SARS-CoV-2 Found in Sputum/Feces After Negative Pharyngeal Specimens

The outbreak of coronavirus disease 2019 (COVID-19) has become a global public health problem. In the absence of a specific therapy or vaccine, timely diagnosis and the establishment of a sufficient isolation period for infected individuals are critical to containment efforts.

Real-time quantitative fluorescence polymerase chain reaction (RT-qPCR) testing of respiratory specimens for SARS–CoV-2 RNA is currently used for case diagnosis and to guide the duration of patient isolation or hospital discharge. However, specimens that are positive on RT-qPCR have, however, also been reported from blood, feces, and urine.


A large team of scientists led by those at Beijing Ditan Hospital (Beijing, China) retrospectively identified a convenience sample of patients admitted to Beijing Ditan Hospital, Capital Medical University with a diagnosis of COVID-19 and paired RT-PCR testing of pharyngeal swabs with either sputum or feces. The RT-qPCR assay targeted the open reading frame 1ab (ORF1ab) region and nucleoprotein (N) gene with a negative control. A cycle threshold value of 37 or less was interpreted as positive for SARS–CoV-2.

The team reported that among 133 patients admitted with COVID-19 from 20 January to 27 February 2020, they identified 22 with an initial or follow-up positive sputum or fecal samples paired with a follow-up negative pharyngeal sample. Of these patients, 18 were aged 15 to 65 years, and four were children; 14 were male; and 11 had a history of either travel to or exposure to an individual returning from Hubei Province in the past month. Fever was the most common initial onset symptom. Five patients had at least one preexisting medical condition.

The scientists collected 545 specimens from 22 patients, including 209 pharyngeal swabs, 262 sputum samples, and 74 feces samples. In these patients, sputum and feces remained positive for SARS–CoV2 on RT-qPCR up to 39 and 13 days, respectively, after the obtained pharyngeal samples were negative. It is important to emphasize, however, that it is not known whether the positive RT-qPCR results for SARS–CoV2 observed here indicate that a patient continues to pose a risk for infection to others. The study was published on March 30, 2020 in the journal Annals of Internal Medicine.

Related Links:
Beijing Ditan Hospital