scholarly journals Evaluation of Sample Pooling for Screening of SARS-CoV-2

2020 ◽  
Author(s):  
Andargachew Mulu ◽  
Dawit Hailu Alemayehu ◽  
Fekadu Alemu ◽  
Dessalegn Abeje Tefera ◽  
Sinknesh Wolde ◽  
...  
Keyword(s):  
Ad Hoc ◽  
Clinical Sample ◽  
Diagnostic Testing ◽  
Positive Sample ◽  
Clinical Samples ◽  
Global Public Health ◽  
Rt Pcr ◽  
Resource Saving ◽  
Public Health Importance ◽  
Ct Value

Abstract Background: The coronavirus disease (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability efficient method is urgently needed.Objectives: To establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2 Methods: Direct clinical sample and NA pooling approach was used for the standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 targeting the envelop (E) and open reading frame (ORF1ab) genomic region of the virus. In this approach, experimental pools were created using SARS CoV-2 positive clinical samples spiked with up to 9 negative samples prior to NA extraction step to have a final extraction volume of 200μL (maximum dilution factor of 10). Viral NA was also subsequently extracted from each pool and tested using the SARS CoV-2 RT-PCR assay.Results: We found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the ct value of the original sample, corresponding to high, medium, and low SARS CoV-2 viral copies/reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend poling of 4 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 4 in 1 was expected to retain accuracy of the test irrespective of the ct value (relative ribonucleic acid RNA copy number) of the sample spiked and result in a 237% increase in testing efficiency. Conclusions: The approaches showed its concept in easily customized and resource-saving manner and would allow expanding of current screening capacities and enable the expansion of detection in the community.

scholarly journals Evaluation of Sample Pooling for Screening of SARS CoV-2

2020 ◽  
Author(s):  
Andargachew Mulu ◽  
Dawit Hailu Alemayehu ◽  
Fekadu Alemu ◽  
Dessalegn Abeje Tefera ◽  
Sinknesh Wolde ◽  
...  
Keyword(s):  
Ad Hoc ◽  
Clinical Sample ◽  
Diagnostic Testing ◽  
Positive Sample ◽  
Clinical Samples ◽  
Global Public Health ◽  
Rt Pcr ◽  
Resource Saving ◽  
Public Health Importance ◽  
Ct Value

AbstractBackgroundThe coronavirus disease (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability efficient method is urgently needed.ObjectivesTo establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2MethodsDirect clinical sample and NA pooling approach was used for the standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 targeting the envelop (E) and open reading frame (ORF1ab) genomic region of the virus. In this approach, experimental pools were created using SARS CoV-2 positive clinical samples spiked with up to 9 negative samples prior to NA extraction step to have a final extraction volume of 200 μL (maximum dilution factor of 10). Viral NA was also subsequently extracted from each pool and tested using the SARS CoV-2 RT-PCR assay.ResultsWe found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the ct value of the original sample, corresponding to high, medium, and low SARS CoV-2 viral copies/reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend poling of 4 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 4 in 1 was expected to retain accuracy of the test irrespective of the ct value (relative RNA copy number) of the sample spiked and result in a 237% increase in testing efficiency.ConclusionsThe approaches showed its concept in easily customized and resource-saving manner and would allow expanding of current screening capacities and enable the expansion of detection in the community.

scholarly journals Evaluation of sample pooling for screening of SARS CoV-2

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247767
Author(s):  
Andargachew Mulu ◽  
Dawit Hailu Alemayehu ◽  
Fekadu Alemu ◽  
Dessalegn Abeje Tefera ◽  
Sinknesh Wolde ◽  
...  
Keyword(s):  
Clinical Sample ◽  
Diagnostic Testing ◽  
Positive Sample ◽  
Clinical Samples ◽  
Global Public Health ◽  
Rt Pcr ◽  
Resource Saving ◽  
Public Health Importance ◽  
Ct Value ◽  
Sample Pooling

