Pathogens
Pan-Coronavirus Molecular Surveillance in Stool Samples from Patients with Acute Gastroenteritis: SARS-CoV-2 as the Only Coronavirus Detected
By Seda Tezcan Ülger, Şeyma AKBULUT, Aslıhan Bekçi and 3 others.
Abstract
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.