Prolonged presence of SARS-CoV-2 viral RNA in faecal samples

Abstract

We present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR results of all respiratory and faecal samples from patients with coronavirus disease 2019 (COVID-19) at the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China, throughout the course of their illness and obligated quarantine period. Real-time RT-PCR was used to detect COVID-19 following the recommended protocol (appendix 2, p 1). Patients with suspected SARS-CoV-2 were confirmed after two sequential positive respiratory tract sample results. Respiratory and faecal samples were collected every 1–2 days (depending on the availability of faecal samples) until two sequential negative results were obtained. We reviewed patients’ demographic information, underlying diseases, clinical indices, and treatments from their official medical records. The study was approved by the Medical Ethical Committee of The Fifth Affiliated Hospital of Sun Yat-sen University (approval number K162-1) and informed consent was obtained from participants. Notably, patients who met discharge criteria were allowed to stay in hospital for extended observation and health care. Between Jan 16 and March 15, 2020, we enrolled 98 patients. Both respiratory and faecal samples were collected from 74 (76%) patients. Faecal samples from 33 (45%) of 74 patients were negative for SARS CoV-2 RNA, while their respiratory swabs remained positive for a mean of 15·4 days (SD 6·7) from first symptom onset. Of the 41 (55%) of 74 patients with faecal samples that were positive for SARS-CoV-2 RNA, respiratory samples remained positive for SARS-CoV-2 RNA for a mean of 16·7 days (SD 6·7) and faecal samples remained positive for a mean of 27·9 days (10·7) after first symptom onset (ie, for a mean of 11·2 days [9·2] longer than for respiratory samples). The full disease course of the 41 patients with faecal samples that were positive for SARS-CoV-2 RNA is shown in the figure. Notably, patient 1 had positive faecal samples for 33 days continuously after the respiratory samples became negative, and patient 4 tested positive for SARS-CoV-2 RNA in their faecal sample for 47 days after first symptom onset (appendix 2, pp 4–5). A summary of clinical symptoms and medical treatments is shown in the appendix 2 (pp 2–3, 6–8). The presence of gastrointestinal symptoms was not associated with faecal sample viral RNA positivity (p=0·45); disease severity was not associated with extended duration of faecal sample viral RNA positivity (p=0·60); however, antiviral treatment was positively associated with the presence of viral RNA in faecal samples (p=0·025; appendix 2, pp 2–3). These associations should be interpreted with caution because of the possibility of confounding. Additionally, the Ct values of all three targeted genes (RdRp, N, E) in the first faecal sample that was positive for viral RNA were negatively associated with the duration of faecal viral RNA positivity (RdRp gene r = –0·34; N gene See Online for appendix 2