CORD-19_Custom_license_subset  

CORD-19:2343e42a324724f6f6c6d3f76b564f41e4596261 JSONTXT 9 Projects

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Id Subject Object Predicate Lexical cue
T1 0-153 Sentence denotes Comparison of the performance of 2 commercial multiplex PCR platforms for detection of respiratory viruses in upper and lower tract respiratory specimens
T2 155-163 Sentence denotes Abstract
T3 164-452 Sentence denotes The performance of the CLART® PneumoVir system with that of the Luminex xTAG RVP Fast v1 assay for detection of most common respiratory viruses in upper and lower tract respiratory specimens (n = 183) from unique patients with influenza-like syndrome or lower tract respiratory infection.
T4 453-537 Sentence denotes Nested PCR coupled to automated sequencing was used for resolution of discrepancies.
T5 538-715 Sentence denotes Fully concordant results were obtained for a total of 122 specimens, whereas 56 specimens gave partially (n = 21) or fully discordant (n = 35) results (Kappa coefficient, 0.62).
T6 716-1061 Sentence denotes The overall specificity of the Luminex xTAG RVP Fast v1 assay was slightly higher than that of the CLART® PneumoVir assay for human bocavirus, influenza A virus/H3N2, influenza B virus, human metapneumovirus, and parainfluenza virus, whereas the sensitivity of the latter was higher for most targeted viruses except, notably, for picornaviruses.
T7 1062-1181 Sentence denotes This was irrespective of either the origin of the respiratory specimen or the age group to which the patients belonged.
T8 1183-1332 Sentence denotes Acute respiratory tract infections caused by respiratory viruses (RVs) are the most common infections attended in hospitals and primary care centers.
T9 1333-1528 Sentence denotes They can range from mild self-limiting illness to severe disease, the latter particularly in pediatric and severely immunosuppressed patients (Ison and Hayden, 2002; Vallières and Renaud, 2013) .
T10 1529-1738 Sentence denotes A great diversity of RVs produces clinically indistinguishable symptoms; thus, laboratory diagnosis based on the simultaneous detection of multiple targets has become the best option for etiological diagnosis.
T11 1739-1970 Sentence denotes Molecular methods are being increasingly used for the diagnosis of respiratory viral infections due to their fine sensitivity, specificity, and timely turnover and are progressively replacing conventional methods (Caliendo, 2011) .
T12 1971-2087 Sentence denotes The decision to choose one or other molecular system is complex and requires systematic and comparative evaluations.
T13 2088-2656 Sentence denotes In this context, the Luminex xTAG RVP Fast assay (Luminex Molecular Diagnostics, Austin, TX, USA) has been extensively evaluated in recent years, and comparative studies have been also published showing high reliability for detection of 19 RVs in different clinical settings (Babady et al., 2012; Dabisch-Ruthe et al., 2012; Gadsby et al., 2010; Hwang et al., 2014; Jokela et al., 2012; Krunic et al., 2007; Merante et al., 2007; Pabbaraju et al., 2008 Pabbaraju et al., , 2011 Pillet et al., 2013; Popowitch et al., 2013; Rand et al., 2011; Raymaekers et al., 2011) .
T14 2657-2850 Sentence denotes The CLART® PneumoVir assay (Genomica, Coslada, Spain) is a reverse transcription-polymerase chain reaction (RT-PCR) DNA microarray method that makes it possible to detect simultaneously 17 RVs.
T15 2851-3069 Sentence denotes The reliability of this procedure for the detection of RVs in children and adults has been previously shown (Culebras et al., 2013; Frobert et al., 2011; Pillet et al., 2013; Renois et al., 2010; Tokman et al., 2014) .
T16 3070-3162 Sentence denotes Nevertheless, little is known as to how this system compares with other multiplex platforms.
T17 3163-3434 Sentence denotes In the current study, the performance characteristics of the CLART® PneumoVir assay was compared to that of the xTAG RVP Fast v1 assay for detection of RVs in clinical specimens from children and adults with influenza-like syndromes or lower tract respiratory infections.
T18 3435-3731 Sentence denotes This was a retrospective study including a total of 183 nonconsecutive upper (n = 125) or lower tract (n = 58) respiratory specimens obtained from unique patients received at the Microbiology Services of the Hospital Ramon y Cajal from Madrid and the Hospital Clínico Universitario from Table 1 .
T19 3732-3906 Sentence denotes Throat and nasopharyngeal swabs were collected with flocked swabs in universal transport medium (Beckton Dickinson, Sparks, MD, USA, or Copan Diagnostics, Murrieta, CA, USA).