Background The coronavirus disease 2019 (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability, an efficient method is urgently needed. Objectives To establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2. Methods We evaluated pooling approach on both direct clinical and NA samples. The standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 was employed targeting the nucleocapsid (N) and open reading frame (ORF1ab) genomic region of the virus. The experimental pools were created using SARS CoV-2 positive clinical samples and extracted RNA spiked with up to 9 negative samples. For the direct clinical samples viral NA was extracted from each pool to a final extraction volume of 200μL, and subsequently both samples tested using the SARS CoV-2 RT-PCR assay. Results We found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the cycle threshold (Ct) value of the original sample, corresponding to high, and low SARS CoV-2 viral copies per reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend pooling of 4/5 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 5 in 1 was expected to retain accuracy of the test irrespective of the Ct value samples spiked, and result in a 137% increase in testing efficiency. Conclusions The approaches showed its concept in easily customized and resource-saving manner and would allow expanding of current screening capacities and enable the expansion of detection in the community. We recommend clinical sample pooling of 4 or 5 in 1. However, we don’t advise pooling of clinical samples when disease prevalence is greater than 7%; particularly when sample size is large.

scholarly journals Correlation between Cycle Threshold (Ct) Value and IL-6 and D-Dimer in Chip-based RT-PCR Positive COVID-19 Cases: Study from a Stand-alone Laboratory

2021 ◽  
pp. 1-9
Author(s):  
Chhavi Gandhi ◽  
H. N. Ravikumar ◽  
Vani Ravikumar ◽  
C. Vani
Keyword(s):  
Interleukin 6 ◽  
Clinical Sample ◽  
Threshold Value ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Ct Value ◽  
Asymptomatic Patients ◽  
Significant Difference ◽  
D Dimer

Background: Novel Coronavirus (SARS-COV-2) is a leading cause of morbidity and mortality since the beginning of 2020 leading to range of symptoms from mild flu to respiratory distress, which is called COVID-19. RTPCR being the main diagnostic test can confirm the presence of the virus in the clinical samples, while various studies have defined Interleukin-6 and D-dimer as potent biomarker for severity. In this study, we have attempted to correlate the severity of COVID-19 with the presence of IL-6 and D-dimer and the Cycle threshold (Ct vlue) as determined by chip based RTPCR. Aim: The study aims to correlate the Cycle threshold value obtained after chip-based RT-PCR with markers such as IL-6 and D-Dimers.                                                      Methodology: It is a retrospective, observational study done in 799 subjects  in a span of three months (August 2020 to October 2020) at R V Metropolis Diagnostic and Healthcare Pvt Ltd. All symptomatic patients who tested positive in the Laboratory for COVID-19 by chip-based RT-PCR were included. Chip based RTPCR or Truenat test was performed on Nasopharyngeal swabs of the suspected subjects. Interleukin-6 was determined by Electrochemiluminiscence assay while D-dimer was done on the principle of Chemiluminiscence. Statistical Analysis Used: SPSS 12.0 version. Results: Total number of subjects enrolled were 799, with mean age of the subjects being 46.80± 17.55 years. In the study, males were found to be affected by COVID-19 more than females with ratio of male to female being 1.65:1. 498 (62.3%) of males presented with COVID-19 while it was observed in 301 (37.6%) females. Out of 799 subjects, 289 (36.2%) were symptomatic and out of 289 subjects, 140 (17.5% of total subjects) required hospitalisation. Cycle threshold values of both screening as well as confirmatory genes were determined separately in the cases of symptomatic and asymptomatic cases and there was no significant difference between the Ct values in cases of symptomatic and asymptomatic patients. Symptomatic patients were subcategorised under hospitalised and non-hospitalised and Again, no significant difference was seen between the two subset of patients in terms of Ct-value and, indirectly, the viral load of their clinical sample. The results convey that IL-6 and D-Dimer was significantly high (p=0.001 and <0.001 respectively) in case of symptomatic patients.D-Dimer was significantly high (p= <0.001) in the patients who needed hospitalisation. IL-6 was significantly raised as well (p=0.02). Screening and confirmatory gene were found to have no significant relationship with IL-6 and D-Dimer, neither any correlation was observed with them. Conclusion: Biomarkers such as Interleukin-6 and D-dimer can very well help in determining the severity and need for hospitalisation in a COVID-19 affected patient, but they have been found to have no relationship with cycle threshold value of RTPCR in our study.

