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All Journal Althea Medical Journal
Chaidir, Lidya
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Medicine & Pharmacology

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Reliability of RT-qPCR Pooling Method for COVID-19 Detection in Various Cycle Threshold Values Radjawali, Muhammad Fauzan Alif; Jihadah, Muti'ah; Chaidir, Lidya
Althea Medical Journal Vol 10, No 2 (2023)
Publisher : Faculty of Medicine Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15850/amj.v10n2.2940

Abstract

Background: Reverse Transcriptase Quantitative Real-time Polymerase Chain Reaction (RT-qPCR) is a standard method to detect SARS-CoV-2, the cause of COVID-19 disease, albeit expensive for some laboratory settings. The pooling test is widely used for large-scale screening to speed up the turn-around time and reduce the cost of the RT-qPCR. However, the pooling test involves mixing a certain number of specimens which theoretically increases the possibility of false-negative results. This study aimed to evaluate the accuracy of the pooling test compared with the non-pooling test in different Ct values as a surrogate for viral load.Methods: RT-qPCR was performed in three groups of samples: non-pooling (individual samples), pooling of 5 samples and 11 samples, with various ranges of Ct value in the respective group: x<25 (n=4); 25<x<30 (n=5), x<30 (n=16), and negative sample (n=5). Agreement and kappa values were calculated. Four of twenty-five individual samples resulted in false-negative after pooling.Results: By taking all samples without applying the cut-off value to the calculation, the agreement in pooling of 5 samples was 0.86 (Kappa 0.31) and of 11 samples was 0.64 (Kappa 0.96). When the cut-off value of Ct<37 was applied, percent agreement and kappa were 1.00, respectively, for both pooling methods.Conclusions: Pooling up to 11 samples shows high concordance with RT-qPCR with individual samples with Ct<37. Interpreting pooling results in a very low viral load (Ct≥37) must be considered due to the increased possibility of inconclusive results.
Viability Test of Mycobacterium Tuberculosis Bacteria Stored in Various Cryopreservation Periods Annisa, Jessi; Susilawati, Neng Rina; Asarina, Shinta; Jihadah, Muti'ah Nurul; Chaidir, Lidya
Althea Medical Journal Vol 11, No 1 (2024)
Publisher : Faculty of Medicine Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15850/amj.v11n1.2949

Abstract

Background: The specimen storage room serves as bioarchive for prospective research purposes. Cryopreservation or preservation at very low temperatures has been used to preserve research isolates for decades. A quality assessment must be conducted to ensure the isolates conditions. This study aimed to assess the quality of isolates by testing the level of viability and contamination from different cryopreservation periods.Methods: This was an experimental study with a total sample of 92 Mycobacterium tuberculosis (Mtb) isolates which were sampled randomly using cryopreservation, aged 8–10 years (in Tryptic Soy Broth media, TSB/) and aged 3–5 years (in Middlebrook 7H9) which was re-cultured in Ogawa Medium at the Tuberculosis Laboratory, Universitas Padjadjaran in May–November 2019. After observing confluent growths, the pure isolate was stained using the Ziehl-Neelsen (ZN) method to confirm the presence of Mtb growth or contamination. A Simple ratio was used to count the recovery rate as a viability parameter and contamination rate of each batch.Results: Test results showed a recovery rate of 66.67–100% of positive cultures stored despite they had been cryopreserved for 10 years. There was no significant difference in the percentage of positive cultures between preservation period groups.Conclusion: Mtb isolates can survive and remain viable after being stored for up to 10 years at -80 ° C in cryopreservation media.
Co-Authors Annisa, Jessi Asarina, Shinta Jihadah, Muti'ah Jihadah, Muti'ah Nurul Radjawali, Muhammad Fauzan Alif Susilawati, Neng Rina