Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023.

BackgroundThe COVID-19 pandemic was largely driven by genetic mutations of SARS-CoV-2, leading in some instances to enhanced infectiousness of the virus or its capacity to evade the host immune system. To closely monitor SARS-CoV-2 evolution and resulting variants at genomic-level, an innovative pipeline termed SARSeq was developed in Austria.AimWe discuss technical aspects of the SARSeq pipeline, describe its performance and present noteworthy results it enabled during the pandemic in Austria.MethodsThe SARSeq pipeline was set up as a collaboration between private and public clinical diagnostic laboratories, a public health agency, and an academic institution. Representative SARS-CoV-2 positive specimens from each of the nine Austrian provinces were obtained from SARS-CoV-2 testing laboratories and processed centrally in an academic setting for S-gene sequencing and analysis.ResultsSARS-CoV-2 sequences from up to 2,880 cases weekly resulted in 222,784 characterised case samples in January 2021-March 2023. Consequently, Austria delivered the fourth densest genomic surveillance worldwide in a very resource-efficient manner. While most SARS-CoV-2 variants during the study showed comparable kinetic behaviour in all of Austria, some, like Beta, had a more focused spread. This highlighted multifaceted aspects of local population-level acquired immunity. The nationwide surveillance system enabled reliable nowcasting. Measured early growth kinetics of variants were predictive of later incidence peaks.ConclusionWith low automation, labour, and cost requirements, SARSeq is adaptable to monitor other pathogens and advantageous even for resource-limited countries. This multiplexed genomic surveillance system has potential as a rapid response tool for future emerging threats.

Effectiveness of a fourth SARS-CoV-2 vaccine dose in previously infected individuals from Austria.

INTRODUCTION: Evidence is limited on the effectiveness of a fourth vaccine dose against coronavirus disease 2019 (COVID-19) in populations with prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We estimated the risk of COVID-19 deaths and SARS-CoV-2 infections according to vaccination status in previously infected individuals in Austria. METHODS: This is a nationwide retrospective observational study. We calculated age and gender adjusted Cox proportional hazard ratios (HRs) of COVID-19 deaths (primary outcome) and SARS-CoV-2 infections (secondary outcome) from 1 November to 31 December 2022, primarily comparing individuals with four versus three vaccine doses. Relative vaccine effectiveness (rVE) was calculated as (1-HR) X 100. RESULTS: Among 3,986,312 previously infected individuals, 281,291 (7,1%) had four and 1,545,242 (38.8%) had three vaccinations at baseline. We recorded 69 COVID-19 deaths and 89,056 SARS-CoV-2 infections. rVE for four versus three vaccine doses was -24% (95% CI: -120 to 30) against COVID-19 deaths, and 17% (95% CI: 14-19) against SARS-CoV-2 infections. This latter effect rapidly diminished over time and infection risk with four vaccinations was higher compared to less vaccinated individuals during extended follow-up until June 2023. Adjusted HR (95% CI) for all-cause mortality for four versus three vaccinations was 0.79 (0.74-0.85). DISCUSSION: In previously infected individuals, a fourth vaccination was not associated with COVID-19 death risk, but with transiently reduced risk of SARS-CoV-2 infections and reversal of this effect in longer follow-up. All-cause mortality data suggest healthy vaccinee bias.

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.

