The performance of gargling for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcriptase (RT)-PCR testing has not been previously reviewed. This review systematically assessed the performance of saline and water gargling for SARS-CoV-2 RT-PCR testing in the settings of diagnosing and monitoring viral shedding.

Introduction: Mass testing is essential in the surveillance strategy for fighting the COVID-19 pandemic. It allows early detection of suspected cases and subsequently early isolation to mitigate spread. However, the high cost and limited consumables and reagents hinder the mass testing strategy in developing countries such as Indonesia. The specimen pooling strategy is an option to perform mass screening with limited resources. This study aims to determine the positivity rate cut-off and to evaluate the efficiency of pooling strategy for the laboratory diagnosis of COVID-19.

Methodology: Between August 4th, 2020, and November 11th, 2020, a four-sample pooling strategy testing to detect SARS-CoV-2 was carried out at the Microbiology Diagnostic Laboratory of Diponegoro National Hospital, Semarang, Indonesia. Pools with positive results were subjected to individual specimen retesting. Spearman’s correlation and linear regression analysis were used to determine the best positivity rate cut-off to apply pooling strategy.

Results: A total of 15,216 individual specimens were pooled into 3,804 four-sample pools. Among these pools, 1,007 (26.47%) were positive. Five hundred and ten (50.64%) were 1/4 positive. A maximum positivity rate of 22% is needed to save at least 50% extraction and qRT-PCR reactions in a four-sample pooling strategy. CT values between individual specimens and pools showed a good interval agreement.

Conclusions: Pooling strategy could reduce personnel workload and reagent cost, and increase laboratory capacity by up to 50% when the positivity rate is less than 22%.

OBJECTIVE: Real-time reverse transcription-polymerase chain reaction (RT-PCR) is the gold standard examination to confirm coronavirus disease 2019 (COVID-19). This study aimed to determine the association between RT-PCR Ct value and COVID-19 clinical severity in the second week of illness.

PATIENTS AND METHODS: This study was a cross-sectional study. Data were collected from medical records of COVID-19 patients at the tertiary COVID-19 referral hospital of West Java, Dr. Hasan Sadikin Hospital Bandung, from January to May 2021. A total of 207 patients who met inclusion criteria were divided into four severity groups. The data were analyzed with One Way ANOVA Test.

RESULTS: There was no significant difference in RT-PCR Ct value among mild, moderate, severe and critical groups measured in the second week of illness, with p=0.825 for Ct Helicase/ORF1b gene, p=0.821 for Ct RdRp gene and p=0.870 for the lowest Ct gene.

CONCLUSIONS: Although Ct value reflects viral load, its role is concluded to be clinically insignificant in terms of association with the severity of COVID-19 in the second week of illness.

Scaling up SARS-CoV-2 testing and tracing continues to be plagued with the limitation of the sample collection method, which requires trained healthcare workers to perform and causes discomfort to the patients. In response, we assessed the performance and user preference of gargle specimens for qRT-PCR-based detection of SARS-CoV-2 in Indonesia. Inpatients who had recently been diagnosed with COVID-19 and outpatients who were about to perform qRT-PCR testing were asked to provide nasopharyngeal and oropharyngeal (NPOP) swabs and self-collected gargle specimens. We demonstrated that self-collected gargle specimens can be an alternative specimen to detect SARS-CoV-2 and the viral RNA remained stable for 31 days at room temperature storage. The developed method was validated for use on multiple RNA extraction kits and commercially available COVID-19 RT-PCR kits. Our developed method achieved a sensitivity of 91.38% when compared to paired NPOP swab specimens (Ct < 35), with 97.10% of patients preferring the self-collected gargle method.