An RT-PCR Test for Detecting SARS-CoV-2 in Stool for Fecal Microbiota Transplantation

To support the continuation of fecal microbiota transplantation (FMT) programs, an integrated screening approach should be included that involves reverse transcriptase polymerase chain reaction (RT-PCR) tests for detecting SARS-CoV-2 in stool specimens, according to a study published in Clinical and Translational Gastroenterology.

As SARS-CoV-2 can be found in stool and may be transmissible via FMT, the United States Food and Drug Administration (FDA) requires screening of potential stool donors for SARS-CoV-2. Thus, researchers sought to develop and validate a high-sensitivity SARS-CoV-2 RT-PCR procedure for testing stool specimens.

A modified extraction method was used with an RT-PCR assay adapted from the Centers for Disease Control and Prevention (CDC) PCR protocol for respiratory specimens. Specimens were created using pre-COVID-19 banked stool samples, collected from May 2020 through September 2020, and spiking in known concentrations of SARS-CoV-2-specific nucleic acids.

The highest transcript concentration at which 2/2 or 1/2 SARS-CoV-2 targets were detected in 9/10 replicates was defined as the dual-target limit and single-target limit of detection, respectively. The researchers then evaluated the clinical performance of the stool samples collected from 17 nasopharyngeal swab RT-PCR-positive patients and 14 nasopharyngeal RT-PCR-negative patients.

Investigators found that the dual-target and single-target limits of detection were 56 copies/µL and 3 copies/µL, respectively. SARS-CoV-2 was detected at concentrations as low as 0.6 copies/µL , and clinical stool samples from known COVID-19-positive patients demonstrated the detection of SARS-CoV-2 in stool up to 29 days from symptom onset, with a high agreement with nasopharyngeal swab tests (kappa statistic of 0.95; P <.001).

In the 17 nasopharyngeal swab RT-PCR-positive patients, SARS-CoV-2 was detected in 16, with 14/16 patients testing positive for both dual- and single-target limits of detection. Among the 14 nasopharyngeal RT-PCR-negative patients, SARS-CoV-2 was not detected in any stool samples. This result demonstrated high agreement between nasopharyngeal and stool RT-PCR testing (P <.001).

Investigators acknowledge limitations to their study, including the small sample size.

“Further studies are required to explore the true prevalence of fecal shedding in those with confirmed COVID-19, duration of shedding in stool and, most importantly, the role of virus found (via RT-PCR or culture) as a source of transmission,” the authors concluded.

Disclosure: This study was funded in part by the Centers for AIDS Research and the National Institute of Allergy and Infectious Diseases of the National Institutes of Health. Please refer to the original reference for a full list of funding sources.


Babiker A, Ingersoll JM, Adelman MW, et al. Validation of high-sensitivity severe acute respiratory syndrome coronavirus 2 testing for stool—toward the new normal for fecal microbiota transplantation. Clin Transl Gastroenterol. 2021;12(6): e00363. doi: 10.14309/ctg.0000000000000363