severe autumn AR cases, respectively, children experienced significantly shorter symptomatic periods and lower VAS scores than those in the self-medication group (all P<0.01). For children with AR+AA, clinical indicators (symptomatic days, VAS score, and C-ACT score) were significantly improved after initiating medication 15 days in advance for mild spring cases and 20 days in advance for other subgroups (all P<0.01). The proportions of pre-season symptoms in the prophylactic medication groups were lower, and TMS scores were higher (all P<0.01). Conclusion: Stratified prophylactic medication based on disease severity before the pollen season can delay symptom onset, alleviate symptom severity, and shorten the duration of symptoms in children with AR and AA.