Performance of the GeneXpert Ebola Assay for Diagnosis of Ebola Virus Disease in Sierra Leone: A Field Evaluation Study

Abstract

BackgroundThroughout 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 FindingsThis 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.ConclusionsThe 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 ...

Diagnosis of Ebola Virus Disease: Past, Present, and Future

“…The field performance of the Xpert Ebola assay was recently evaluated on whole blood and buccal swab samples submitted for routine clinical RT-PCR testing in a field biocontainment laboratory in Sierra Leone (73). Compared to the benchmark Trombley RT-PCR assay (NP gene target) (74), the Xpert assay showed 100% sensitivity with 95.8% specificity in fresh venipuncture whole-blood specimens (n ϭ 211; 22 Ebola virus-positive specimens), and 100% sensitivity with 100% specificity in buccal swab specimens (mixture of fresh and frozen specimens; n ϭ 64; 20 Ebola virus-positive specimens).…”

Bolstering Community Cooperation in Ebola Resurgence Protocols: Combining Field Blood Draw and Point-of-Care Diagnosis

“…In 2015, the United States Food and Drug Administration and the WHO authorized emergency use of the Cepheid GeneXpert Ebola assay, a point-of-care diagnostic test that uses whole blood versus serum or plasma and accelerates results [26–28]. The sensitivity and specificity of the assay are comparable to those of the standard real-time RT-PCR, with enhanced sensitivity for the nucleoprotein target [21,26].…”

“…In 2015, the United States Food and Drug Administration and the WHO authorized emergency use of the Cepheid GeneXpert Ebola assay, a point-of-care diagnostic test that uses whole blood versus serum or plasma and accelerates results [26–28]. The sensitivity and specificity of the assay are comparable to those of the standard real-time RT-PCR, with enhanced sensitivity for the nucleoprotein target [21,26]. Specifically, compared to the benchmark Trombley real-time RT-PCR (rRT-PCR) assay for detection of the nucleoprotein of the Ebola virus [29], sensitivity and specificity on whole blood samples were found to be 100% (95% CI: 84.6%–100%) and 95.8% (95% CI: 91.8%–98.2%), respectively, for GeneXpert [26].…”

Ebola Virus Disease: Biology, Diagnosis, Treatment and Prevention of Epidemics

“…RT-PCR of urine and breast milk of lactating mothers and semen of men recovering from Ebola infection has been recommended (Bausch et al, 2007;Moreau et al, 2015). New automated RT-PCR blood tests, quick and easy to perform have proved accurate in field applications (Semper et al, 2016;Ahrberg et al, 2016). A 37 minutes test detects Ebola RNA load from finger prick in diseased and semen, breast milk and eye fluids in post-recovery patients (Ahrberg et al, 2016).…”