A two minute liquid based sample preparation for rapid SARS-CoV2 real-time PCR screening: A multicentre evaluation

Diagnostic performance of the Qiaprep amp Viral RNA UM kit for the detection of COVID-19 compared to RT-PCR

Background

RT-PCR is the currently recommended laboratory method for diagnosing acute SARS-CoV-2 infection. Nevertheless, to carry out this assay, numerous manual steps are necessary, but they are long lasting and error-prone. A new sample preparation solution was launched, the Qiaprep & amp Viral RNA UM kit, that combines a short, liquid-based sample preparation with one-step RT-PCR amplification and detection of SARS-CoV-2. Such alternative allows reducing the handling of samples and obtaining a result in a shorter period of time. The objective of the study was to compare the performance of the kit with RT-PCR.

Methods

A prospective trial was carried out in the clinical microbiology laboratory of a tertiary care hospital. The pharyngeal and nasopharyngeal swabs included in the study were taken from patients who underwent medical consultation because compatible COVID-19 symptoms. Samples were processed simultaneously for the reference RT-PCR and by the QIA P&A kit.

Results

190 samples were included in the clinical trial. The reference RT-PCR method indicated that 125 (66%) samples, out of the 190, were positive. The QIA P&A kit showed 112 positive samples for SARS-CoV-2. The QIA P&A kit has a sensitivity of 86% to detect SARS-CoV-2 and a 100% specificity, the positive predictive value was of 96%, the negative predictive value 78%, and the obtained Kappa value was 0,76. QIA P&A kit showed a lower mean cycle threshold compared with the diagnostic standard, with a statistically significant difference (p < 0.05).

Conclusion

The QIA P&A kit has an acceptable, yet not optimal performance for sample preparation and amplification of SARS-CoV-2 and further studying is required for it to be validated as a cost-effective, rapid diagnostic method for detecting infections.

Rapid Extraction of Viral Nucleic Acids Using Rotating Blade Lysis and Magnetic Beads

The complex and lengthy protocol of current viral nucleic acid extraction processes limits their use outside laboratory settings. Here, we describe a rapid and reliable method for extracting nucleic acids from viral samples using a rotating blade and magnetic beads. The viral membrane can be instantly lysed using a high-speed rotating blade, and nucleic acids can be immediately isolated using a silica magnetic surface. The process was completed within 60 s by this method. Routine washing and eluting processes were subsequently conducted within 5 min. The results achieved by this method were comparable to those of a commercially available method. When the blade-based lysis and magnetic bead adsorption processes were performed separately, the RNA recovery rate was very low, and the Ct value was delayed compared to simultaneous lysis and RNA adsorption. Overall, this method not only dramatically shortens the conventional extraction time but also allows for its convenient use outside the laboratory, such as at remote field sites and for point-of-care testing.

SARS-CoV-2 and RT-PCR Testing in Travelers: Results of a Cross-sectional Study of Travelers at Iraq's International Borders

BACKGROUND

In late 2019, a novel coronavirus was detected in Wuhan, China, that caused a pandemic by September 2021, resulting in 224,180,411 cases and more than 4,600,000 deaths worldwide. In response to the pandemic, the Autonomous Kurdistan Regional Government of Iraq (KRG) imposed strict infection control measures at its borders for all travelers from neighboring countries, wherein each traveler was subjected to a mandatory reverse transcription polymerase chain reaction (RT-PCR) test on arrival to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected travelers. The aim of this study is to determine the rate of infection with SARS-CoV-2 among the travelers entering Kurdistan region through Ibrahim Al-Khalil crossing point with Turkey as a predictor for the upcoming infection waves.

METHODS

The data of RT-PCR tests to detect SARS-CoV-2 in all travelers arriving at the Ibrahim Al-Khalil Border Crossing between Iraq and the Republic of Turkey were reviewed from August 21, 2020 to August 21, 2021.

RESULTS

It was found that there were 9873 cases of SARS-CoV-2 infections among 1,082,074 travelers during the study period.

CONCLUSIONS

This study shows the importance of mass testing of travelers at border crossings to control the spread of SARS-CoV-2 infection.

Strategies for Scaling up SARS-CoV-2 Molecular Testing Capacity

Scaling up SARS-CoV-2 testing during the COVID-19 pandemic was critical to maintaining clinical operations and an open society. Pooled testing and automation were two critical strategies used by laboratories to meet the unprecedented demand. Here, we review these and other cutting-edge strategies that sought to expand SARS-CoV-2 testing capacity while maintaining high individual test performance.

A single-center report of COVID-19 disease course and management in liver transplanted pediatric patients

BACKGROUND

In 2019, SARS-CoV-2 causing COVID-19 emerged. Severe COVID-19 symptoms may evolve by virtue of hyperactivation of the immune system. Equally, immunocompromised patients may be at increased risk to develop COVID-19. However, treatment guidelines for children following liver transplantation are elusive.

METHODS

As a liver transplantation center, we diagnosed and followed up 10 children (male/female: 8/2) with a median age of 8.5 years (IQR: 5.2-11.0), with COVID-19 post-liver transplant between March 2019 and December 2020. COVID-19 diagnosis was based on PCR test and or florid X-ray findings compatible with COVID-19 in the absence of other cause. We retrospectively collected clinical and laboratory data from electronic patient records following written consent from patients/parents.

RESULTS

Nine patients were diagnosed as definitive (PCR positive) with one patient being diagnosed as probable COVID-19. Seven patients recovered without any support whereas three were admitted for non-invasive oxygenation. Lymphopenia and/or high levels of serum IL-6 were detected in four patients. Six patients mounted anti-SARS-CoV-2 antibodies at median 30 days (IQR: 26.5-119.0) following COVID-19 diagnosis. Antibiotic therapy, favipiravir, anakinra, and IVIG were used as treatment in 4,1,1 and 2 patients, respectively. Furthermore, we kept the tacrolimus with or without everolimus but stopped MMF in 2 patients. Importantly, liver allograft function was retained in all patients.

CONCLUSIONS

We found that being immunocompromised did not affect disease severity nor survival. Stopping MMF yet continuing with tacrolimus was an apt treatment modality in these patients.