Detection of MPXV DNA was performed as previously described [15] (link). In brief, specimens were either extracted on the Chemagic MSMI instrument (PerkinElmer) followed by amplification on the QuantStudio 12 K Flex (ThermoFisher) or extraction and amplification was performed on the cobas 6800 platform (Roche Diagnostics). Both assays used lab-developed primers and probes which targeted a conserved region of the viral polymerase gene common to the Orthopoxvirus genus [16] (link).
Cobas 6800 platform
Manufactured by Roche
Sourced in Switzerland, Italy
The Cobas 6800 platform is a fully automated, high-throughput molecular diagnostic system designed for clinical laboratories. It is capable of processing a wide range of sample types and performing various nucleic acid testing (NAT) assays. The Cobas 6800 platform provides efficient sample handling, accurate results, and reliable performance to support clinical decision-making.
Automatically generated - may contain errors
Lab products found in correlation
Quantstudio 5 platform, by Thermo Fisher Scientific (2 mentions)
Quantstudio 12k flex, by Thermo Fisher Scientific (1 mentions)
Chemagic msm 1 instrument, by PerkinElmer (1 mentions)
Starlet, by Seegene (1 mentions)
Maxwell rsc viral rna kit, by Promega (1 mentions)
Lc480 thermocycler, by Roche (1 mentions)
Taqman fast virus 1 step master mix, by Thermo Fisher Scientific (1 mentions)
Miseq platform, by Illumina (1 mentions)
10 protocols using cobas 6800 platform
1
MPXV DNA Detection Protocol
2
Comparative Analysis of SARS-CoV-2 Diagnostic Assays
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The Eastern Ontario Regional Laboratory Association (EORLA) virology laboratory provides centralized microbiology testing for the Eastern Ontario region. For the purpose of this study, nasopharyngeal swabs collected in appropriate media for viral nucleic acid stability were tested by qRT-PCR or transcription mediated amplification (TMA) on various automated platforms. Of the 270 samples received, 211 were extracted and tested for SARS-CoV-2 using either the Seegene AllplexTM SARS-CoV-2 Assay (E gene, N gene and RdRP gene detection) (Seegene, Toronto, ON), 24 were tested using the cobas® SARS-CoV-2 Test (E gene, Orf1a gene) on the cobas® 6800 platform (Roche Diagnostics Canada, Laval, QC), and the remaining 35 were tested with either the Panther Fusion® SARS-CoV-2 Assay (Orf1a and Orf1b gene regions) or the Aptima® SARS-CoV-2 Assay (TMA) (Orf1a and Orf1b gene regions) (Hologics Canada ULC, Mississauga, ON). Internal validation studies have demonstrated similar SARS-CoV-2 limits of detection for these devices (data not shown). For the Seegene AllplexTM assay, nucleic acid was extracted either on a Starlet (SeeGene) (107 samples) or MGI (BGI, Cambridge, MA) (105 samples) liquid handler, and the amplification reactions were done in a CFX96 Touch Real-Time PCR Detection System.
3
Post-Infection Symptom Monitoring Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
At the follow-up blood collections (five months and ten months post-infection), participants were asked to complete a written questionnaire, providing information about vaccination and infection status, and the duration of persistent symptoms (Long-COVID symptoms).
If participants had any symptoms during the study period, they were encouraged to visit the Liechtenstein National Testing Facility for reverse transcription-polymerase chain reaction (RT-PCR) testing, which was performed with either the COBAS 6800 platform (Roche Diagnostics, Rotkreuz, Switzerland) or the TaqPath assay on a QuantStudio 5 platform (Thermo Fisher Scientific, Allschwil, Switzerland) [24 (link),25 (link),26 (link)]. Positively tested participants (PCR and antibody tests, or only antibody tests) were subsequently contacted by the study team and asked to report their symptoms (fever, fever degree, chills, cough, sniff, dyspnea, anosmia, ageusia, pressure in the chest, sore throat, muscle pain, headache, fatigue, general feeling of illness, diarrhea, sickness, vomiting) and hospitalization status by a standardized questionnaire commissioned by telephone interview (Figure 2 ).
