RT-qPCR and RNA extraction for SARS-CoV-2 diagnosis were performed on a Roche Cobas8800 (Roche Diagnostics, Switzerland), on a GeneXpert Infinity (Cepheid, Sunnyvale, USA), or on a MagExStar (Hamilton, Bonaduz, Switzerland). Roche Cobas8800 and GeneXpert Infinity are fully automated systems for RNA extraction and amplification, with integrated detection systems based on RT-qPCR. For SARS-CoV-2 diagnosis, we used the Xpert Xpress SARS-CoV-2 assay (Cepheid, Sunnyvale, USA) detecting the N2 gene and the E gene on the GeneXpert Infinity and the cobas® SARS-CoV-2 Test Kit detecting orf1a/b gene (SARS-CoV-2) and E gene (pan-Sarbecoviren) on the Cobas8800. When samples were analyzed on a MagExStar, RNA was extracted with an RNAdvance Kit from Beckman Coulter (Beckman Coulter, Indianapolis, USA) as previously described [11 (link)]. Detection of RNA was carried out by conventional RT-qPCR using the ampliCube Coronavirus SARS-CoV-2 assay from Mikrogen Diagnostik (Mikrogen, Neuried, Germany). RNA extraction and PCR assay detecting the envelope (E) gene of B-lineage betacoronavirus (FAM) and the Orf1a gene (HEX) were performed according to the manufacturer’s instructions. RT-qPCR was carried out on a Bio-Rad CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Feldkirchen, Germany).
Xpert xpress sars cov 2 assay
Manufactured by Cepheid
Sourced in United States, France
The Xpert Xpress SARS-CoV-2 assay is a real-time reverse transcription-polymerase chain reaction (RT-PCR) in-vitro diagnostic test designed for the qualitative detection of SARS-CoV-2 viral nucleic acids in respiratory specimens.
Automatically generated - may contain errors
Lab products found in correlation
Cobas sars cov 2 assay, by Roche (3 mentions)
Genexpert system, by Cepheid (3 mentions)
Cdc 2019 novel coronavirus real time rt pcr assay, by Thermo Fisher Scientific (2 mentions)
Taqpath covid 19 rt pcr assay, by Thermo Fisher Scientific (2 mentions)
Simplexa covid 19 assay, by DiaSorin (2 mentions)
Lyra direct sars cov 2 assays, by Quidel (2 mentions)
Aptima sars cov 2 assay, by Hologic (2 mentions)
Alinity m sars cov 2 assay, by Abbott (2 mentions)
Neumodx sars cov 2 assay, by Qiagen (2 mentions)
Simplexa covid 19 direct assay, by DiaSorin (2 mentions)
Cfx96 touch real time pcr detection system, by Bio-Rad (2 mentions)
Rnadvance kit, by Beckman Coulter (1 mentions)
Genexpert infinity, by Cepheid (1 mentions)
Kingfisher, by Thermo Fisher Scientific (1 mentions)
Taqpath covid 19 ce ivd rt pcr kit, by Thermo Fisher Scientific (1 mentions)
Panther fusion sars cov 2 assay, by Hologic (1 mentions)
Genexpert xvi system, by Cepheid (1 mentions)
Minion device, by Oxford Nanopore (1 mentions)
Reliance one step multiplex supermix, by Bio-Rad (1 mentions)
Dsp virus pathogen mini kit, by Qiagen (1 mentions)
25 protocols using xpert xpress sars cov 2 assay
1
Automated SARS-CoV-2 Diagnosis Protocols
2
SARS-CoV-2 Detection from Frozen Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Frozen remnant clinical specimens were tested according to the manufacturer’s instructions (3 ). Briefly, 50 μl of specimen was used as input for sample extraction. Samples were extracted by adding the specimen to 50 μl of CNL (lysis) solution and heating for 2 min at 95°C in the Solas 8 instrument. For detection, 5 μl of the heated lysate is used as input for the COVID-19 2SF assay. Discordant results were resolved by repeat testing of the clinical specimen by the reference method, the Cepheid Xpert Xpress SARS-CoV-2 assay (4 ).