BACKGROUND: The aim of external quality assessment (EQA) schemes is to evaluate the analytical performance of laboratories and test systems in a near-to-real-life setting. This monitoring service provides feedback to participant laboratories and serves as a control measure for the epidemiological assessment of the regional incidence of a pathogen, particularly during epidemics. Using data from EQA schemes implemented as a result of the intensive effort to monitor SARS-CoV-2 infections in Austria, we aimed to identify factors that explained the variation in laboratory performance for SARS-CoV-2 detection over the course of the COVID-19 pandemic. METHODS: For this observational study, we retrospectively analysed 6308 reverse transcriptase quantitative PCR (RT-qPCR) test results reported by 191 laboratories on 71 samples during 14 rounds of three SARS-CoV-2 pathogen detection EQA schemes in Austria between May 18, 2020, and Feb 20, 2023. We calculated the overall rates of false and true-negative, false and true-positive, and inconclusive results. We then assessed laboratory performance by estimating the sensitivity by testing whether significant variation in the odds of obtaining a true-positive result could be explained by virus concentration, laboratory type, or assay format. We also assessed whether laboratory performance changed over time. FINDINGS: 4371 (93·7%) of 4663 qPCR test results were true-positive, 241 (5·2%) were false-negative, and 51 (1·1%) were inconclusive. The mean per-sample sensitivity was 99·7% in samples with high virus concentrations (1383 [99·4%] true-positive, three [0·2%] false-negative, and five [0·4%] inconclusive results for 1391 tests in which the sample cycle threshold was ≤32), whereas detection rates were lower in samples with low virus concentrations (mean per-sample sensitivity 92·5%; 2988 [91·3%] true-positive, 238 [7·3%] false-negative, and 46 [1·4%] inconclusive results for 3272 tests in which the cycle threshold was >32). Of the 1645 results expected to be negative, 1561 (94·9%) were correctly reported as negative, 10 (0·6%) were incorrectly reported as positive, and 74 (4·5%) were reported as inconclusive. Notably, the overall performance of the tests did not change significantly over time. The odds of reporting a correct result were 2·94 (95% CI 1·75-4·96) times higher for a medical laboratory than for a non-medical laboratory, and 4·60 (2·91-7·41) times greater for automated test systems than for manual test systems. Automated test systems within medical laboratories had the highest sensitivity when compared with systems requiring manual intervention in both medical and non-medical laboratories. INTERPRETATION: High rates of false-negativity in all PCR analyses evaluated in comprehensive, multiple, and repeated EQA schemes outline a clear path for improvement in the future. The performance of some laboratories (eg, non-medical laboratories or those using non-automated test systems) should receive additional scrutiny-for example, by requiring additional EQA schemes for certification or accreditation-if the aggregated data from EQA rounds suggest lower sensitivity than that recorded by others. This strategy will provide assurances that epidemiological data as a whole are reliable when testing on such a large scale. Although performance did not improve over time, we cannot exclude extenuating circumstances-such as shortages and weakened supply chains-that could have prevented laboratories from seeking alternative methods to improve performance. FUNDING: None.

Implementation of a Surveillance System for Severe Acute Respiratory Infections at a Tertiary Care Hospital in Austria: Protocol for a Retrospective Longitudinal Feasibility Study.

BACKGROUND: The risk of a large number of severe acute respiratory infection (SARI) cases emerging is a global concern. SARI can overwhelm the health care capacity and cause several deaths. Therefore, the Austrian Agency for Health and Food Safety will explore the feasibility of implementing an automatic electronically based SARI surveillance system at a tertiary care hospital in Austria as part of the hospital network, initiated by the European Centre for Disease Prevention and Control. OBJECTIVE: We aim to investigate the availability of routinely collected health record data pertaining to respiratory infections and the optimal approach to use such available data for systematic surveillance of SARI in a real-world setting, describe the characteristics of patients with SARI before and after the beginning of the COVID-19 pandemic, and investigate the feasibility of identifying the risk factors for a severe outcome (intensive care unit admission or death) in patients with SARI. METHODS: We will test the feasibility of a surveillance system, as part of a large European network, at a tertiary care hospital in the province of Lower Austria (called Regional Hospital Wiener Neustadt). It will be a cross-sectional study for the inventory of the electronic data records and implementation of automatic data retrieval for the period of January 2019 through the end of December 2022. The analysis will include an exploration of the database structure, descriptive analysis of the general characteristics of the patients with SARI, estimation of the SARI incidence rate, and assessment of the risk factors and different levels of severity of patients with SARI using logistic regression analysis. RESULTS: This will be the first study to assess the feasibility of SARI surveillance at a large 800-bed tertiary care hospital in Austria. It will provide a general overview of the potential for establishing a hospital-based surveillance system for SARI. In addition, if successful, the electronic surveillance will be able to improve the response to early warning signs of new SARI, which will better inform policy makers in strengthening the surveillance system. CONCLUSIONS: The findings will support the expansion of the SARI hospital-based surveillance system to other hospitals in Austria. This network will be of use to Austria in preparing for future pandemics. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/47547.