If participants had any symptoms during the study period, they were encouraged to visit the Liechtenstein National Testing Facility for reverse transcription-polymerase chain reaction (RT-PCR) testing, which was performed with either the COBAS 6800 platform (Roche Diagnostics, Rotkreuz, Switzerland) or the TaqPath assay on a QuantStudio 5 platform (Thermo Fisher Scientific, Allschwil, Switzerland) [24 (link),25 (link),26 (link)]. Positively tested participants (PCR and antibody tests, or only antibody tests) were subsequently contacted by the study team and asked to report their symptoms (fever, fever degree, chills, cough, sniff, dyspnea, anosmia, ageusia, pressure in the chest, sore throat, muscle pain, headache, fatigue, general feeling of illness, diarrhea, sickness, vomiting) and hospitalization status by a standardized questionnaire commissioned by telephone interview (
4
Feasibility and Outcomes of Point-of-Care Viral Load Testing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To assess trial feasibility, we evaluated the proportion of potentially eligible participants who were enrolled, who completed follow-up, and who had same-day VL testing (point-of-care arm only). We obtained approvals to retrospectively assess routine, deidentified laboratory, and clinical data from PCZ CDC to determine the total number of potentially eligible participants during the study period, allowing us to calculate the proportion we managed to enroll. To provide exploratory estimates of the potential effect of point-of-care VL testing, we assessed the primary outcome of viral suppression <50 copies/mL at 24 weeks after enrolment in each arm according to intention-to-treat. Outcome VLs were measured retrospectively testing stored samples with the cobas HIV-1 assay on the cobas 6800 platform (Roche, Basel, Switzerland). Additional prespecified exploratory outcomes were HIV drug resistance in each arm at study exit, time to detection of viral failure (consecutive VLs ≥1000 copies/mL), switch to second-line ART, and appropriate switch/transition to dolutegravir-based ART.
5
Roche cobas 6800 COVID-19 Detection
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The study was approved by the Comité d’Ethique Hospitalo-Facultaire Universitaire de Liège (reference number CE 2020/137). COVID-19 detection was routinely performed using the cobas 6800 platform (Roche). For this, 400 μl of nasopharyngeal swabs in a preservative medium (Amies or UTM) were first incubated at room temperature for 30 min with 400 μl of cobas PCR media kit (Roche) for viral inactivation. Samples were then loaded on the cobas 6800 platform using the cobas SARS-CoV-2 assay for the detection of the ORF1ab and E genes.
For qRT-PCR control and sequencing analysis, RNA was extracted from clinical samples (300 μl) on a Maxwell 48 device using the Maxwell RSC viral RNA kit (Promega) following a viral inactivation step using proteinase K according to the manufacturer’s instructions. RNA elution occurred in 50 μl RNase-free water, and 5 μl was used for the RT-PCR. Reverse transcription and RT-PCR were performed on a LC480 thermocycler (Roche) based on the Corman et al. (9 (link)) protocol for the detection of RdRP and E genes using the TaqMan fast virus 1-step master mix (Thermo Fisher). Primers and probes (Eurogentec, Belgium) were used as described by the authors (9 (link)).
For qRT-PCR control and sequencing analysis, RNA was extracted from clinical samples (300 μl) on a Maxwell 48 device using the Maxwell RSC viral RNA kit (Promega) following a viral inactivation step using proteinase K according to the manufacturer’s instructions. RNA elution occurred in 50 μl RNase-free water, and 5 μl was used for the RT-PCR. Reverse transcription and RT-PCR were performed on a LC480 thermocycler (Roche) based on the Corman et al. (9 (link)) protocol for the detection of RdRP and E genes using the TaqMan fast virus 1-step master mix (Thermo Fisher). Primers and probes (Eurogentec, Belgium) were used as described by the authors (9 (link)).
6
Quantitative SARS-CoV-2 Diagnostic Assays
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Nasal PCRs were conducted using Roche SARS CoV-2 qualitative real-time PCR (Cobas 6800 platform, Roche Diagnostics, Indianapolis, IN). Serology testing was performed using Roche Elecsys Anti-SARS-CoV-2 (Cobas platform) immunoassay. The immunoassay utilizes “high-affinity” antibodies, with a reported specificity of 99.8% and sensitivity of 100% at >14 days after PCR confirmation.
