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In 2020 a new coronavirus disease spread to millions of people worldwide causing a pandemic. Some experienced long-term consequences of the infection with prolonged symptoms affecting the ability to function in everyday life. However, it is not known if long-term consequences are different than other infectious diseases. The purpose of this study was to assess whether COVID-19 infection could induce long-term effects on physical and mental health that differed significantly from other infectious diseases with similar initial symptoms. We conducted a questionnaire study approximately two years after testing patients for COVID-19 infection in the period between March 1st and May 31st, 2020. The participants had been tested for COVID-19 in a hospital in Denmark during the first wave of the pandemic because they had considerable symptoms of a respiratory infection. They all received questionnaires approximately two years after being tested. The survey consisted of validated questionnaires providing data on self-assessed health status (SF-12) and data on self-evaluated work-related functional ability (WORQ). The answers were compared between two groups: COVID-positive and non-COVID-positive. Data on COVID-status was retrieved from a PCR test in 2020 and from the questionnaire sent out during spring 2022. A total of 463 participants answered the questionnaire (response rate 17%). Compared with nonworking participants, occupational active participants had a higher rate of COVID-19 infection. We found no significant differences in work-related functional ability (WORQ) or in self-assesed health status (PCS) between PCR-COVID-negative participants and the PCR-positive participants when adjusted for relevant confounders. The mental health status (MCS) was slightly higher in non-COVID-19 participants compared to COVID-positive participants when adjusted for working status (49.3 vs. 47.5, p < 0.009). Our study indicates that the impact from COVID-19 infection on long-term self-rated physical health and work-related functioning is comparable between participants tested positive for COVID-19 and participants who had similar acute symptoms but tested negative for COVID-19. Our results emphasize the need for comprehensive rehabilitation strategies focusing on symptom management, irrespective of the specific viral cause.