Identification of the SARS-CoV-2 Genome in Various Systemic Samples from the Laboratory of Confirmed COVID-19 Patients in Iran

Background: COVID-19 is a highly contagious respiratory illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While nasopharyngeal swab testing remains the primary method for identifying SARS-CoV-2 carriers, the virus’s genetic material can be detected in various bodily samples, suggesting potential transmission through non-respiratory routes. Objectives: This study aimed to investigate the presence and quantity of SARS-CoV-2 RNA in stool, endotracheal tube (ETT) samples, cerebrospinal fluid (CSF), bronchoalveolar lavage (BAL), and sputum. The research sought to correlate these findings with clinical characteristics and the severity of illness. Methods: We retrospectively collected 1,567 samples, including 550 BAL samples, 464 ETT samples, 45 fecal samples, 21 CSF samples, and 487 sputum samples from patients admitted to Namazi Hospital between April 1, 2020, and the end of September 2022. Clinical characteristics, patient demographics, radiographic, and laboratory results were among the medical data gathered and assessed. We used reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect and measure SARS-CoV-2 RNA shedding in different samples of individuals infected with COVID-19. Results: Among the 550 BAL samples collected from patients, 20.7% tested positive for SARS-CoV-2. Additionally, the virus’s genome was detected in 17.8% of 45 CSF samples, 11% of 464 ETT samples, 4.76% of 21 fecal samples, and 2.9% of 487 sputum samples. Notably, patients with SARS-CoV-2-positive BAL samples exhibited a significantly higher frequency of cough and dyspnea than those who tested negative. Conclusions: These findings revealed that SARS-CoV-2 has been detected in diverse specimens collected from the upper and lower respiratory systems (sputum, ETT, and BAL samples), the central nervous system (CSF), and the digestive tract (fecal samples) during the infection’s progression. This widespread presence significantly impacts our understanding of the disease’s pathogenesis and enhances diagnostic capabilities, proving a valuable asset in managing the infection.