All tests were performed retrospectively on aliquots of whole CSF stored at −80°C immediately after lumbar puncture. Total nucleic acid (NA) was extracted from 100 µl of CSF specimens using an automated easyMAG system (bioMérieux, Marcy l'Étoile, France), following the manufacturer's instructions. Internally controlled real-time (RT-) PCRs were utilized to detect several meningitis/encephalitis-associated viruses [including HSV, cytomegalovirus (CMV), VZV, Epstein-Barr Virus (EBV), EVs, Nipah virus, influenza A and B virus, flaviviruses (generic) and Mumps virus] as well as four bacterial pathogens (including Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae type b and Streptococcus suis). If clinically indicated, saliva was collected and tested by rabies PCR. All the PCR procedures were carried out as described in our previous studies [8] (link), [9] (link), [21] (link), [22] (link).
Easymag system
Manufactured by bioMérieux
Sourced in France
The EasyMag system is a compact and automated nucleic acid extraction instrument designed for clinical laboratories. It utilizes magnetic separation technology to extract and purify nucleic acids from various sample types. The EasyMag system is capable of processing multiple samples simultaneously, providing efficient and consistent results.
Automatically generated - may contain errors
Lab products found in correlation
Simplexa flu a b rsv kit, by DiaSorin (3 mentions)
Seeplex rv7 kit, by Seegene (3 mentions)
Allplex 2019 ncov assay, by Seegene (2 mentions)
Magna pure system, by Roche (1 mentions)
Abi 7500 system, by Thermo Fisher Scientific (1 mentions)
Qiamp dna mini kit, by Qiagen (1 mentions)
Nuclisens lysis buffer, by bioMérieux (1 mentions)
15 protocols using easymag system
1
Comprehensive Viral and Bacterial Meningitis/Encephalitis Detection
2
Lentiviral shRNA Delivery and Transfection
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For preparation of shRNA, 293T cells were co-transfected with the lentiviral vector containing the shRNA, a plasmid encoding the lentiviral Gag/Pol, and a plasmid encoding the VSV-G at a 10:6.5:3.5 ratios respectively. Supernatants contaning the viral particles were collected after 48 hours. A549 cells were selected for puromycin resistance at 5μg/ml. Viral RNA that was transfected was isolated from cell free purified viral stocks by easyMag system (BioMerieux). Viral RNA transfection was performed on cells that were plated in 24 well plates, at 50K cells/well, which were subsequently transfected with 1μg/ml of DNA with 2μl/μg of LT-1 (MirusBio) transfection reagent per DNA, according to manufacturer's recommendations. UV inactivation prior to viral infection or viral RNA transfection, was performed with the UV Stratalinker 2400 (StrataGene) at 0.99 Joule.
3
Comprehensive Viral Pathogen Screening in NP Swabs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
All NP swab samples were tested with the BioFire FilmArray RP, GenMark eSensor RVP, and Luminex NxTAG RPP assays according to their respective package inserts. Targets included for each test are shown in Table 3 . Fresh specimens were tested at the time of collection with the GenMark eSensor RVP and reported in the patient chart according to routine laboratory protocol. Testing by BioFire RP and Luminex NxTAG RPP was batched and performed on thawed frozen specimens in 2016. Nucleic acid extraction for the GenMark and Luminex tests was performed using the EasyMag system (bioMérieux, Durham, NC) and was completed within 72 h after collection (GenMark) or within 24 h after thawing of the sample (Luminex). Aliquots were created and refrozen at the time of thawing for future shipments to Memorial Sloan Kettering Cancer Center, where the BioFire testing was conducted. Shipments were batched and sent overnight on dry ice. All samples were also tested using our adenovirus-specific LDT; extraction for this test was performed using the MagNA Pure system (Roche, Indianapolis, IN). The LDT utilized the ABI 7500 real-time PCR system with primers and probes described previously (21 (link)). Adenovirus typing was performed by sequencing the hexon gene according to the protocol of Lu and Erdman (22 (link)).
4
Multiplex Detection of Respiratory Viruses
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Respiratory viruses were detected in nasopharyngeal swabs from all the patients by means of multiplex RT-PCR. Any bronchoalveolar lavage fluid samples or tracheal aspirates ordered by the physician in charge were also tested.
Samples were first tested in the virology laboratory of each participating hospital by means of real-time influenza A and B PCR after manual nucleic acid extraction. All samples were then sent to the French National Influenza Reference Centre (CNR-Lyon) for influenza confirmation and screening for other respiratory viruses. RNA and DNA were extracted with the automated Easymag system from BioMérieux (Marcy l’Etoile, France), and influenza viruses were detected with an in-house real-time RT-PCR protocol [15] (link). The samples were also screened for a panel of other respiratory viruses (adenoviruses, bocaviruses, coronaviruses, human metapneumovirus, parainfluenza viruses 1–4, picornavirus and RSV) by real-time PCR using the Respiratory Multiwell System r-gene® on an ABI 7300 analyser.
Samples were first tested in the virology laboratory of each participating hospital by means of real-time influenza A and B PCR after manual nucleic acid extraction. All samples were then sent to the French National Influenza Reference Centre (CNR-Lyon) for influenza confirmation and screening for other respiratory viruses. RNA and DNA were extracted with the automated Easymag system from BioMérieux (Marcy l’Etoile, France), and influenza viruses were detected with an in-house real-time RT-PCR protocol [15] (link). The samples were also screened for a panel of other respiratory viruses (adenoviruses, bocaviruses, coronaviruses, human metapneumovirus, parainfluenza viruses 1–4, picornavirus and RSV) by real-time PCR using the Respiratory Multiwell System r-gene® on an ABI 7300 analyser.