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.

Diagnostic Study to Assess the Performance of a New Urinary Legionella Antigen Test-A National Study in Three Referral University Hospitals in Austria during 2014-2017.

BACKGROUND: We evaluated the performance of a rapid diagnostic antigen test (Coris) as an index test versus the urinary Antigen ELISA (Bartels) as the reference test. METHODS: Prospective diagnostic accuracy study (2014-2017) at three university hospitals in Austria. RESULTS: A total of 996 patients were included in the study. Legionellosis was diagnosed in 49/996 (4.9%) using the reference test. The sensitivity and specificity of the Coris test were 75.5% (95% CI 61.1-86.7%) and 100% (95%CI 99.6-100%), respectively. The PPV was 100% and when using the lower 95% CI limit of the estimate for sensitivity, the resulting PPV was 61.1%. The NPV was 98.7% and the accuracy was 98.8%. The index test showed a PPV > 97% during the period of summer and autumn (May through November) and ≥88% during winter (December through February). The NPV was >97% during all of the periods. The median of the monthly incidence in the general population was 0.1 per 100,000 (IQR 0.1; 0.3). CONCLUSION: The new rapid test gave a high level of diagnostic accuracy in a rapid fashion. The test can be applied at the bedside by non-laboratory staff.

Impact of COVID-19 Pandemic on Initiation of Immunosuppressive Treatment in Immune-Mediated Inflammatory Diseases in Austria: A Nationwide Retrospective Study.

Objective: Conventional immunosuppressive and advanced targeted therapies, including biological medications and small molecules, are a mainstay in the treatment of immune-mediated inflammatory diseases (IMID). However, the COVID-19 pandemic caused concerns over these drugs' safety regarding the risk and severity of SARS-CoV-2 infection. Thus, we aimed to assess the impact of the COVID-19 pandemic on the initiation of these treatments in 2020. Study Design and Setting: We conducted a population-based retrospective analysis of real-world data of the Austrian health insurance funds on the initiation of conventional immunosuppressive and advanced targeted therapies. The primary objective was to compare the initiation of these medications in the year 2020 with the period 2017 to 2019. Initiation rates of medication were calculated by comparing a certain unit of time with an average of the previous ones. Results: 95,573 patients were included. During the first lockdown in Austria in April 2020, there was a significant decrease in the initiations of conventional immunosuppressives and advanced targeted therapies compared to previous years (p < 0.0001). From May 2020 onwards, numbers rapidly re-achieved pre-lockdown levels despite higher SARS-CoV-2 infection rates and subsequent lockdown periods at the end of 2020. Independent from the impact of the COVID-19 pandemic, a continuous increase of starts of advanced targeted therapies and a continuous decrease of conventional immunosuppressants during the observation period were observed. Conclusions: In IMID patients, the COVID-19 pandemic led to a significant decrease of newly started conventional immunosuppressive and advanced targeted therapies only during the first lockdown in Austria.

Inadequate design of mutation detection panels prevents interpretation of variants of concern: results of an external quality assessment for SARS-CoV-2 variant detection.