Detecting SARS-CoV-2 by Realtime RT-PCR in clinical samples collected in the North of Vietnam

2021 ◽  
Vol 30 (9) ◽  
pp. 11-17
Author(s):  
Hoang Vu Mai Phuong ◽  
Ung Thi Hong Trang ◽  
Nguyen Vu Son ◽  
Le Thi Thanh ◽  
Nguyen Le Khanh Hang ◽  
...  
Keyword(s):  
Viral Load ◽  
Average Rate ◽  
Clinical Samples ◽  
Viet Nam ◽  
Rt Pcr ◽  
Ct Value ◽  
The North ◽  
Viral Load Data ◽  
The Mean ◽  
High Level

From January to August 2020, Northern Viet Nam faced a COVID-19 outbreak, up to September 2020, there were 1122 confrmed cases of SARS-CoV-2, of which 465 cases were imported from Europe, America and Asia, 657 cases were identifed domestically. A total of 30,686 samples were collected during the SARS-CoV-2 outbreak in Northern Viet Nam and examined by Real-time RT-PCR using primers and probe from Charite - Berlin protocol. This study showed the initial results of SARS-CoV-2 detection and RNA quantitative in positive samples. The positive rate was 0.8%, ranging from 0.4 to 3.5% according to collection sites. Out of 251 positive samples, the mean Ct value was 28 (IQR: 22.3-32; range 14 - 38). The positive samples had a Ct value below 30 was 68.5%, there was no signifcant difference between the Ct value of the group ≤ 30 and > 30. The mean of the RNA copies/µl was 8.4.107, (IQR: 2.29.106 - 1.83.109 RNA copies/µl, range: 1.95.103 – 4.95.1011). In the group of imported COVID-19 cases, the rate of virus at low level was 29%, an average was 56% and at high level was 15%. In the community groups, the viral load data showed that the average rate at low, intermediate and high level were 20%, 63% and 17% respectively. The proportion of high-level viral load may raise an alert to start the quarantine process to reduce the transmission of SARS-CoV-2

scholarly journals Investigation of pooling strategies using clinical COVID-19 samples for more efficient diagnostic testing

2020 ◽  
Author(s):  
Samantha H Adikari ◽  
Emily Z Alipio Lyon ◽  
Attelia D Hollander ◽  
Alina Deshpande ◽  
Elizabeth Hong-Geller
Keyword(s):  
Diagnostic Testing ◽  
Rna Extraction ◽  
Positive Sample ◽  
Viral Rna ◽  
Clinical Samples ◽  
Extraction Column ◽  
Diagnostic Assay ◽  
Significant Difference ◽  
Pooling Strategies ◽  
Single Positive

When testing large numbers of clinical COVID-19 samples for diagnostic purposes, pooling samples together for processing can offer significant reductions in the materials, reagents, time, and labor needed. We have evaluated two different strategies for pooling independent nasopharyngeal swab samples prior to testing with an EUA-approved SARS-CoV-2 RT-qPCR diagnostic assay. First, in the Dilution Study, we assessed the assay's ability to detect a single positive clinical sample diluted in multiple negative samples before the viral RNA extraction stage. We observed that positive samples with Ct values at ~30 can be reliably detected in pools of up to 30 independent samples, and positive samples with Ct values at ~35 can be detected in pools of 5 samples. Second, in the Reloading Study, we assessed the efficacy of reloading QIAamp viral RNA extraction columns numerous times using a single positive sample and multiple negative samples. We determined that one RNA extraction column can be reloaded with up to 20 clinical samples (1 positive and 19 negatives) sequentially without any loss of signal in the diagnostic assay. Furthermore, we found there was no significant difference in assay readout whether the positive sample was loaded first or last in a series of 20 samples. These results demonstrate that different pooling strategies can lead to increased process efficiencies for COVID-19 clinical diagnostic testing.