7
Evaluating SARS-CoV-2 Variant Detection
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Nasopharyngeal sites were swabbed from 150 consecutive outpatients presenting to the CoVID-19 Triage and Test Center at UHB for SCoV2 specific NAT testing from January 25th to February 28th 2022 (6 (link)). Swabs were collected in universal transport medium (UTM; Copan; Brescia, Italy), and analyzed using the cobas SARS-CoV-2 test on the cobas6800 platform (Roche) as described (3 (link)). Cobas SARS-CoV-2 Target 1 (ORF1a/b) Ct-values were used to assess RAT performance. Omicron BA.1 was confirmed in the 100 SCoV2-positive nasopharyngeal swabs. As Omicron BA.2 and BA.5 harbor the additional nucleocapsid mutation S413R, we obtained 100 Omicron BA.2 and 100 Omicron BA.5 positive nasopharyngeal swabs from consecutive outpatients at UHB from March 8 to July 15, 2022.
8
Characterizing SARS-CoV-2 Omicron Variants
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Nasopharyngeal sites were swabbed from 150 consecutive outpatients presenting to the CoVID-19 Triage and Test Center at UHB for SCoV2 specific NAT testing from January 25th to February 28th 2022 (6 (link)). Swabs were collected in universal transport medium (UTM; Copan; Brescia, Italy), and analyzed using the cobas SARS-CoV-2 test on the cobas6800 platform (Roche) as described (3 (link)). Cobas SARS-CoV-2 Target 1 (ORF1a/b) Ct-values were used to assess RAT performance. Omicron BA.1 was confirmed in the 100 SCoV2-positive nasopharyngeal swabs. As Omicron BA.2 and BA.5 harbor the additional nucleocapsid mutation S413R, we obtained 100 Omicron BA.2 and 100 Omicron BA.5 positive nasopharyngeal swabs from consecutive outpatients at UHB from March 8 to July 15, 2022.
9
Seroconversion and COVID-19 Symptom Duration
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
SARS-CoV-2 antibody tests were assessed at baseline (starting April 2020) and during follow-up (starting December 2020) by the medical laboratory Dr. Risch Ostschweiz AG (Buchs SG, Switzerland). The tests were assessed with an orthogonal test algorithm that employed electrochemiluminescence assays. These assay test for pan-immunoglobulins directed against the N antigen and the receptor-binding domain of the SARS-CoV-2 spike protein.19 (link) Seroconversion was assumed if the first blood sample was negative for SARS-CoV-2 antibodies and the second sample was positive.
If participants had any symptoms during the study period, they were encouraged to visit the Liechtenstein National Testing Facility for RT-PCR testing. The testing facility was open daily allowing for higher testing frequencies than that in other European countries.20 (link) RT-PCR was performed on either the COBAS 6800 platform (Roche Diagnostics, Rotkreuz, Switzerland) or the TaqPath assay on a QuantStudio 5 platform (Thermo Fisher Scientific, Allschwil, Switzerland).20–22 (link) Participants diagnosed with COVID-19 contacted the study team to discuss their symptoms and health statuses. Additionally, participants provided their date of SO and overall symptom duration, enabling us to calculate the symptom end (SE) date.
If participants had any symptoms during the study period, they were encouraged to visit the Liechtenstein National Testing Facility for RT-PCR testing. The testing facility was open daily allowing for higher testing frequencies than that in other European countries.20 (link) RT-PCR was performed on either the COBAS 6800 platform (Roche Diagnostics, Rotkreuz, Switzerland) or the TaqPath assay on a QuantStudio 5 platform (Thermo Fisher Scientific, Allschwil, Switzerland).20–22 (link) Participants diagnosed with COVID-19 contacted the study team to discuss their symptoms and health statuses. Additionally, participants provided their date of SO and overall symptom duration, enabling us to calculate the symptom end (SE) date.
10
Detecting HIV Drug Resistance Mutations
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
We tested VL with the cobas HIV‐1 assay (lower limit of quantitation 20 copies/ml) using the cobas 6800 platform (Roche) in the National Health Laboratory Service at the Inkosi Albert Luthuli Hospital in Durban. For all samples with VL ≥1000 copies/ml, we attempted sequencing of HIV‐1 pol (protease [PR], reverse transcriptase [RT] and integrase [IN]) at the KwaZulu‐Natal Research Innovation and Sequencing Plaform (KRISP). Following RNA extraction, we amplified PR, RT and IN genes using the amplification module of the Applied Biosystems HIV‐1 Genotyping Kit with Integrase (Thermo Fisher Scientific); and sequenced on the Illumina MiSeq platform (Illumina). We identified drug resistance mutations at >20% frequency using Stanford HIVdb (version 9.1).
The person conducting all the above tests was blinded to the results from other methods.
The person conducting all the above tests was blinded to the results from other methods.
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!