5
Multiplex RT-PCR for Respiratory Pathogens
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Nasopharyngeal and tracheal aspirates were obtained from all patients for detection and identification of respiratory viruses. Nasopharyngeal aspirates were obtained 2–3 days before surgery in the complete absence of respiratory symptoms. Tracheal aspirates were collected in the operating room just after orotracheal intubation. Nucleic acid extraction was performed using the EASYMAG system (bioMérieux, France) according to the manufacturer’s instructions. Samples were subjected to real-time polymerase chain reaction (RT-PCR, one step) using the ABI 7500 system (Applied Biosystems, CA, USA). A Multiplex Kit (XGen, Pinhais, PR, Brazil) was used for detection of 19 respiratory pathogens including 18 viruses and Mycoplasma pneumoniae.
6
Molecular Diagnostics for Typhoid, Leptospirosis, and Meningitis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA was extracted from the stored whole blood samples (2 mL in adults and 1 mL from children) with a QIAmp DNA mini kit (Qiagen, Manchester, UK). A real-time PCR for S.enterica Typhi and S.enterica Paratyphi was performed using 25 μL reactions containing 5 μL of extracted DNA targeting STY0201 (Putative fimbrial adhesion in S. Typhi CT18) or SSPA2308 (hypothetical protein in SPA AKU-12601) as previously described [21 (link)]. Probe-based real-time PCR was also performed on the DNA extracted from blood to detect Leptospira spp, R.typhi and O.tsustugamushi [22 (link)–24 (link)]. Low-positive plasmid controls determined adequate detection limits of each assay.
Total nucleic acid was isolated from 100 μL of CSF specimens using the automated easyMAG® system (bioMérieux), and diagnostic PCRs were performed [25 (link)]. Four real-time PCR protocols were used for detection of S pneumoniae, H influenzae type B, Neisseria meningitidis, and Streptococcus suis. Real time-PCRs were used to detect herpes simplex virus 1 and 2, varicella zoster virus, enteroviruses (generic and 71-specific) [26 (link)], and human parechoviruses (generic).
Total nucleic acid was isolated from 100 μL of CSF specimens using the automated easyMAG® system (bioMérieux), and diagnostic PCRs were performed [25 (link)]. Four real-time PCR protocols were used for detection of S pneumoniae, H influenzae type B, Neisseria meningitidis, and Streptococcus suis. Real time-PCRs were used to detect herpes simplex virus 1 and 2, varicella zoster virus, enteroviruses (generic and 71-specific) [26 (link)], and human parechoviruses (generic).
7
TBEV detection in tick samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Because the meadows the goats used for grazing during the time before the outbreak (between April and May 2016) were documented by the farm owner, ticks were sampled around all suspected meadows between July and September 2016 by flagging along the vegetation. Ticks were identified and pooled according to stage and sex (three to 10 nymphs and two to five adult females or males per pool, all larvae in one pool). Pools were crushed using a MM400 mixer mill (Retsch, Germany) and three steel beads per pool, and nucleic acid was extracted using the EasyMag system (Biomerieux, Germany). Extracted nucleic acid was tested for TBEV RNA by a RT-qPCR [16 (link)].
8
Viral and Bacterial Co-infections in Hospitalized Patients
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Viral respiratory infection was diagnosed by PCR from combined pharyngeal and nasopharyngeal swabs introduced into UTM tubes and transported to the laboratory. RNA extraction was by the easyMAG® system (BioMérieux, Marcy-l'Étoile, France). RSV was diagnosed by the Simplexa™ Flu A/B & RSV kit (DiaSorin) or the Seeplex® RV7 kit (Seegene).
All positive cultures (blood, sputum, urine and others) from the first seven days of hospitalization were extracted for identification of bacterial or fungal super-infections. The list was reviewed independently by two internal medicine physicians to exclude positive cultures that were considered to be contaminants.
All positive cultures (blood, sputum, urine and others) from the first seven days of hospitalization were extracted for identification of bacterial or fungal super-infections. The list was reviewed independently by two internal medicine physicians to exclude positive cultures that were considered to be contaminants.
9
Molecular Diagnosis of Viral Respiratory Infections
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The diagnosis of viral respiratory infection was done by PCR. Samples were collected by combined pharyngeal and nasopharyngeal swabs that were inoculated into UTM tubes and immediately transported to the laboratory. RNA extraction was done using the easyMAG® system (BioMérieux, Marcy-l'Étoile, France). The diagnosis of SARS-CoV-2 was done by RT-PCR using mostly the Allplex™ 2019-nCoV Assay (Seegene). The diagnosis of Influenza A&B and RSV was done using the Simplexa™ Flu A/B & RSV kit (DiaSorin) or the Seeplex® RV7 kit (Seegene).
10
qRT-PCR Quantification of Norovirus GII
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The automated EasyMag system (bioMerieux, Durham, NC) was used for RNA extraction as per manufacturer instructions, with a final RNA reconstitution volume of 25μl in NucliSENS® elution buffer. Viral RNA was amplified by RT-qPCR targeting the conserved ORF1-ORF2 junction of hNoV GII as previously described (Jothikumar et al., 2005 (link); Escudero-Abarca et al., 2020 (link)). For quantification, the resulting CT values were extrapolated to log10 genome equivalent copies (GEC) by comparison to a standard curve produced by serial dilutions of hNoV GII.4 Sydney RNA obtained from the initial inoculum. Reduction in hNoV GEC as a function of treatment was calculated by subtracting the remaining virus log10 GEC for each treatment from that obtained for the dry control (baseline).
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!