scholarly journals SalivaSTAT: Direct-PCR and pooling of saliva samples collected in healthcare and community setting for SARS-CoV-2 mass surveillance

2020 ◽  
Author(s):  
Nikhil S Sahajpal ◽  
Ashis K Mondal ◽  
Sudha Ananth ◽  
Allan Njau ◽  
Pankaj Ahluwali ◽  
...  
Keyword(s):  
Clinical Sample ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Community Setting ◽  
Absolute Quantification ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Direct Pcr ◽  
Sample Pooling ◽  
Saliva Collection

BackgroundThe limitations of widespread current COVID-19 diagnostic testing lie at both pre-analytical and analytical stages. Collection of nasopharyngeal swabs is invasive and is associated with exposure risk, high cost, and supply-chain constraints. Additionally, the RNA extraction in the analytical stage is the most significant rate-limiting step in the entire testing process. To alleviate these limitations, we developed a universal saliva processing protocol (SalivaSTAT) that would enable an extraction free RT-PCR test using any of the commercially available RT-PCR kits.MethodsWe optimized saliva collection devices, heat-shock treatment and homogenization. The effect of homogenization on saliva samples for extraction-free RT-PCR assay was determined by evaluating samples with and without homogenization and preforming viscosity measurements. Saliva samples (872) previously tested using the FDA-EUA method were reevaluated with the optimized SalivaSTAT protocol using two widely available commercial RT-PCR kits. Further, a five-sample pooling strategy was evaluated as per FDA guidelines using the SalivaSTAT protocol.ResultsThe saliva collection (done without any media) performed comparable to the FDA-EUA method. The SalivaSTAT protocol was optimized by incubating saliva samples at 95°C for 30-minutes and homogenization, followed by RT-PCR assay. The clinical sample evaluation of 630 saliva samples using the SalivaSTAT protocol with PerkinElmer (600-samples) and CDC (30-samples) RT-PCR assay achieved positive (PPA) and negative percent agreement (NPA) of 95.8% and 100%, respectively. The LoD was established as ∼20-60 copies/ml by absolute quantification. Further, a five-sample pooling evaluation using 250 saliva samples achieved a PPA and NPA of 92% and 100%, respectively.ConclusionWe have optimized an extraction-free direct RT-PCR assay for saliva samples that demonstrated comparable performance to FDA-EUA assay (Extraction and RT-PCR). The SalivaSTAT protocol is a rapid, sensitive, and cost-effective method that can be adopted globally, and has the potential to meet testing needs and may play a significant role in management of the current pandemic.

scholarly journals SalivaSTAT: Direct-PCR and Pooling of Saliva Samples Collected in Healthcare and Community Setting for SARS-CoV-2 Mass Surveillance

Diagnostics ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 904
Author(s):  
Nikhil S. Sahajpal ◽  
Ashis K. Mondal ◽  
Sudha Ananth ◽  
Allan Njau ◽  
Pankaj Ahluwalia ◽  
...  
Keyword(s):  
Clinical Sample ◽  
Diagnostic Testing ◽  
Community Setting ◽  
Absolute Quantification ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Direct Pcr ◽  
Comparable Performance ◽  
Sample Pooling ◽  
Saliva Collection

Objectives: Limitations of widespread current COVID-19 diagnostic testing exist in both the pre-analytical and analytical stages. To alleviate these limitations, we developed a universal saliva processing protocol (SalivaSTAT) that would enable an extraction-free RT-PCR test using commercially available RT-PCR kits. Methods: We optimized saliva collection devices, heat-shock treatment, and homogenization. Saliva samples (879) previously tested using the FDA-EUA method were reevaluated with the optimized SalivaSTAT protocol using two widely available commercial RT-PCR kits. A five-sample pooling strategy was evaluated as per FDA guidelines. Results: Saliva collection (done without any media) showed performance comparable to that of the FDA-EUA method. The SalivaSTAT protocol was optimized by incubating saliva samples at 95 °C for 30-min and homogenization, followed by RT-PCR assay. The clinical sample evaluation of 630 saliva samples using the SalivaSTAT protocol with PerkinElmer (600-samples) and CDC (30-samples) RT-PCR assay achieved positive (PPA) and negative percent agreements (NPAs) of 95.0% and 100%, respectively. The LoD was established as ~60–180 copies/mL by absolute quantification. Furthermore, a five-sample-pooling evaluation using 250 saliva samples achieved a PPA and NPA of 92% and 100%, respectively. Conclusion: We have optimized an extraction-free RT-PCR assay for saliva samples that demonstrates comparable performance to FDA-EUA assay (Extraction and RT-PCR).