3
SARS-CoV-2 Detection from Frozen Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Frozen remnant clinical specimens were tested according to the manufacturer’s instructions (3 ). Briefly, 50 μl of specimen was used as input for sample extraction. Samples were extracted by adding the specimen to 50 μl of CNL (lysis) solution and heating for 2 min at 95°C in the Solas 8 instrument. For detection, 5 μl of the heated lysate is used as input for the COVID-19 2SF assay. Discordant results were resolved by repeat testing of the clinical specimen by the reference method, the Cepheid Xpert Xpress SARS-CoV-2 assay (4 ).
4
SARS-CoV-2 Detection by mRT-PCR
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
SARS-CoV-2 RNA present in nasopharyngeal swab specimens was assayed by mRT-PCR using the Cepheid® Xpert Xpress SARS-CoV-2 assay on Infinity. This assay consists of two amplicons with specific sets of primers/probes. Amplicon 1 targets the region in the viral nucleocapsid gene unique to SARS-CoV-2. Amplicon 2 targets a conserved region of the viral protein envelope gene homologous to all coronaviruses of the Sarbecovirus sub-genus. In addition, a Sample Processing Control and a Probe Check Control are also included for the assay performance. The assay analytical sensitivity was determined by serial dilutions of ZeptoMetrix virus stock—NATSARS(CoV2)-ERC with a known concentration. The limit of detection is 30 virions per assay.
5
Comparative SARS-CoV-2 Testing Evaluation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
De-identified frozen specimens were shared with the Cornell COVID-19 Testing Laboratory (CCTL) by three other COVID-19 testing laboratories in the United States. A total of 201 nasopharyngeal (NP) swabs and 24 anterior nares (AN) swabs were included in this study. Sixty NP swabs were tested in originating laboratory 1 using the Xpert® Xpress SARS-CoV-2 assay (Cepheid, Sunnyvale, CA), and of these, 30 were positive and 30 were negative for SARS-CoV-2. The other 141 NP swabs were tested in originating laboratory 2 using the TaqPath COVID-19 Combo Kit Multiplex Real-Time RT-PCR assay (Thermo Fisher Scientific Inc., Waltham, MA); 70 were positive and 71 were negative SARS-CoV-2. The AN swabs were originally tested using the New York State Department of Health (NYSDOH) (laboratory 3) SARS-CoV-2 RT-PCR assay; 12 were positive and 12 were negative for SARS-CoV-2.
6
SARS-CoV-2 Detection via Molecular Assays
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Nasopharyngeal swabs or combined oropharyngeal and nares swabs were sent to the Clinical Virology Laboratory at CHLA for testing. The molecular assays used were the CDC 2019-Novel Coronavirus Real-Time RT-PCR assay, the Taqpath COVID-19 RT-PCR assay (Thermo Fisher, Walham, MA), the Xpert Xpress SARS-CoV-2 assay (Cepheid, Sunnyvale, CA), and the Simplexa COVID-19 assay (Diasorin Molecular, Cypress, CA). Total nucleic acid was extracted according to manufacturer's instructions as outlined in the respective Emergency Use Authorization [[11] , [12] , [13] , [14] ]. Viral loads (copies/mL) were calculated based on a standard curve generated by testing samples with known viral copy numbers for each assay as previously described [11 ].
7
Comparative Analysis of SARS-CoV-2 RT-PCR Assays
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
SARS-CoV-2 RT-PCR testing was performed using the RealStar SARS-CoV-2 RT-PCR Kit 1.0 reagent system (Altona, Hamburg, Germany) which targets on the S gene and E gene, the Cobas SARS-CoV-2 Assay (Roche Molecular Systems, Inc., Branchburg, NJ) which targets the ORF1ab and E genes, and the Xpert Xpress SARS-CoV-2 Assay (Cepheid, Inc., Sunnyvale, CA) which targets the N2 and E genes [16 (link)]. The ORF1ab and N2 genes are specific for SARS-Cov-2, while the E gene is a pan-Sarbecovirus marker. Based on the previous data [16 (link)], the diagnostic performance of both the Cobas 6800 and the Xpert Xpress SARS-CoV-2 Assays are considered equivalent. SARS-CoV-2 RT-PCR cycle threshold (CT) values of the SARS-CoV-2-specific target, which correlate inversely with the quantitative viral load [17 (link)], were obtained using the Cobas SARS-CoV-2 Assay and Xpert Xpress SARS-CoV-2 RT-PCR Assay, as the values for the SARS-CoV-2-specific gene were comparable between platforms [16 (link)]. CT values from the RealStar SARS-CoV-2 RT-PCR assay were excluded from the analysis as the values are not directly comparable to the other two platforms.
