Abstract
Objective:To determine the stability of respiratory samples for SARS-CoV-2 PCR at standard laboratory ultra-freezer temperatures (-80°C).Methods:Five hundred and sixty-five archived, SARS-CoV-2 PCR positive patient specimens received at the Pathology Department of the Indus Hospital & Health Network between January 2021 and June 2021 were retested in June 2021. Samples had been stored at -70°C or below throughout this duration. Sample integrity following storage was assessed as the percentage of samples with reproducible results, and as consistency of cycle threshold (Ct) values between the original testing and the repeat testing.Results:Of the 565 samples evaluated in this study, 86% gave reproducible results upon retesting. However, there was no correlation between the duration of storage and result reproducibility, though the majority (69% for PCR Target-I and 78% for PCR Target-II respectively) of non-reproducible results had Ct values above 30. Similarly, there was a consistent increase of Ct values upon storage at ultra-freezer temperatures, though the effect again was more contingent upon freezing the sample in the ultra-freezer rather than the duration of storage.Conclusion:SARS-CoV-2 positive respiratory specimens for PCR can be stored for up to six months at -70°C or below without loss of sample integrity, though there is some loss of PCR-detected viral targets as evidenced by an immediate increased in the PCR-generated Ct values. In addition, samples with initial Ct values above 30 are more likely to give non-reproducible results.
Highlights
SARS-CoV-2 positive respiratory specimens for PCR can be stored for up to six months at -70°C or below without loss of sample integrity, though there is some loss of PCR-detected viral targets as evidenced by an immediate increased in the PCR-generated cycle threshold (Ct) values
69% and 78% of discrepant results, i.e. positive results which turned negative on repeat testing, had a Ct value above 30 for Target-I and Target-II respectively
The average Ct values obtained for Target-I and Target-II during the initial run and subsequent run, along with the standard deviation and coefficient of variation are presented in Table-II
Summary
Five hundred and sixty-five randomly selected, anonymous, archived, SARS-CoV-2 PCR positive nasopharyngeal patient specimens stored in viral transport, media were used in this study These specimens had been sent to the Pathology Department at Indus Hospital & Health Network, Karachi, after approval by the Institutional Review Board (IHHN_IRB_2021_07_001) for routine testing for SARS-CoV-2 between January 2021 and June 2021. Real-time PCR testing on these samples was done either on Roche Cobas 6800 using cobas SARS-CoV-2 kit or on GeneXpert using Xpert® Xpress SARS-CoV-2. Both systems are fully automated, including sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection systems. Both systems detect two targets in the virus genome – a ‘Target-I’ which is a nucleic acid sequence specific to SARS-CoV-2, and a ‘TargetII’ which is a nucleic acid sequence not specific to SARS-CoV-2, but is common to all Sarbecoviruses
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call