Spores of the genus Alternaria, which are a common component of the atmospheric microbiome, are among the important fungal aeroallergens. The study aimed to (1) compare the characteristics of the Alternaria Main Spore Season (MSS) in an urban and rural area, (2) assess the correlation between the airborne concentration of Alternaria spores and Alt a 1 allergen, and (3) identify the environmental factors influencing the intensity of MSS and daily variation of airborne spore and Alt a 1 allergen levels. The airborne spores and allergen were recorded over two years (2022–2023) in the Kaplna village, and over three years (2021–2023) in Bratislava city (Slovakia), using Hirst-type samplers for spores and cyclone samplers for allergen. The intensity of the MSS varied significantly between individual years and locations, demonstrating the influence of environmental conditions. Higher values of the Seasonal Spore Integral (SSIn) were recorded in Kaplna, which has more plant biomass, but higher Spore Allergen Potency (SAP) levels were recorded in Bratislava, with a higher degree of urbanisation. In general, we found a positive correlation between the spore and Alt a 1 levels, but the SAP was negatively correlated with the concentration of spores. Meteorological parameters and air pollutants influenced the levels of spores, allergen, and SAP to a varying degree based on the individual year and location, with the most noticeable influence of relative humidity and precipitation decreasing the concentration of spores and increasing SAP.
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