Pan-Coronavirus Molecular Surveillance in Stool Samples from Patients with Acute Gastroenteritis: SARS-CoV-2 as the Only Coronavirus Detected

Background: Coronaviruses (CoVs) are important human and animal pathogens with respiratory and gastrointestinal tropism and considerable potential for cross-species transmission. Broad molecular surveillance approaches may complement virus-specific assays by facilitating the detection of both known and potentially emerging CoVs in diverse clinical specimens. This study aimed to investigate and molecularly characterize CoVs in stool samples from patients with acute gastroenteritis using a broad-range pan-coronavirus (panCoV) RT-PCR approach and to provide baseline data relevant to future One Health surveillance. Methods: A total of 280 stool samples collected from patients with acute gastroenteritis between November 2021 and October 2022 were analyzed. Viral nucleic acids were subjected to semi-nested panCoV RT-PCR targeting a conserved approximately 600 bp region of the RNA-dependent RNA polymerase (RdRp) gene within the subfamily Orthocoronavirinae. Confirmed amplicons were characterized by Sanger sequencing and BLASTn analysis, and sequences of sufficient quality were further evaluated by phylogenetic analysis. Results: CoV RNA was detected in 20 of 280 stool samples (7.14%, 95% exact CI, 4.42–10.82%). Sequence analysis identified all 20 positive samples as SARS-CoV-2, while phylogenetic analysis of 16 high-quality sequences supported species-level identification. No endemic non-SARS-CoV-2 or zoonotic CoVs were detected by the applied assay in this cohort. In an exploratory analysis, SARS-CoV-2 RNA detection was more frequent among patients receiving chemotherapy and/or immunosuppressive treatment than among those not receiving these therapies (18.4% vs. 5.4%; p = 0.010). Conclusions: Broad-range molecular screening of stool specimens from patients with acute gastroenteritis detected SARS-CoV-2 RNA, whereas no endemic non-SARS-CoV-2 or zoonotic CoVs were detected by the applied assay in this cohort. These findings provide baseline data on coronavirus RNA detection in an underexplored clinical specimen type and support the potential complementary role of stool-based molecular surveillance in future integrated One Health surveillance strategies. Detection of viral RNA alone does not demonstrate viral infectivity or fecal–oral transmission.