Validation of High-Sensitivity Severe Acute Respiratory Syndrome Coronavirus 2 Testing for Stool - Toward the New Normal for Fecal Microbiota Transplantation

Ahmed Babiker, Jessica M. Ingersoll, Max W. Adelman, Andrew S. Webster, Kari J. Broder, Victoria Stittleburg, Jesse J. Waggoner, Colleen S. Kraft, Michael H. Woodworth

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


INTRODUCTION:Mounting evidence demonstrates potential for fecal-oral transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The US Food and Drug Administration now requires SARS-CoV-2 testing of potential feces donors before the use of stool manufactured for fecal microbiota transplantation. We sought to develop and validate a high-sensitivity SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) procedure for testing stool specimens.METHODS:A modified extraction method was used with an RT-PCR assay adapted from the Centers for Disease Control and Prevention PCR protocol for respiratory specimens. Contrived specimens were created using pre-COVID-19 banked stool specimens and spiking in known concentrations of SARS-CoV-2-specific nucleic acid. 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 clinical performance of the assay was evaluated with stool samples collected from 17 nasopharyngeal swab RT-PCR-positive patients and 14 nasopharyngeal RT-PCR-negative patients.RESULTS:The dual-target and single-target limit of detection were 56 copies/L and 3 copies/L, respectively. SARS-CoV-2 was detected at concentrations as low as 0.6 copies/L. 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 value < 0.001).DISCUSSION:The described RT-PCR test is a sensitive and flexible approach for the detection of SARS-CoV-2 in stool specimens. We propose an integrated screening approach that incorporates this stool test to support continuation of fecal microbiota transplantation programs.

Original languageEnglish (US)
Pages (from-to)E00363
JournalClinical and translational gastroenterology
Issue number6
StatePublished - Jun 9 2021

ASJC Scopus subject areas

  • Gastroenterology


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