Detection of SARS-CoV-2 RNA in stool samples from patients with acute gastroenteritis during a low prevalence endemic period in summer 2023

Introduction

Following its emergence in 2020, we are currently undergoing a transition from a pandemic to an endemic state for SARS-CoV-2. In order to comprehend the endemic nature of the virus, it is feasible to derive epidemiological insights not only from surveillance but also from diagnostic screening tests.

To examine whether persistent shedding of SARS-CoV-2 virus RNA in stool samples occurs in patients with gastroenteritic symptoms during a low prevalence period following the declared end of the SARS-CoV-2 pandemic.

Material and Methods

Stool samples, collected for gastroenteritis screening between June 12, 2023, and July 20, 2023, and initially tested negatively for Adenovirus, Norovirus, Rotavirus, Campylobacter spp., Salmonella spp., Yersinia enterocolitica, Clostridioides difficile, enterohemorrhagic E. coli, enteropathogenic E. coli, and enteroinvasive E. coli, were subjected to testing for SARS-CoV-2 and influenza A/B RNA at our diagnostic laboratory in a tertiary care center in Cologne. Automated nucleic acid extraction using the Maxwell®RSC Blood DNA Kit (Promega), followed by the RIDA®GENE Flu & SARS-CoV-2 PCR assay (R-Biopharm) conducted on a CFX96 real-time cycler (Bio-Rad) was performed.

Routine surveillance data of SARS-CoV-2 positive cases were used.

Results

After the substantial Omicron waves, SARS-CoV-2 RNA and influenza RNA was found in one each out of 103 (0.97%; CI95% 0; 0.029) consecutive stool samples from patients presenting gastroenteritic symptoms during a period of low prevalence.The weekly prevalence of admissions was less than 0.5 per 100 admissions, and there were no occurrences of nosocomial cases throughout the investigation period.

Summary

Given that a substantial portion of the population had been infected by the time the extensive Omicron wave ended, there was a possibility that persistent SARS-CoV-2 in the gastrointestinal tract could be identified in symptomatic patients. However, this expectation did not align with the actual findings.