Detection of SARS-CoV-2 from Indonesia with colorimetric saliva based RT-LAMP method using thermal cycler

Arif Bimantara (Universitas 'Aisyiyah Yogyakarta)
Ika Afifah Nugraheni (Universitas 'Aisyiyah Yogyakarta)
Luluk Rosida (Universitas 'Aisyiyah Yogyakarta)
Tasya Muliasari (Universitas 'Aisyiyah Yogyakarta)

International Journal of Health Science and Technology
Vol 4, No 2 (2022): November

Coronavirus disease 2019 (COVID-19) is an acute respiratory syndrome disease caused by the SARS-CoV-2 virus (severe acute respiratory syndrome coronavirus 2). This virus has mutations that cause its transmission to speed up so it requires a fast detection method to prevent such transmission. The detection method that becomes gold standard is RT-qPCR (reverse transcription-quantitative polymerase chain reaction). The disadvantage of the RT-qPCR method is that the long detection time and nasopharyngeal swab sampling cause discomfort in the patient. One alternative method of detection of the SARS-CoV-2 virus is colorimetric saliva based RT-LAMP (reverse transcription loop-mediated isothermal amplification). The advantage of the RT-LAMP method is that it is fast and accurate. The purpose of this study is to determine the ability of the RT-LAMP saliva-based colorimetric method to use thermal cyclers as an alternative to SARS-CoV-2 detection in Indonesia. This study used the primary design of SARS-CoV-2 Indonesia. The samples used were positive and negative saliva for COVID-19 based on RT-qPCR test results from PKU Muhammadiyah Hospital, Yogyakarta City. The research stages include optimization of RT-LAMP conditions, saliva sampling followed by colorimetric visualization of results and electrophoresis. Colorimetric testing was carried out with the addition of phenol red and observed a change in color from pink to yellow. The results showed that RT-LAMP can run optimally at 65 °C for 45 minutes. Colorimetric RT-LAMP testing in this study was ineffective because it could not detect positive samples compared to electrophoresis results. Factors that cause this include a small number of amplicons, incompatible RT-LAMP reagents used for colorimetric methods using phenol red, and phenol red which cannot work optimally so that it requires a new or more appropriate pH indicator. It is necessary to conduct further research by replacing other visualization methods such as replacing pH indicators or by fluorescence methods.