Impact of storage temperature and duration on rRT-PCR Cycle Threshold (Ct) values in SARS-CoV-2-positive nasopharyngeal Samples: A study at a provincial hospital in Morocco

Oumaima Mallouk; Aicha Qasmaoui; Rachid Amgoun; Said Hilali; Samira Natoubi

doi:10.63095/NBSEH.26.338615

Authors

Oumaima Mallouk Department of Applied Biology, Faculty of Science and Technology, University Hassan I, Settat, Morocco (https://ror.org/03cdvht47).
Aicha Qasmaoui Department of Medical Bacteriology, Laboratory of Epidemic Diseases, National Institute of Hygiene, Rabat, Morocco.
Rachid Amgoun Microbiology Laboratory, Provincial Hassan II Hospital, Delegation of the Health Ministry, Settat, Morocco.
Said Hilali Department of Applied Biology, Faculty of Science and Technology, University Hassan I, Settat, Morocco (https://ror.org/03cdvht47).
Samira Natoubi Laboratory of Care, Health and Sustainable Development 2S2D, Higher Institute of Nursing Professions and Techniques of Health (ISPITS) Casablanca, Annexe Settat Morocco (https://ror.org/007h8y788).

DOI:

https://doi.org/10.63095/NBSEH.26.338615

Keywords:

SARS-CoV-2, RT-PCR, CT value, Storage temperature, Storage duration

Abstract

Reverse transcription polymerase chain reaction (RT-PCR) is the gold standard for SARS-CoV-2 diagnosis of infection. Pre-analytical factors such as storage temperature and duration may affect RNA stability and, consequently, RT-PCR performance. This study aimed to assess the impact of these factors on cycle threshold (Ct) values to ensure reliable diagnostic results. Eighteen SARS-CoV-2–positive nasopharyngeal swab samples were stored at +4 °C and −20 °C and analyzed by RT-PCR over a period of 1 to 7 days. Detection of the S (Spike) and RdRp (RNA-dependent RNA polymerase) genes was performed, and Ct values were compared before and after storage. All analyses were conducted using the same standardized protocol for RNA extraction, amplification, and result interpretation. All initially positive samples remained positive after storage. Ct values showed only minor variations, with mean decreases of −1.02 cycles for RdRp and −1.05 cycles for the S gene after storage. Variations of up to 2–3 Ct cycles were observed in some samples. These findings suggest that short-term storage under standard conditions is unlikely to affect SARS-CoV-2 detection by RT-PCR. Because of the limited sample size, the analysis was mainly descriptive. Therefore, short-term storage of SARS-CoV-2 samples under routine laboratory conditions did not alter RT-PCR qualitative results.

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