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The nasopharyngeal swab is commonly used for the diagnosis of SARS-CoV-2 infection. Since the swab is performed in this site, of course, it cannot detect the presence of the virus in other tissue districts such as the lung, brain, or bowel. In the present case report, the nasopharyngeal swab was negative twice. From this, the patient discontinued antiviral therapy. Nasopharyngeal swabs were maintained negative until five days later, when we recorded a severe impairment of the patient’s clinical condition. At this time, the bronchoalveolar lavage was positive for SARS-CoV-2. The purpose of the case herein described is to suggest paying attention to the nasopharyngeal swab result. A negative detection in nasopharyngeal swab could not be indicative of COVID-19 recovery.