8
COVID-19 Testing Protocols and Assay Comparison
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The majority of COVID-19 testing was performed using Quidel Lyra Direct SARS-CoV-2 Assays.
Dry nasal swabbing was obtained by trained urgent care technicians or trained swab-clinic staff. The assay was approved by the FDA under emergency use authorization (EAU). No peer-reviewed, published data on specificity / sensitivity was available for this specific assay. FDA provided data demonstrates 100% positive and negative percent agreement with controlled spike samples at 5x level of detection (LoD), and 1 false negative at 1x LoD. A comparison study to similar EAU assays was conducted resulting in 96% positive percent agreement (PPA) and 100% negative percent agreement (NPA). 8 A COVID-19 Pretest Probability Calculator Frederick K. Hayden Jr., MMSc, PA-C
In the later period of sampled data, the Cepheid Xpert Xpress SARS-CoV-2 assay used in limited case by case basis for rapid results-mostly for patients requiring stat admission testing for other non-COVID-19 problems. It is undetermined if any of this study's samples include results from this assay. These swabs were obtained via nasopharyngeal samples by the same trained staff. Similarly, there is no peer-reviewed published data; however, FDA EUA documentation reveals the Cephid assay has 97% PPA and 95% NPA to other EUA samples. 9
Dry nasal swabbing was obtained by trained urgent care technicians or trained swab-clinic staff. The assay was approved by the FDA under emergency use authorization (EAU). No peer-reviewed, published data on specificity / sensitivity was available for this specific assay. FDA provided data demonstrates 100% positive and negative percent agreement with controlled spike samples at 5x level of detection (LoD), and 1 false negative at 1x LoD. A comparison study to similar EAU assays was conducted resulting in 96% positive percent agreement (PPA) and 100% negative percent agreement (NPA). 8 A COVID-19 Pretest Probability Calculator Frederick K. Hayden Jr., MMSc, PA-C
In the later period of sampled data, the Cepheid Xpert Xpress SARS-CoV-2 assay used in limited case by case basis for rapid results-mostly for patients requiring stat admission testing for other non-COVID-19 problems. It is undetermined if any of this study's samples include results from this assay. These swabs were obtained via nasopharyngeal samples by the same trained staff. Similarly, there is no peer-reviewed published data; however, FDA EUA documentation reveals the Cephid assay has 97% PPA and 95% NPA to other EUA samples. 9
9
SARS-CoV-2 Detection from Nasopharyngeal Swabs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The material for analysis corresponded to the stored remnants of nasopharyngeal swabs that had been taken for diagnostic purposes. RNA was purified from 300 μL of nasopharyngeal exudate in a KingFisher (Thermo Fisher Scientific) equipment. Cepheid Xpert Xpress SARS-CoV-2 Assay (Cepheid, CA) and TaqPath COVID-19 CE-IVD RT-PCR kit (Thermo Fisher Scientific) were applied for SARS-CoV-2 RT-PCR based detection as per the manufacturer’s instructions.
10
SARS-CoV-2 RNA Detection in Respiratory Swabs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
COVID-19 was diagnosed by the presence of SARS-CoV-2 RNA in respiratory swabs. RNA was detected via the Abbott ID Now SARS-CoV-2 reverse-transcription polymerase chain reaction (PCR) high-throughput assay or the Cepheid Xpert Xpress SARS-CoV-2 assay, conducted at the LECOM Health Senior Living Center Laboratory, supported by the Regional Response Health Collaborative (RRHC) Program of the Pennsylvania Department of Human Services, Pennsylvania Department of Health, Pennsylvania Emergency Management Agency, and additional health systems RRHC Program, 2020).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!