Non-Invasive Specimen Collection in COVID-19 RT-PCR Testing: An Observational Study at an Indonesian Tertiary Hospital

Background: COVID-19 is a disease of SARS-CoV2 beta coronavirus infection. One way to control the progression of COVID-19 symptoms is a rapid and accurate diagnosis. The current gold standard of COVID-19 diagnostic method uses RT-PCR from nasopharyngeal (NP) swabs and sputum specimens. Objective: To assess the efficacy of saliva and rectal swabs as non-invasive alternatives to the conventional nasopharyngeal swab for RTPCR testing in COVID-19 diagnosis, with a focus on the potential benefits for healthcare providers and patient comfort. Methods: This observational study was conducted with 80 confirmed cases at a tertiary hospital in Indonesia, the study compared RTPCR positivity rates among different collection methods. Results: A high positivity rate of 92% for nasopharyngeal swabs, with saliva and rectal swabs yielding 36% and 34%, respectively. Notably, the positivity rates for saliva and rectal samples increased to 60% and 50% when testing occurred between five to seven days post-symptom onset. Crucially, in older patients, both saliva and rectal swabs demonstrated higher positivity rates than in younger patients within the initial four days of symptom onset, with rates of 43% and 17%, respectively. Furthermore, a significant correlation was found between rectal swab positivity on day one and mortality in the older cohort, where lower Ct values on day seven were significantly associated with the deceased group. Conclusion: These findings support the potential of saliva and rectal swabs in predicting disease severity and patient outcomes, suggesting a safer and more convenient testing strategy for COVID- 19.