Background: Reverse transcription polymerase chain reaction (RT-PCR) using lower gastrointestinal (GI) specimens can detect SARS-CoV-2 RNA in patients with gastrointestinal symptoms. However, the association between cycle threshold (Ct) values from such specimens and the presence of GI manifestations remains unclear.

Materials and methods: An analytical cross-sectional study was conducted using secondary, de-identified hospital records from three Indonesian medical centers (July–November 2020). Adult patients with positive lower GI RT-PCR results and available Ct values were included. Ct values were dichotomized as low (<25) or high (≥25). GI symptoms assessed included nausea, vomiting, abdominal pain, diarrhea, and constipation. The primary outcome was the association between Ct category and the presence of any GI symptom, analyzed using Fisher’s exact test. Results are presented as prevalence ratios (PRs) with 95% confidence intervals (CIs).

Results: A total of 37 patients met the inclusion criteria (43.2% male; mean age 44.8 ± 13.2 years). Only one patient (2.7%) exhibited a low Ct value, while 36 (97.3%) had high Ct values. Overall, 22 patients (59.5%) reported at least one GI symptom. The most frequently reported symptom was nausea (54.1%), followed by vomiting (18.9%), abdominal pain (16.2%), and diarrhea (13.5%); constipation was not observed. No significant association was found between Ct category and the presence of GI symptoms (p = 0.595; PR 1.048, 95% CI 0.956–1.148).

Conclusion: Among adults with SARS-CoV-2 detected via RT-PCR from lower GI specimens, Ct value category was not significantly associated with GI symptom presence. These findings underscore the limited prognostic value of Ct values from lower GI sampling and emphasize the need for larger, prospectively designed studies with standardized protocols.