OBJECTIVES: Mutation-specific PCR assays have quickly found their way into laboratory diagnostics due to their capacity to be a fast, easy to implement and high-throughput method for the detection of known SARS-CoV-2 variants of concern (VoCs). However, little is known about the performance of such assays in routine laboratory analysis. METHODS: The results reported in a recent round of an external quality assessment (EQA) scheme for SARS-CoV-2 mutation-specific PCR were retrospectively analyzed. For the determination of individual variant-specific sequences as well as for the interpretation results for certain virus variants, correct, incorrect, and unreported results were evaluated, and their possible causes were investigated. RESULTS: A total of 34 laboratories participated in this study. For five samples containing the VoC Alpha + E484K, Beta, Gamma, Delta, or B.1.1.318 (as a variant of interest), 848 results for SARS-2-CoV mutation detection were reported, 824 (97.2%, range per sample 88-100%) of which were correct. Melting curve assays gave 99% correct results, real-time RT-qPCR 94%, microarray-based assays 100%, and MALDI-TOF MS 96%. A total of 122/167 (73%) reported results for SARS-CoV-2 variant determination were correct. Of the 45 inconclusive or incorrect results, 33 (73%) were due to inadequate selection of targets that did not allow identification of contemporary VoC, 11 (24%) were due to incorrect results, and one (3%) was due to correct results of mutation-specific PCR. CONCLUSIONS: Careful and up-to-date selection of the targets used in mutation-specific PCR is essential for successful detection of current SARS-CoV-2 variants.

RT-PCR based SARS-CoV-2 variant screening assays require careful quality control.

BACKGROUND: Distinctive genotypes of SARS-CoV-2 have emerged that are or may be associated with increased transmission, pathogenicity, and/or antibody escape. In many countries, clinical and diagnostic laboratories are under mandate to identify and report these so-called variants of concern (VOC). OBJECTIVES: We used an external quality assessment scheme to determine the scope, accuracy, and reliability of laboratories using various molecular diagnostic assays to identify current VOC (03 March 2021). STUDY DESIGN: Participant laboratories were sent the same five patient-derived samples and were asked to provide their variant detection methods, variant detection results and interpretation of results. RESULTS: Twenty-five laboratories reported a range of RT-qPCR-based assays to identify specific variations in the SARS-CoV-2 spike protein that are characteristic of three VOC lineages. Laboratories that detected VOC-associated nucleotide mutations at four specific sites had the highest ratio of correct classification. Low template copy number and additional variation in target regions resulted in loss of confidence and accuracy in sample classification. CONCLUSIONS: Melting-curve-based assays to identify genomic variants are less time-consuming and require less bioinformatic analysis compared to partial or whole genome sequencing. However, our results suggest that correct classification of a given genotype/lineage (e.g., a VOC) relies on the ability to detect more than one variant site, adequate template in the sample (i.e., relatively high viral load/copy number) and results may be unclear in certain samples with additional genetic variations. These initial results suggest that some diagnostic laboratories may require additional training to interpret and report complex genetic information about a dynamic emerging virus.

The versatility of external quality assessment for the surveillance of laboratory and in vitro diagnostic performance: SARS-CoV-2 viral genome detection in Austria.

OBJECTIVES: External quality assessment (EQA) schemes provide information on individual and general analytical performance of participating laboratories and test systems. The aim of this study was to investigate the use and performance of SARS-CoV-2 virus genome detection systems in Austrian laboratories and their preparedness to face challenges associated with the pandemic. METHODS: Seven samples were selected to evaluate performance and estimate variability of reported results. Notably, a dilution series was included in the panel as a measure of reproducibility and sensitivity. Several performance criteria were evaluated for individual participants as well as in the cohort of all participants. RESULTS: A total of 109 laboratories participated and used 134 platforms, including 67 different combinations of extraction and PCR platforms and corresponding reagents. There were no false positives and 10 (1.2%) false negative results, including nine in the weakly positive sample (Ct ∼35.9, ∼640 copies/mL). Twenty (22%) laboratories reported results of mutation detection. Twenty-five (19%) test systems included amplification of human RNA as evidence of proper sampling. The overall linearity of Ct values from individual test systems for the dilution series was good, but inter-assay variability was high. Both operator-related and systematic failures appear to have caused incorrect results. CONCLUSIONS: Beyond providing certification for participating laboratories, EQA provides the opportunity for participants to evaluate their performance against others so that they may improve operating procedures and test systems. Well-selected EQA samples offer additional inferences to be made about assay sensitivity and reproducibility, which have practical applications.