Direct Evidence of Active SARS-CoV-2 Replication in the Intestine

Clin Infect Dis. 2021 Aug 2;73(3):361-366. doi: 10.1093/cid/ciaa925.


Background: Currently, there is no direct evidence to prove the active replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the intestinal tract and relevant pathological changes in the colon and rectum. We investigated the presence of virions and pathological changes in surgical rectal tissues of a patient with clinically confirmed coronavirus disease 2019 (COVID-19) with rectal adenocarcinoma.

Methods: The clinical data were collected during hospitalization and follow-up of this patient. Quantitative reverse transcriptase-polymerasechain reaction (RT-PCR) was performed on the rectal tissue specimens obtained from surgical resection, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa during follow-up after recovery. Ultrathin sections of surgical samples were observed for SARS-CoV-2 virions using electron microscopy. Histopathological examination was performed using hematoxylin-eosin stain. Immunohistochemical analysis and immunofluorescence were carried out on rectal tissues to evaluate the distribution of SARS-CoV-2 antigen and immune cell infiltrations.

Results: The patient had fever and cough on day 3 postoperatively, was diagnosed with COVID-19 on day 7, and was discharged from the hospital on day 41. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens but not in samples collected 37 days after discharge. Notably, coincident with rectal tissues of surgical specimens testing nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Moreover, abundant lymphocytes and macrophages (some were SARS-CoV-2 positive) infiltrating the lamina propria were found with no significant mucosal damage.

Conclusions: We first report the direct evidence of active SARS-CoV-2 replication in a patient's rectum during the incubation period, which might explain SARS-CoV-2 fecal-oral transmission.

Keywords: COVID-19; SARS-CoV-2; coronavirus disease 2019; intestinal infection rectal cancer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19*
  • Hospitalization
  • Humans
  • Intestines
  • Patient Discharge
  • RNA, Viral
  • SARS-CoV-2*


  • RNA, Viral