Performance of SARS-CoV-2 nucleic acid amplification testing in Austria as measured by external quality assessment schemes during 3 years of the COVID-19 pandemic: an observational retrospective study

Buchta, Christoph; Aberle, Stephan W; Allerberger, Franz; Benka, Bernhard; Görzer, Irene; Griesmacher, Andrea; Hübl, Wolfgang; Huf, Wolfgang; Kapiotis, Stylianos; Müller, Mathias M; Neuwirth, Erich; Puchhammer-Stöckl, Elisabeth; Weseslindtner, Lukas; Camp, Jeremy V

doi:10.1016/s2666-5247(23)00286-0

Cited by 4 publications

(2 citation statements)

References 15 publications

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“…EQA schemes on SARS-CoV-2 genome detection served to inform public health authorities about the quality of epidemic data generated by diagnostic laboratories, but, equally importantly, informed participants about their performance relative to other labs so that they may identify areas for improvement ( Buchta et al, 2023a ). This is a critical process when new assays or techniques are implemented, as seen during the COVID-19 pandemic when the performance of a given assay was unknown and their implementation unfamiliar to some diagnostic laboratories ( Buchta et al, 2023b ).…”

Section: Introductionmentioning

confidence: 99%

Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria

Camp,

Puchhammer-Stöckl,

Aberle

et al. 2024

Front. Mol. Biosci.

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Introduction: A notable feature of the 2019 coronavirus disease (COVID-19) pandemic was the widespread use of whole genome sequencing (WGS) to monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Countries around the world relied on sequencing and other forms of variant detection to perform contact tracing and monitor changes in the virus genome, in the hopes that epidemic waves caused by variants would be detected and managed earlier. As sequencing was encouraged and rewarded by the government in Austria, but represented a new technicque for many laboratories, we designed an external quality assessment (EQA) scheme to monitor the accuracy of WGS and assist laboratories in validating their methods.Methods: We implemented SARS-CoV-2 WGS EQAs in Austria and report the results from 7 participants over 5 rounds from February 2021 until June 2023. The participants received sample material, sequenced genomes with routine methods, and provided the sequences as well as information about mutations and lineages. Participants were evaluated on the completeness and accuracy of the submitted sequence and the ability to analyze and interpret sequencing data.Results: The results indicate that performance was excellent with few exceptions, and these exceptions showed improvement over time. We extend our findings to infer that most publicly available sequences are accurate within ≤1 nucleotide, somewhat randomly distributed through the genome.Conclusion: WGS continues to be used for SARS-CoV-2 surveillance, and will likely be instrumental in future outbreak scenarios. We identified hurdles in building next-generation sequencing capacity in diagnostic laboratories. EQAs will help individual laboratories maintain high quality next-generation sequencing output, and strengthen variant monitoring and molecular epidemiology efforts.

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Section: Introductionmentioning

confidence: 99%

Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria

Camp,

Puchhammer-Stöckl,

Aberle

et al. 2024

Front. Mol. Biosci.

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“…Our Department of Respiratory Medicine mostly treats patients with pulmonary diseases such as lung cancer, interstitial pneumonia, and nontuberculous mycobacterial infections. PCR is quite sensitive and specific for the detection of SARS-CoV-2 [ 10 ]. We adopted a policy to perform PCR screening for hospital admission at the beginning of 2022 in order to identify and isolate patients infected with SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

The Utility and Limitations of Universal Polymerase Chain Reaction Screening for SARS-CoV-2 During Hospital Admission

Ogo,

Ikegame,

Hotta

et al. 2024

Cureus

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Objective: Universal polymerase chain reaction (PCR) screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on hospital admission is an effective approach to preventing coronavirus disease 2019 (COVID-19) outbreaks in medical facilities. However, false-positive test results due to a recent infection are a concern. We investigated the usefulness and limitations of universal PCR screening for SARS-CoV-2 on hospital admission in a real-world setting.Methods: We retrospectively analyzed 1320 attempted hospital admissions for 775 patients at the

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External quality assessments for SARS-CoV-2 genome detection in Austria

Buchta,

Aberle,

Görzer

et al. 2024

Wien Klin Wochenschr

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Summary Background External quality assessment (EQA) schemes provide objective feedback to participating laboratories about the performance of their analytical systems and information about overall regional analytical performance. The EQAs are particularly important during pandemics as they also assess the reliability of individual test results and show opportunities to improve test strategies. With the end of the COVID-19 pandemic, the testing frequency significantly decreased in Austria. Here, we analyzed whether this decrease had an effect on participation and/or performance in SARS-CoV‑2 virus detection EQAs, as compared to the pandemic era. Material and methods Identical samples were sent to all participating laboratories, and the EQA provider evaluated the agreement of the reported results with defined targets. The EQA was operated under two schemes with identical samples and therefore we analyzed it as a single EQA round. The performance of testing was reported as true positive ratios, comparing the post-pandemic data to previous rounds. Furthermore, subgroups of participants were analyzed stratified by laboratory type (medical or nonmedical) and the test system format (fully automated or requiring manual steps). Results While the frequency of false negative results per sample did not change during the 3 years of the pandemic (5.7%, 95% confidence interval [CI] 3.1–8.4%), an average per sample false negative ratio of 4.3% was observed in the first post-pandemic EQA (0%, 1.8%, and 11% for the 3 positive samples included in the test panel, n = 109 test results per sample). In this first post-pandemic EQA medical laboratories (average 0.4% false negative across 3 samples, n = 90) and automated test systems (average 1.2% false negative, n = 261) had lower false negative ratios than nonmedical laboratories (22.8%, n = 19) and manual test systems (16.7%, n = 22). These lower average ratios were due to a low concentration sample, where nonmedical laboratories reported 36.8% and manual test systems 54.5% true positive results. Conclusion Overall ratios of true positive results were below the mean of all results during the pandemic but were similar to the first round of the pandemic. A lower post-pandemic true positive ratio was associated with specific laboratory types and assay formats, particularly for samples with low concentration. The EQAs will continue to monitor the laboratory performance to ensure the same quality of epidemiological data after the pandemic, even if vigilance has decreased.

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Performance of SARS-CoV-2 nucleic acid amplification testing in Austria as measured by external quality assessment schemes during 3 years of the COVID-19 pandemic: an observational retrospective study

Cited by 4 publications

References 15 publications

Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria

Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria

The Utility and Limitations of Universal Polymerase Chain Reaction Screening for SARS-CoV-2 During Hospital Admission

External quality assessments for SARS-CoV-2 genome detection in Austria

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