T20 3907-3967 Sentence denotes The remaining types of specimens were transported undiluted.
T21 3968-4121 Sentence denotes In all cases, specimens were received at the laboratory within 30 min of collection and were conserved at 4°C until processed (within 18 h of reception).
T22 4122-4501 Sentence denotes Nucleic acid extraction was performed using the Qiagen EZ-1 Viral extraction kit on the EZ1 Robot instrument (Qiagen, Valencia, CA, USA) at Hospital Clínico Universitario or the NucliSENS® easyMAG™ method (BioMérieux, Madrid, Spain) at the Hospital Ramón y Cajal, following routine diagnostic protocols established at each center and according to the manufacturer's instructions.
T23 4502-4670 Sentence denotes Both nucleic acid extraction platforms have been validated for the Luminex xTAG RVP Fast assay by the manufacturer (package insert; www.luminexcorp.com/Assays/xTAGRVP).
T24 4671-4837 Sentence denotes Likewise, the NucliSENS® easyMAG™ method has been previously validated for its use coupled to the CLART® PneumoVir assay (Frobert et al., 2011; Pillet et al., 2013) .
T25 4838-5108 Sentence denotes In turn, the Qiagen EZ-1 Viral extraction kit has been validated by the manufacturer (personal communication) and by our group (unpublished results) against the manual nucleic acid extraction and purification method recommended by the manufacturer in the package insert.
T26 5109-5243 Sentence denotes Sample volumes of 200 and 250 μL were used for nucleic acid extraction by the EZ1 and the NucliSENS® easyMAG™ platforms, respectively.
T27 5244-5286 Sentence denotes Both methods use isopropanol as a solvent.
T28 5287-5405 Sentence denotes The nucleic acids were eluted in a volume of 60 and 55 μL for the EZ-1 and the NucliSENS® easyMAG™ kits, respectively.
T29 5406-5512 Sentence denotes Both leftover specimens and nucleic acid extracts were then conserved at −70°C for further investigations.
T30 5513-5604 Sentence denotes Initial testing at both laboratories was performed with the Luminex xTAG RVP Fast v1 assay.
T31 5605-5737 Sentence denotes Frozen nucleic acid extracts that had been stored for a maximum of 6 months were thawed for testing with the CLART® PneumoVir assay.
T32 5738-5885 Sentence denotes Either original specimens stored at −70°C (new extraction) or frozen nucleic acid extracts (when available) were used to analyze the discrepancies.
T33 5886-6233 Sentence denotes In order to determine whether long-term storage and repeated freezing and thawing (maximum, 3 cycles) had any effect on RVs detectability, 10 randomly selected nucleic acid extracts that were subjected to nested PCR sequencing for analysis of discrepancies were reanalyzed by both the Luminex xTAG RVP Fast v1 assay and the CLART® PneumoVir assay.
T34 6234-6295 Sentence denotes Reanalyses gave similar results to those obtained previously.
T35 6296-6361 Sentence denotes The Luminex xTAG RVP Fast v1 assay was used in the current study.
T36 6362-6524 Sentence denotes In this assay, nucleic acids from the sample are converted to complementary DNA and mixed with short sequences (TAG primers) of DNA specific to each viral target.
T37 6525-6653 Sentence denotes If the target is present, the primer will bind and will be lengthened through a process called target specific primer extension.
T38 6654-6701 Sentence denotes During this extension, a label is incorporated.
T39 6702-6761 Sentence denotes Color-coded beads are added to identify the tagged primers.
T40 6762-6870 Sentence denotes Attached to each differently colored bead is an anti-TAG sequence specific to 1 of the extended TAG primers.
T41 6871-6944 Sentence denotes Each anti-TAG only binds to the complementary TAG sequence on the primer.
T42 6945-7037 Sentence denotes Samples are then placed in a Luminex instrument where beads are read and analyzed by lasers.
T43 7038-7163 Sentence denotes The lasers identify the color of the bead (specific to a virus of subtype) and the presence or absence of the labeled primer.
T44 7164-7325 Sentence denotes The MS2 phage genome (ssRNA, size 3569 nt.) is added to the specimens and serves as a control for nucleic acid extraction efficiency (internal positive control).
T45 7326-7426 Sentence denotes The bacteriophage Lambda is added to the amplification reactions as a control for RT-PCR efficiency.
