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dc.contributor.authorSemper, Amanda E.en_US
dc.contributor.authorBroadhurst, M. Janaen_US
dc.contributor.authorRichards, Jadeen_US
dc.contributor.authorFoster, Geraldine M.en_US
dc.contributor.authorSimpson, Andrew J. H.en_US
dc.contributor.authorLogue, Christopher H.en_US
dc.contributor.authorKelly, J. Danielen_US
dc.contributor.authorMiller, Annen_US
dc.contributor.authorBrooks, Tim J. G.en_US
dc.contributor.authorMurray, Meganen_US
dc.contributor.authorPollock, Nira R.en_US
dc.date.accessioned2016-05-02T17:02:20Z
dc.date.issued2016en_US
dc.identifier.citationSemper, A. E., M. J. Broadhurst, J. Richards, G. M. Foster, A. J. H. Simpson, C. H. Logue, J. D. Kelly, et al. 2016. “Performance of the GeneXpert Ebola Assay for Diagnosis of Ebola Virus Disease in Sierra Leone: A Field Evaluation Study.” PLoS Medicine 13 (3): e1001980. doi:10.1371/journal.pmed.1001980. http://dx.doi.org/10.1371/journal.pmed.1001980.en
dc.identifier.issn1549-1277en
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:26860324
dc.description.abstractBackground: Throughout the Ebola virus disease (EVD) epidemic in West Africa, field laboratory testing for EVD has relied on complex, multi-step real-time reverse transcription PCR (RT-PCR) assays; an accurate sample-to-answer RT-PCR test would reduce time to results and potentially increase access to testing. We evaluated the performance of the Cepheid GeneXpert Ebola assay on clinical venipuncture whole blood (WB) and buccal swab (BS) specimens submitted to a field biocontainment laboratory in Sierra Leone for routine EVD testing by RT-PCR (“Trombley assay”). Methods and Findings: This study was conducted in the Public Health England EVD diagnostic laboratory in Port Loko, Sierra Leone, using residual diagnostic specimens remaining after clinical testing. EDTA-WB specimens (n = 218) were collected from suspected or confirmed EVD patients between April 1 and July 20, 2015. BS specimens (n = 71) were collected as part of a national postmortem screening program between March 7 and July 20, 2015. EDTA-WB and BS specimens were tested with Xpert (targets: glycoprotein [GP] and nucleoprotein [NP] genes) and Trombley (target: NP gene) assays in parallel. All WB specimens were fresh; 84/218 were tested in duplicate on Xpert to compare WB sampling methods (pipette versus swab); 43/71 BS specimens had been previously frozen. In all, 7/218 (3.2%) WB and 7/71 (9.9%) BS samples had Xpert results that were reported as “invalid” or “error” and were excluded, leaving 211 WB and 64 BS samples with valid Trombley and Xpert results. For WB, 22/22 Trombley-positive samples were Xpert-positive (sensitivity 100%, 95% CI 84.6%–100%), and 181/189 Trombley-negative samples were Xpert-negative (specificity 95.8%, 95% confidence interval (CI) 91.8%–98.2%). Seven of the eight Trombley-negative, Xpert-positive (Xpert cycle threshold [Ct] range 37.7–43.4) WB samples were confirmed to be follow-up submissions from previously Trombley-positive EVD patients, suggesting a revised Xpert specificity of 99.5% (95% CI 97.0%–100%). For Xpert-positive WB samples (n = 22), Xpert NP Ct values were consistently lower than GP Ct values (mean difference −4.06, 95% limits of agreement −6.09, −2.03); Trombley (NP) Ct values closely matched Xpert NP Ct values (mean difference −0.04, 95% limits of agreement −2.93, 2.84). Xpert results (positive/negative) for WB sampled by pipette versus swab were concordant for 78/79 (98.7%) WB samples, with comparable Ct values for positive results. For BS specimens, 20/20 Trombley-positive samples were Xpert-positive (sensitivity 100%, 95% CI 83.2%–100%), and 44/44 Trombley-negative samples were Xpert-negative (specificity 100%, 95% CI 92.0%–100%). This study was limited to testing residual diagnostic samples, some of which had been frozen before use; it was not possible to test the performance of the Xpert Ebola assay at point of care. Conclusions: The Xpert Ebola assay had excellent performance compared to an established RT-PCR benchmark on WB and BS samples in a field laboratory setting. Future studies should evaluate feasibility and performance outside of a biocontainment laboratory setting to facilitate expanded access to testing.en
dc.language.isoen_USen
dc.publisherPublic Library of Scienceen
dc.relation.isversionofdoi:10.1371/journal.pmed.1001980en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811569/pdf/en
dash.licenseLAAen_US
dc.subjectBiology and Life Sciencesen
dc.subjectAnatomyen
dc.subjectBody Fluidsen
dc.subjectBlooden
dc.subjectMedicine and Health Sciencesen
dc.subjectPhysiologyen
dc.subjectHematologyen
dc.subjectMolecular Biologyen
dc.subjectMolecular Biology Techniquesen
dc.subjectArtificial Gene Amplification and Extensionen
dc.subjectPolymerase Chain Reactionen
dc.subjectReverse Transcriptase-Polymerase Chain Reactionen
dc.subjectBiology and life sciencesen
dc.subjectOrganismsen
dc.subjectVirusesen
dc.subjectRNA virusesen
dc.subjectFilovirusesen
dc.subjectEbola Virusen
dc.subjectMicrobiologyen
dc.subjectMedical Microbiologyen
dc.subjectMicrobial Pathogensen
dc.subjectViral Pathogensen
dc.subjectHemorrhagic Fever Virusesen
dc.subjectPathology and Laboratory Medicineen
dc.subjectPathogensen
dc.subjectTropical Diseasesen
dc.subjectNeglected Tropical Diseasesen
dc.subjectViral Hemorrhagic Feversen
dc.subjectEbola Hemorrhagic Feveren
dc.subjectInfectious Diseasesen
dc.subjectViral Diseasesen
dc.subjectExtraction techniquesen
dc.subjectRNA extractionen
dc.subjectPeople and placesen
dc.subjectGeographical locationsen
dc.subjectAfricaen
dc.subjectSierra Leoneen
dc.subjectDiagnostic Medicineen
dc.subjectClinical Laboratory Sciencesen
dc.subjectClinical Laboratoriesen
dc.subjectBlood Plasmaen
dc.titlePerformance of the GeneXpert Ebola Assay for Diagnosis of Ebola Virus Disease in Sierra Leone: A Field Evaluation Studyen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalPLoS Medicineen
dash.depositing.authorMiller, Annen_US
dc.date.available2016-05-02T17:02:20Z
dc.identifier.doi10.1371/journal.pmed.1001980*
dash.authorsorderedfalse
dash.contributor.affiliatedMurray, Megan
dash.contributor.affiliatedMiller, Ann


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