SARS-CoV-2 Direct real-time Polymerase Chain Reaction Testing in Laboratories With Shortage Challenges

Abstract

Aim: In our study, we propose the use of direct real-time polymerase chain reaction (RT-PCR), this test does not require extraction or a preheating step, which saves a lot of cost, labor, processing time and provides a solution for supply shortage. Materials & methods: We assayed 185 nasopharyngeal samples stored in viral transport media. The indirect method was done with RNA extraction step, and the direct RT-PCR was done without an extraction step, both assays were evaluated on a commercially validated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kit targeting E gene. Results: Our assay showed a sensitivity of 79%, a specificity of 100% and the agreement between methods was 72%. Conclusion: Overall, this simple direct RT-PCR approach can be utilized as a qualitative diagnostic tool for emergency SARS-CoV-2 surveillance in countries with limited resources and may help laboratories to continue testing and at greater frequency despite supply shortages, although with delay in cycle threshold value in comparison with indirect RT-PCR.

Examining the Relationship Between Workplace Industry and COVID-19 Infection

“…Because PCR diagnostic testing is typically initiated upon symptom onset, these measures may miss individuals who may be unaware of their COVID-19 status and/or have not tested via PCR, especially more recently in the course of the pandemic, which was characterized by PCR test shortages. 30,31 As such, it is reassuring that we have observed largely consistent relationships in our main analysis and the sensitivity analysis, with more pronounced signals in certain industries.…”

“…Reliance on PCR is especially problematic considering the global test shortages in recent COVID-19 waves. 30,31 Rapid antigen screening (RAS) is becoming increasingly recognized as a useful tool for reducing COVID-19 spread in the workplace. [32][33][34] Regular, frequent RAS is a scalable method to control SARS-CoV-2 transmission, because of early detection and isolation of asymptomatic cases, 2,35 which is particularly important in light of VOC-related transmission.…”

“…With the high prevalence of asymptomatic transmission, these may miss individuals who may be unaware of their COVID-19 status and/or have not tested via PCR. Reliance on PCR is especially problematic considering the global test shortages in recent COVID-19 waves 30,31 …”

Evaluation and Clinical Validation of Guanidine-Based Inactivation Transport Medium for Preservation of SARS-CoV-2

“…One source of this shortage is the limited resource available recommended by WHO and the Centre for Disease Control and Prevention (CDC). For COVID-19 diagnostic testing, WHO and the CDC recommend nasal or pharyngeal swabs that are stored in a viral transport medium (VTM) and tested using a nucleic acid amplification test (NAAT) [ 5 , 9 , 14 – 16 ]. Unfortunately, NAAT for SARS-CoV-2 detection has several limitations in terms of sensitivity among its various protocols [ 17 , 18 ].…”

“…Diagnostic test laboratories have used several alternative methods to NAAT [ 10 , 16 , 29 – 39 ]. However, all alternative methods still require the sample collection step and, therefore, require a swab and transport medium.…”