T46 7427-7606 Sentence denotes RT-PCR was performed according to the xTAG RVP Fast assay product insert instructions (10-μL template volume) on a UnoCycler thermocycler (VWR International BVBA, Leuve, Belgium).
T47 7607-7742 Sentence denotes RT-PCR was followed by a single-step hybridization of PCR products to the fluorescent bead array and incubation with reporter reagents.
T48 7743-7887 Sentence denotes The plate was then analyzed using the xMAP 200 IS instrument (Luminex Molecular Diagnostics, Toronto, Canada) using the xPONENT software (v3.1).
T49 7888-8324 Sentence denotes The Luminex xTAG RVP Fast v1 assay allows the detection of adenovirus (Adv); human bocavirus (hBoV); human coronavirus (hCov) E-229, HKU1, NL63, and OC43; seasonal influenza A virus (InfA) A/H1N1, InfA/H3N2, and other InfA viruses (non-subtypificable); influenza B virus (InfB); human metapneumovirus (hMPV) A and B; parainfluenza virus (PIV) 1, 2, 3, and 4A-4B; respiratory syncytial virus (RSV) A-B; and enterovirus/rhinovirus (EvRh).
T50 8325-8464 Sentence denotes The CLART® PneumoVir DNA array assay (Genomica, Coslada, Spain) was performed and interpreted following the manufacturer's recommendations.
T51 8465-8606 Sentence denotes This assay is based on the amplification of specific fragments (120-330 bp) of the viral genome by means of 2 multiplex PCRs (RT-PCR or PCR).
T52 8607-8694 Sentence denotes During a 5-h RT-PCR/PCR amplification, the amplified products were labeled with biotin.
T53 8695-8805 Sentence denotes Following amplification, hybridization with specific probes immobilized sites of the microarray was performed.
T54 8806-9018 Sentence denotes After incubation with a streptavidin-peroxidise conjugate, the addition of tetramethylbenzidine resulted in the appearance of an insoluble product, which precipitated at the hybridization sites on the microarray.
T55 9019-9141 Sentence denotes The hybridization profile was read on the clinical array reader and interpreted by means of the CLART® pneumoVir Software.
T56 9142-9266 Sentence denotes Amplification reactions were performed on a UnoCycler thermocycler (VWR International BVBA) using a template volume of 5 μL.
T57 9267-9362 Sentence denotes An internal control was added to the amplification reactions, as specified by the manufacturer.
T58 9363-9590 Sentence denotes The CLART® PneumoVir DNA array assay differs from the Luminex xTAG RVP Fast assay in that it detects influenza C virus but does not allow the detection of the alphacoronavirus NL63 virus and the betacoronaviruses HKU1 and OC43.
T59 9591-9741 Sentence denotes The CLART® PneumoVir is able to discriminate between rhinovirus and enterovirus genus, and it permits the identification of the new influenza A/H1N1v.
T60 9742-9994 Sentence denotes Discrepancies between both methods were resolved by means of an "in-house"-developed nested PCR assays and direct sequencing of amplicons following previously published protocols (Coiras et al., 2003 (Coiras et al., , 2004 López-Huertas et al., 2005) .
T61 9995-10099 Sentence denotes Only viral agents missed by either one or the other assay were targeted in the analysis of discordances.
T62 10100-10215 Sentence denotes Hence, the presence of viral agents detected by both systems was not confirmed by nested PCR coupled to sequencing.
T63 10216-10278 Sentence denotes We distinguished between fully and partial discordant results.
T64 10279-10442 Sentence denotes The former referred to qualitative discrepancies (positive by one method, but negative by the other assay, or when the virus detected was different in each assay).
T65 10443-10583 Sentence denotes The latter were those in which both assays were coincident in at least 1 virus, although 1 assay could identify more viruses than the other.
T66 10584-10689 Sentence denotes Full concordance was defined as obtaining identical results by both methods (including negative results).
T67 10690-10886 Sentence denotes A true positive was defined as either being positive (identical result) by the 2 assays or by a single assay if confirmed by the corresponding "in house" RT-PCR assay coupled to direct sequencing.
T68 10887-11045 Sentence denotes Agents not included in CLART® PneumoVir panel and detected by the Luminex xTAG RVP Fast v1 (hCov HKU1, NL63, and OC43) were excluded for comparative analyses.
T69 11046-11168 Sentence denotes Pairwise differences in sensitivity were determined by the McNemar test, with P values b0.05 being considered significant.
T70 11169-11256 Sentence denotes The level of agreement between both assays was calculated by means of Kappa statistics.
