Nationwide external quality assessment of SARS-CoV-2 nucleic acid amplification tests in Japan

Exploring the causes of variability in quality of oropharyngeal swab sampling for SARS-CoV-2 nucleic acid testing and proposed improvement measures: a multicenter, double-blind study

Although coronavirus disease 2019 (COVID-19) has not been considered a public health emergency of international concern since last year, intermittent regional impacts still persist, and accurate testing remains crucial. Ribonuclease P protein subunit P30 (RPP30) RNA, known for its broad and stable expression in tissue cells, was used to evaluate samples from 10 hospitals with over 3,000 negative nucleic acid tests. The results revealed that the overall pass rate for the collected samples was consistently low and exhibited significant heterogeneity. After reassessing the evaluative effectiveness of RPP30 RNA Ct values from the samples of 132 positive individuals under quarantine observation, it was used to identify factors affecting sampling quality. These factors included different stages ranging from sample collection to PCR processing, various characteristics of both samplers and individuals being sampled, as well as sampling season and location. The results indicated that post-sampling handling had minimal impact, winter and fever clinic samples showed higher quality, whereas children's samples had lower quality. The key finding was that the characteristics of samplers were closely related to sampling quality, emphasizing the role of subjectivity. Quality control warnings led to substantial improvements, confirming this finding. Consequently, although there are various factors during the testing process, the most critical aspect is to improve, supervise, and maintain standardized practices among sampling staff.IMPORTANCEThis study further confirmed the reliability of internal references (IRs) in assessing sample quality, and utilized a large sample IR data to comprehensively and multidimensionally identify significant interference factors in nucleic acid test results. By further reminding and intervening in the subjective practices of specimen collectors, good results could be achieved.

Continuous quality improvement with a two-step strategy effective for mass SARS-CoV-2 screening at the Tokyo 2020 Olympic and Paralympic Games

The Tokyo 2020 Olympic and Paralympic Games (Games) were held during the height of the coronavirus disease 2019 (COVID-19) pandemic. To detect people infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) early enough to contain the spread and to facilitate the timely arrival of athletes at their game venues, all participating athletes staying in the Olympic Village (up to 14,000) were screened daily for the infection. Toward this aim, a two-step strategy was adopted comprising screening of self-collected saliva samples using a chemiluminescence enzyme immunoassay, followed by confirmatory testing using polymerase chain reaction. The testing system was integrated with an information management system covering all steps. To ensure the accuracy of the test results, rigorous quality assurance measures and monitoring of performance/specimen quality were implemented. A chronological chart analysis was implemented to monitor the holistic process and to give feedback to improve the sampling. Nearly all test results for 418,506 saliva samples were reported within 12 hours of sample collection, achieving the target mean turnaround time of 150 minutes for confirmatory testing. As a result, athlete activity and performance for the Games were ensured. The chronological chart confirmed that no athletes were withdrawn due to a false-positive result, and no infection clusters were identified among the athletes in the Olympic Village. In conclusion, continuous quality improvement as part of the two-step strategy for mass screening for COVID-19 contributed to the success of the Games during the pandemic. The quality practice, systems, and workflows described here may offer a model for future mass-gathering sporting events during similar major infectious disease epidemics.

External quality assessment survey for SARS-CoV-2 nucleic acid amplification tests in clinical laboratories in Tokyo, 2021

INTRODUCTION

Nucleic acid amplification tests (NAATs) play a pivotal role in clinical laboratories for diagnosing COVID-19. This study aimed to elucidate the accuracy of these tests.

METHODS

In 2021, an external quality assessment of NAATs for SARS-CoV-2 was conducted in 47 laboratories in Tokyo, Japan. In open testing, where the laboratories knew that the samples were intended for the survey, a simulated nasopharyngeal swab suspension sample was used, featuring a positive sample A with a viral concentration of 50 copies/μL, positive sample B with 5 copies/μL, and a negative sample. Laboratories employing real-time RT-PCR were required to report cycle threshold (Ct) values. In blind testing, where the samples were processed as normal test samples, a positive sample C with 50 copies/μL was prepared using a simulated saliva sample.

RESULTS

Of the 47 laboratories, 41 were engaged in open testing. For sample A, all 41 laboratories yielded positive results, whereas for sample B, 36 laboratories reported positive results, 3 laboratories reported "test decision pending", 1 laboratory reported "suspected positive", and 1 laboratory did not respond. All 41 laboratories correctly identified the negative samples as negative. The mean Ct values were 32.2 for sample A and 35.2 for sample B. In the blind test, six laboratories received samples. Sample C was identified as positive by five laboratories and negative by one laboratory.

CONCLUSIONS

The nature of the specimen, specifically the saliva, may have influenced the blind test outcomes. The identified issues must be meticulously investigated and rectified to ensure accurate results.