scholarly journals Comparative analysis of the diagnostic performance of five commercial COVID-19 qRT PCR kits used in India

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
J. Singh ◽  
A. K. Yadav ◽  
A. Pakhare ◽  
P. Kulkarni ◽  
L. Lokhande ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Diagnostic Performance ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Clinical Samples ◽  
Diagnostic Process ◽  
Control Group ◽  
Rt Pcr ◽  
Short Period ◽  
Commercial Kits

AbstractTo meet the unprecedented requirement of diagnostic testing for SARS-CoV-2, a large number of diagnostic kits were authorized by concerned authorities for diagnostic use within a short period of time during the initial phases of the ongoing pandemic. We undertook this study to evaluate the inter-test agreement and other key operational features of 5 such commercial kits that have been extensively used in India for routine diagnostic testing for COVID-19. The five commercial kits were evaluated, using a panel of positive and negative respiratory samples, considering the kit provided by National Institute of Virology, Indian Council of Medical Research (2019-nCoV Kit) as the reference. The positive panel comprised of individuals who fulfilled the 3 criteria of being clinically symptomatic, having history of contact with diagnosed cases and testing positive in the reference kit. The negative panel included both healthy and disease controls, the latter being drawn from individuals diagnosed with other respiratory viral infections. The same protocol of sample collection, same RNA extraction kit and same RT-PCR instrument were used for all the kits. Clinical samples were collected from a panel of 92 cases and 60 control patients, who fulfilled our inclusion criteria. The control group included equal number of healthy individuals and patients infected with other respiratory viruses (n = 30, in each group). We observed varying sensitivity and specificity among the evaluated kits, with LabGun COVID-19 RT-PCR kit showing the highest sensitivity and specificity (94% and 100% respectively), followed by TaqPath COVID-19 Combo and Allplex 2019-nCoV assays. The extent of inter-test agreement was not associated with viral loads of the samples. Poor correlation was observed between Ct values of the same genes amplified using different kits. Our findings reveal the presence of wide heterogeneity and sub-optimal inter-test agreement in the diagnostic performance of the evaluated kits and hint at the need of adopting stringent standards for fulfilling the quality assurance requirements of the COVID-19 diagnostic process.

scholarly journals Accuracy of Roche SARS-CoV-2 Rapid Antigen Test in Nasopharyngeal Swab: Clinical Impression Matters

2021 ◽  
Vol 2 (10) ◽  
pp. 929-938
Author(s):  
Khin Phyu Pyar ◽  
Khine Khine Su ◽  
Kyaw Wunna ◽  
Myo Thant ◽  
Kaung Myat ◽  
...  
Keyword(s):  
Predictive Value ◽  
False Negative ◽  
Hospital Setting ◽  
Clinical Samples ◽  
Nasopharyngeal Swab ◽  
Clinical Impression ◽  
Antigen Test ◽  
Rt Pcr ◽  
Ct Value