T71 11257-11489 Sentence denotes Among the 183 respiratory specimens initially included in the study, 5 were positive by the Luminex xTAG RVP v1 assay for human CoVs not included in the CLART® PneumoVir panel (CoV NL63, n = 2; CoV HKU1, n = 1; and CoV OC43, n = 2).
T72 11490-11544 Sentence denotes These were excluded from the analyses described below.
T73 11545-11621 Sentence denotes Thus, the final number of samples included for comparative purposes was 178.
T74 11622-11787 Sentence denotes The total number of viruses detected by the Luminex xTAG RVP Fast assay and the CLART® PneumoVir both was comparable (n = 140 versus n =138, respectively; P = 0.92).
T75 11788-11916 Sentence denotes Likewise, both methods performed comparably for detection of multiple infections (n = 29 versus n = 27, respectively; P = 0.94).
T76 11917-12077 Sentence denotes Fully concordance was obtained for a total of 122/178 (68.5%) specimens (65 identical positive results and 57 samples yielding negative results in both assays).
T77 12078-12150 Sentence denotes Thus, the overall rate of concordance was 80% (Kappa coefficient, 0.62).
T78 12151-12251 Sentence denotes A single RV was detected in 54 out of the 65 specimens (83.0%) yielding concordant positive results.
T79 12252-12323 Sentence denotes Two and 3 RVs were detected in 9 (13.8%) and 2 (3.0%) of these samples.
T80 12324-12443 Sentence denotes Partially or fully discordant results were observed in 21/178 samples (11.8%) and 35/178 samples (19.6%), respectively.
T81 12444-12645 Sentence denotes The latter discrepant results corresponded to 28 specimens testing negative by one method and positive by the other and 7 specimens testing positive by both methods but yielding different viral agents.
T82 12646-12729 Sentence denotes It is of note that InfA H1N1/v was detected by the CLART® PneumoVir in 5 specimens.
T83 12730-12850 Sentence denotes These specimens tested either negative (n = 2) or positive for InfA H1/N1 (n = 3) by the Luminex xTAG RVP Fast v1 assay.
T84 12851-12917 Sentence denotes A detailed description of discrepant results is shown in Table 2 .
T85 12918-12983 Sentence denotes Table 3 shows the number of viral agents detected by each method.
T86 12984-13071 Sentence denotes An excellent concordance (Kappa index N0.90) was found for hMPV, RSV, PIV-3, and PIV-4.
T87 13072-13183 Sentence denotes Conversely, a suboptimal concordance (Kappa index b0.60) was found for InfA A/H1/N1 and picornaviruses (EV/Rh).
T88 13184-13338 Sentence denotes The data clearly proved the superiority of the Luminex xTAG RVP Fast v1 assay over the CLART® PneumoVir assay for detection of picornaviruses (P ≤ 0.001).
T89 13339-13554 Sentence denotes In contrast, the CLART® PneumoVir method appeared to perform slightly better for detection of most of the other RVs included in the panels, although the differences did not reach statistical significance (Table 3 ).
T90 13555-13717 Sentence denotes The performance of both assays was irrespective of either the origin of the respiratory specimen or the age group to which the patients belonged (data not shown).
T91 13718-13850 Sentence denotes A total of 47 out of 56 specimens yielding discordant results were further analyzed by nested PCR coupled with automated sequencing.
T92 13851-13930 Sentence denotes No sufficient volume for analysis was available from the remaining 9 specimens.
T93 13931-14058 Sentence denotes The viral agent missed by either one or the other multiplex PCR assay was confirmed by the reference method in 41/47 specimens.
T94 14059-14300 Sentence denotes In the remaining 6 specimens, the presence of 1 or more viral agents in respiratory specimens, as detected by one or the other method, could not be confirmed by the reference method and thus were considered false-positive results (Table 2) .
T95 14301-14517 Sentence denotes Following resolution of discrepancies, the data indicated that the sensitivity of the Luminex xTAG RVP Fast v1 assay was higher than of the CLART® PneumoVir assay for detection of picornaviruses (89.8% versus 59.3%).
T96 14518-14920 Sentence denotes The opposite was true for Adv (90.0% vs. 100%), hBoV (80% versus 90%), InfB (66.7% versus 100%), 3/0 (2) 4/0 (1) 2/1 (2) 4/0 (3) InfA A/H1N1v 2/2 (2) -3/3 (3) -InfA A/H3N2 1/0 (1) 0 2/0 (0) 0 hMPV 1/1 (1) 0 1/1 (1) 0 PIV-1 1/0 (1) 1/0 (1) 0 0 PIV-2 1/1 (1) 0 0 0 PIV-3 1/0 (1) 0 1/0 (0) 0 RSV A-B 2/1 (1) 0 1/0 (0) 0 a Number of available specimens for confirmation by nested PCR coupled to sequencing.