Optimizing heat inactivation for SARS-CoV-2 at 95 °C and its implications: A standardized approach

Background

Standardized and validated heat inactivation procedure for Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not available. For heat inactivation, various protocols were reported to prepare External Quality Assessment Programme (EQAP) samples without direct comparison between different durations.

Objective

To assess the heat inactivation procedures against SARS-CoV-2. The efficacy of the optimized condition was reflected by the results from laboratories testing the EQAP samples.

Study design

The SARS-CoV-2 strain was exposed to 95 °C in a water bath for three different time intervals, 5 min, 10 min and 15 min, respectively. The efficacy of inactivation was confirmed by the absence of cytopathic effects and decreasing viral load in 3 successive cell line passages. The viral stock inactivated by the optimal time interval was dispatched to EQAP participants and the result returned were analyzed.

Results

All of the three conditions were capable of inactivating the SARS-CoV-2 of viral load at around cycle threshold value of 10. When the 95 °C 10 min condition was chosen to prepare SARS-CoV-2 EQAP samples, they showed sufficient homogeneity and stability. High degree of consensus was observed among EQAP participants in all samples dispatched.

Conclusions

The conditions evaluated in the present study could be helpful for laboratories in preparing SARS-CoV-2 EQAP samples.

The European Organisation of External Quality Assurance Providers in Laboratory Medicine (EQALM) Statement: guidelines for publishing about interlaboratory comparison studies (PubILC)

Data and results from interlaboratory comparison (ILC) studies, external quality assessment (EQA) and proficiency testing (PT) activities are important and valuable contributions both to the further development of all disciplines of medical laboratory diagnostics, and to the evaluation and comparison of in vitro diagnostic assays. So far, however, there are no recommendations as to which essential items should be addressed in publications on interlaboratory comparisons. The European Organization of External Quality Assurance Providers in Laboratory Medicine (EQALM) recognized the need for such recommendations, and these were developed by a group of experts. The result of this endeavor is the EQALM Statement on items recommended to be addressed in publications on interlaboratory comparison activities (PubILC), in conjunction with a user-friendly checklist. Once adopted by authors and journals, the EQALM Statement will ensure essential information and/or study-related facts are included within publications on EQA/PT activities.

High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.

Design of external quality assessment schemes and definition of the roles of their providers in future epidemics

During an epidemic, individual test results form the basis of epidemiological indicators such as case numbers or incidence. Therefore, the accuracy of measures derived from these indicators depends on the reliability of individual results. In the COVID-19 pandemic, monitoring and evaluating the performance of the unprecedented number of testing facilities in operation, and novel testing systems in use, was urgently needed. External quality assessment (EQA) schemes are unique sources of data reporting on testing performance, and their providers are recognised contacts and support for test facilities (for technical-analytical topics) and health authorities (for planning the monitoring of infection diagnostics). To identify information provided by SARS-CoV-2 genome detection EQA schemes that is relevant for public health microbiology, we reviewed the current literature published in PubMed between January, 2020, and July, 2022. We derived recommendations for EQA providers and their schemes for best practices to monitor pathogen-detection performance in future epidemics. We also showed laboratories, test facilities, and health authorities the information and benefits they can derive from EQA data, and from the non-EQA services of their providers.

First Round of External Quality Assessment Scheme for SARS-CoV-2 Laboratories During the COVID-19 Pandemic in Thailand

The emergence of SARS-CoV-2 necessitated the rapid deployment of tests to diagnose COVID-19. To monitor the accuracy of testing across the COVID-19 laboratory network in Thailand, the Department of Medical Sciences under the Ministry of Public Health launched a national external quality assessment (EQA) scheme using samples containing inactivated SARS-CoV-2 culture supernatant from a predominant strain in the early phase of the Thailand outbreak. All 197 laboratories in the network participated; 93% (n=183) of which reported correct results for all 6 EQA samples. Ten laboratories reported false-negative results, mostly for samples with low viral concentrations, and 5 laboratories reported false-positive results (1 laboratory reported false positives and false negatives). An intralaboratory investigation of 14 laboratories reporting incorrect results revealed 2 main causes of error: (1) RNA contamination of the rRT-PCR reaction and (2) poor-quality RNA extraction. Specific reagent combinations were significantly associated with false-negative reports. Thailand's approach to national EQA for SARS-CoV-2 can serve as a roadmap for other countries interested in implementing a national EQA program to ensure laboratories provide accurate testing results, which is crucial in diagnosis, prevention, and control strategies. A national EQA program can be less costly and thus more sustainable than commercial EQA programs. National EQA is recommended to detect and correct testing errors and provide postmarket surveillance for diagnostic test performance.