This study examined the presence and diversity of fungal taxa in the eyes and noses of COVID-19 patients. We collected sixty samples from COVID-19 patients and recovered about 30 fungal isolates. Six species of fungi were identified as Aspergillus niger (40%), A. flavus (23.33%), A. parasiticus (13.33%), Alternaria alternata (10%), Fusarium oxysporum (10%), and Candida albicans (3.33%), respectively.  We initially isolated A. niger from the pulmonary system. Its virulence factors were more prominent than those of other taxa isolated from the eyes, suggesting a significant risk to the patients. We studied the serum immunoglobulin (IgG and IgM) levels of COVID-19 patients and controls. The results showed that a week after infection, the IgG level was 12.74 AU/ml, significantly higher than the healthy control, which ranged from 12–15 AU/ml for negative and 0.73 for positive. During the first week of infection, IgM reached 3.1 AU/ml, and in the fourth week, IgG rose to 53.63 AU/ml, whereas IgM levels fell to 0.73. These findings provide valuable information on COVID-19 patients' immune responses and how they evolve over time. Our study also compared COVID-19 patients' WBC levels to those of the control group. The median was 40, with 10% of patients having low WBC counts and 50% having high ones. Lymphocyte counts differed significantly between 47.5% (low count) and 17.5% (high count). Patients had normal neutrophil counts, with 5% having low counts and 45% having high counts, like the control group. Monocyte, eosinophil, and basophil counts were likewise similar to those in the control group.