Background: In COVID-19 pandemic, the diagnosis and treatment must be as early as possible to save the life of each patient. Moreover, screening of asymptomatic carriers, close contacts or healthy subjects must not be delay to prevent transmission to publics. For confirmation of diagnosis of SARS-CoV-2 infection, nasopharyngeal swab must be tested either by real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR) tests or Rapid Antigen Test (RAT). RAT is faster, easier and cheaper; thus, it is suitable for health service in developing country. Objectives: The aim of this study was to assess the diagnostic accuracy of Roche SARS-CoV-2 Rapid Antigen Test (RAT) in diagnosing SARS-CoV-2 infection. Methods: Hospital based exploratory study was done in out-patient department and fever clinic, and molecular laboratory of No. (1) Defence Services General Hospital. Nasopharyngeal swabs were taken, and the Roche SARS- CoV-2 RAT was conducted in parallel with RT-PCR test (reference standard). Results: Among the 932 patients/subjects recruited, RT-PCR was positive in 468 individuals, corresponding to a prevalence of 50.2%. The RAT was positive in 363 patients (60.4%), false positive in 120 patients; it was negative in 569 individuals (39.6%), false negative in 225 patients. The overall sensitivity of the RAT was 51.9% (95% Confidence Interval [CI] 47.29-56.53) and, the specificity was 74.1% (95% CI 69.9-78.07); positive predictive value was 66.9% and negative predictive value was 60.5%. The sensitivity varied with Ct value; 78% in clinical samples with Ct values < 20, 57.5% in those with Ct values between 21 and 25, 41.8% in samples with Ct values between 26 and 30, and, 36.4% in samples with Ct value > 30. Conclusion: The accuracy of the SARS-CoV-2 Roche RAT in diagnosing SARS-CoV-2 infections was inferior to RT-PCR and manufacturer’s data. The sensitivity was with low Cycle threshold values < 20 which were inversely related to the viral load. RAT test should be used in association with clinical impression of physicians. In hospital setting especially in emergency department, the role of RAT should be reconsidered in those patients presenting with anosmia and some cases of dyspnoea, late symptoms in the course of disease, as the RAT results would be false negative. Other errors may arise if the operator for RAT has to handle more than recommended tests per hour especially in the peak of epidemics.

scholarly journals Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel, the First Rapid Multiplex PCR Commercial Assay for SARS-CoV-2 Detection

2020 ◽  
Vol 58 (8) ◽  
Author(s):  
Benoit Visseaux ◽  
Quentin Le Hingrat ◽  
Gilles Collin ◽  
Donia Bouzid ◽  
Samuel Lebourgeois ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Limit Of Detection ◽  
Clinical Sample ◽  
Point Of Care ◽  
Sample Pretreatment ◽  
Tracheal Aspirate ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Viral Neutralization ◽  
Efficient Detection

ABSTRACT In the race to contain severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), efficient detection and triage of infected patients must rely on rapid and reliable testing. In this work, we performed the first evaluation of the QIAstat-Dx respiratory SARS-CoV-2 panel (QIAstat-SARS) for SARS-CoV-2 detection. This assay is the first rapid multiplex PCR (mPCR) assay, including SARS-CoV-2 detection, and is fully compatible with a non-PCR-trained laboratory or point-of-care (PoC) testing. This evaluation was performed using 69 primary clinical samples (66 nasopharyngeal swabs [NPS], 1 bronchoalveolar lavage fluid sample [BAL], 1 tracheal aspirate sample, and 1 bronchial aspirate sample) comparing SARS-CoV-2 detection with the currently WHO-recommended reverse transcription-PCR (RT-PCR) (WHO-RT-PCR) workflow. Additionally, a comparative limit of detection (LoD) assessment was performed for QIAstat-SARS and WHO-RT-PCR using a quantified clinical sample. Compatibility of sample pretreatment for viral neutralization or viscous samples with the QIAstat-SARS system were also tested. The QIAstat-Dx respiratory SARS-CoV-2 panel demonstrated a sensitivity comparable to that of the WHO-recommended assay with a limit of detection at 1,000 copies/ml. The overall percent agreement between QIAstat-Dx SARS and WHO-RT-PCR on 69 clinical samples was 97% with a sensitivity of 100% (40/40) and specificity at 93% (27/29). No cross-reaction was encountered for any other respiratory viruses or bacteria included in the panel. The QIAstat-SARS rapid multiplex PCR panel provides a highly sensitive, robust, and accurate assay for rapid detection of SARS-CoV-2. This assay allows rapid decisions even in non-PCR-trained laboratory or point-of-care testing, allowing innovative organization.

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