T97 14922-15124 Sentence denotes In the current study, the performance characteristics of 2 commercially available multiplex PCR assays for detection of RVs, the CLART® Pneumovir assay and Luminex xTAG RVP Fast v1 assay, were compared.
T98 15125-15194 Sentence denotes It is of note that this version is no longer available in the market.
T99 15195-15339 Sentence denotes Both assays have a comparable hands-on time and time to result (slightly longer for the CLART® PneumoVir assay; approximately 5.5 h versus 4 h).
T100 15340-15465 Sentence denotes Our data indicated the following: i) the overall degree of concordance between both assays was 80% (Kappa coefficient, 0.62).
T101 15466-15558 Sentence denotes As discussed below, this was mostly due to discrepancies in the detection of picornaviruses.
T102 15559-15674 Sentence denotes In this sense, the Luminex xTAG RVP Fast v1 assay was clearly superior (P b 0.001) over the CLART® PneumoVir assay.
T103 15675-15844 Sentence denotes ii) The sensitivity of the CLART® PneumoVir assay was higher than that of the Luminex xTAG RVP Fast v1 assay for most targeted agents, except notably for picornaviruses.
T104 15845-15975 Sentence denotes In contrast, the overall specificity of the latter assay was slightly higher than that of the CLART® PneumoVir assay for most RVs.
T105 15976-16338 Sentence denotes The results were highly concordant (Kappa index N0.90) for hMPV, RSV, and PIV-3 and PIV-4, whereas striking discrepancies were observed for InfA H1/N1 and picornaviruses. iii) The performance of both assays was comparable irrespective of the origin of the specimen (upper versus lower respiratory tract) and the age of patients (pediatric versus adult patients).
T106 16339-16595 Sentence denotes In line with our data, Pillet et al. (2013) found the CLART® Pneumovir assay to display a better overall sensitivity than the Luminex xTAG RVP Fast v1 assay, mostly due to an increased rate of detection of influenza viruses (specially InfB), Adv, and hBoV.
T107 16596-16877 Sentence denotes A suboptimal sensitivity of the Luminex xTAG RVP Fast v1 assay for detection of Adv, hBoV, InfA viruses, InfB, and RSV A-B in comparison to that of other commercial platforms (eSensor RVP and the FilmArray RVP) has also been reported (Babady et al., 2012; Popowitch et al., 2013) .
T108 16878-16969 Sentence denotes On the contrary, the CLART® PneumoVir was poorly sensitive for detection of picornaviruses.
T109 16970-17162 Sentence denotes This has also been reported in other studies (Pillet et al., 2013; Tokman et al., 2014) and may likely be due to the fact that the assay only detects enterovirus type B (Pillet et al., 2013) .
T110 17163-17343 Sentence denotes False-positive results were scarce, and most frequently obtained with the CLART® PneumoVir assay, especially for hBoV and some PIVs, and notably in the context of mixed infections.
T111 17344-17418 Sentence denotes Mispriming is a likely reason accounting for these false-positive results.
T112 17419-17644 Sentence denotes Nevertheless, given the high overall sensitivity of CLART® PneumoVir, we cannot rule out the possibility of these being true positives that remained undetected by the nested PCR assay employed for resolution of discrepancies.
T113 17645-17738 Sentence denotes This is in contrast to previously published data (Pillet et al., 2013; Tokman et al., 2014) .
T114 17739-17856 Sentence denotes The use of different criteria for resolving discordant results among the studies may account for these discrepancies.
T115 17857-18115 Sentence denotes Limitations of the current study are the relatively scarce number of positive specimens for several viral agents, and its retrospective design, which implied the use of thawed instead of freshly obtained specimens for testing with the CLART® PneumoVir assay.
T116 18116-18230 Sentence denotes In this context, there is also inherent bias associated with selecting archived specimens for comparative studies.
T117 18231-18404 Sentence denotes In addition, due to financial constraints, detection of a given target by both methods was considered a true-positive result without further testing by the reference method.
T118 18405-18652 Sentence denotes Despite the above limitations, our data proved the reliability of the CLART® PneumoVir assay as compared to the Luminex xTAG RVP Fast v1 assay for the diagnosis of upper and lower tract respiratory infections, both in adult and pediatric patients.