(1) Background: After an acute SARS-CoV-2 infection, patients are at risk of developing Long COVID, with fatigue as a frequent and serious health problem. Objectives: To identify symptom clusters in acute SARS-CoV-2 infections and investigate their associations with the development of Long COVID fatigue, and to examine sex-specific differences. (2) Methods: The analysis included a total of 450 COVID-19 outpatients, of whom 54.4% were female. The median ages of the men and women were 51 years (IQR 36.0; 60.0) and 48 years (IQR 33.0; 57.0), respectively. Data collection took place between November 2020 and May 2021, with a median time between acute SARS-CoV-2 infection and examination in the study center of 240 days (IQR 133; 326). The Fatigue Assessment Scale (FAS) was used to identify fatigue and its severity. A multiple correspondence analysis was used to group forty-two COVID-19 symptoms into seven symptom clusters. Logistic and log-linear regressions were used to investigate associations between acute symptom clusters and Long COVID fatigue as dichotomous and continuous outcome, respectively. (3) Results: Fatigue occurred more frequently in women than in men (45% vs. 25%) and the median FAS score, indicating severity of fatigue, was higher in women than in men. The comparison between men and women revealed notable differences in four out of seven clusters. The strongest associations between symptom clusters in infection and Long COVID fatigue were identified for the cluster “cognitive and mental symptoms”. In the log-linear regression model, each additional symptom in this cluster was associated with an increase of the FAS score by 5.13% (95% CI: [0.04; 0.07]; p < 0.001). The results of the logistic regression models supported this finding. Each additional symptom in this symptom cluster increased the odds of fatigue by 42% (95% CI: [1.23; 1.66]; p < 0.001). (4) Conclusions: In our study in COVID-19 outpatients, a strong association was observed between the number of symptoms in the cluster “cognitive and mental symptoms” during acute SARS-CoV-2 infection and the risk of developing fatigue months later. The consequent use of preventive and therapeutic strategies is necessary to decrease the burden of fatigue in the context of Long COVID.
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