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Title: Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus

The recently developed Xpert® Ebola Assay is a novel nucleic acid amplification test for simplified detection of Ebola virus (EBOV) in whole blood and buccal swab samples. The assay targets sequences in two EBOV genes, lowering the risk for new variants to escape detection in the test. The objective of this report is to present analytical characteristics of the Xpert® Ebola Assay on whole blood samples. Our study evaluated the assay’s analytical sensitivity, analytical specificity, inclusivity and exclusivity performance in whole blood specimens. EBOV RNA, inactivated EBOV, and infectious EBOV were used as targets. The dynamic range of the assay, the inactivation of virus, and specimen stability were also evaluated. The lower limit of detection (LoD) for the assay using inactivated virus was estimated to be 73 copies/mL (95% CI: 51–97 copies/mL). The LoD for infectious virus was estimated to be 1 plaque-forming unit/mL, and for RNA to be 232 copies/mL (95% CI 163–302 copies/mL). The assay correctly identified five different Ebola viruses, Yambuku-Mayinga, Makona-C07, Yambuku-Ecran, Gabon-Ilembe, and Kikwit-956210, and correctly excluded all non-EBOV isolates tested. The conditions used by Xpert® Ebola for inactivation of infectious virus reduced EBOV titer by ≥6 logs. In conclusion, we found the Xpert® Ebolamore » Assay to have high analytical sensitivity and specificity for the detection of EBOV in whole blood. It offers ease of use, fast turnaround time, and remote monitoring. The test has an efficient viral inactivation protocol, fulfills inclusivity and exclusivity criteria, and has specimen stability characteristics consistent with the need for decentralized testing. The simplicity of the assay should enable testing in a wide variety of laboratory settings, including remote laboratories that are not capable of performing highly complex nucleic acid amplification tests, and during outbreaks where time to detection is critical.« less
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [4] ;  [4] ;  [5] ;  [5] ;  [5] ;  [5] ;  [5] ;  [5] ;  [6] ;  [6] ;  [6] ;  [7] ;  [8] ;  [9] ;  [10] more »;  [5] « less
  1. Stanford Univ. School of Medicine, CA (United States). Dept. of Pathology; Stanford Univ. School of Medicine, CA (United States). Dept. of Medicine, Division of Infectious Diseases and Geographic Medicine
  2. Stanford Univ. School of Medicine, CA (United States). Dept. of Pathology
  3. Stanford Univ. School of Medicine, CA (United States). Dept. of Pathology; Stanford Health Care and Stanford Children’s Health, Palo Alto, CA (United States)
  4. Cepheid, Solna (Sweden)
  5. Cepheid, Sunnyvale, CA (United States)
  6. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  7. Univ. of Texas Medical Branch, Galveston, TX (United States)
  8. Public Health Agency of Canada, Winnipeg, MB (Canada)
  9. Public Health Agency of Canada, Winnipeg, MB (Canada)
  10. Public Health Agency of Sweden, Solna (Sweden)
Publication Date:
Report Number(s):
LLNL-JRNL-675675
Journal ID: ISSN 1932-6203
Grant/Contract Number:
AC52-07NA27344
Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 10; Journal Issue: 11; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Research Org:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org:
Bill and Melinda Gates Foundation; USDOE National Nuclear Security Administration (NNSA)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; blood; Ebola virus; nucleic acids; viral nucleic acid; RNA viruses; reverse transcriptase-polymerase chain reaction; viral replication; viral genomics; Biological and medical sciences
OSTI Identifier:
1259525
Alternate Identifier(s):
OSTI ID: 1474356

Pinsky, Benjamin A., Sahoo, Malaya K., Sandlund, Johanna, Kleman, Marika, Kulkarni, Medha, Grufman, Per, Nygren, Malin, Kwiatkowski, Robert, Baron, Ellen Jo, Tenover, Fred, Denison, Blake, Higuchi, Russell, Van Atta, Reuel, Beer, Neil Reginald, Carrillo, Alda Celena, Naraghi-Arani, Pejman, Mire, Chad E., Ranadheera, Charlene, Grolla, Allen, Lagerqvist, Nina, and Persing, David H.. Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus. United States: N. p., Web. doi:10.1371/journal.pone.0142216.
Pinsky, Benjamin A., Sahoo, Malaya K., Sandlund, Johanna, Kleman, Marika, Kulkarni, Medha, Grufman, Per, Nygren, Malin, Kwiatkowski, Robert, Baron, Ellen Jo, Tenover, Fred, Denison, Blake, Higuchi, Russell, Van Atta, Reuel, Beer, Neil Reginald, Carrillo, Alda Celena, Naraghi-Arani, Pejman, Mire, Chad E., Ranadheera, Charlene, Grolla, Allen, Lagerqvist, Nina, & Persing, David H.. Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus. United States. doi:10.1371/journal.pone.0142216.
Pinsky, Benjamin A., Sahoo, Malaya K., Sandlund, Johanna, Kleman, Marika, Kulkarni, Medha, Grufman, Per, Nygren, Malin, Kwiatkowski, Robert, Baron, Ellen Jo, Tenover, Fred, Denison, Blake, Higuchi, Russell, Van Atta, Reuel, Beer, Neil Reginald, Carrillo, Alda Celena, Naraghi-Arani, Pejman, Mire, Chad E., Ranadheera, Charlene, Grolla, Allen, Lagerqvist, Nina, and Persing, David H.. 2015. "Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus". United States. doi:10.1371/journal.pone.0142216. https://www.osti.gov/servlets/purl/1259525.
@article{osti_1259525,
title = {Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus},
author = {Pinsky, Benjamin A. and Sahoo, Malaya K. and Sandlund, Johanna and Kleman, Marika and Kulkarni, Medha and Grufman, Per and Nygren, Malin and Kwiatkowski, Robert and Baron, Ellen Jo and Tenover, Fred and Denison, Blake and Higuchi, Russell and Van Atta, Reuel and Beer, Neil Reginald and Carrillo, Alda Celena and Naraghi-Arani, Pejman and Mire, Chad E. and Ranadheera, Charlene and Grolla, Allen and Lagerqvist, Nina and Persing, David H.},
abstractNote = {The recently developed Xpert® Ebola Assay is a novel nucleic acid amplification test for simplified detection of Ebola virus (EBOV) in whole blood and buccal swab samples. The assay targets sequences in two EBOV genes, lowering the risk for new variants to escape detection in the test. The objective of this report is to present analytical characteristics of the Xpert® Ebola Assay on whole blood samples. Our study evaluated the assay’s analytical sensitivity, analytical specificity, inclusivity and exclusivity performance in whole blood specimens. EBOV RNA, inactivated EBOV, and infectious EBOV were used as targets. The dynamic range of the assay, the inactivation of virus, and specimen stability were also evaluated. The lower limit of detection (LoD) for the assay using inactivated virus was estimated to be 73 copies/mL (95% CI: 51–97 copies/mL). The LoD for infectious virus was estimated to be 1 plaque-forming unit/mL, and for RNA to be 232 copies/mL (95% CI 163–302 copies/mL). The assay correctly identified five different Ebola viruses, Yambuku-Mayinga, Makona-C07, Yambuku-Ecran, Gabon-Ilembe, and Kikwit-956210, and correctly excluded all non-EBOV isolates tested. The conditions used by Xpert® Ebola for inactivation of infectious virus reduced EBOV titer by ≥6 logs. In conclusion, we found the Xpert® Ebola Assay to have high analytical sensitivity and specificity for the detection of EBOV in whole blood. It offers ease of use, fast turnaround time, and remote monitoring. The test has an efficient viral inactivation protocol, fulfills inclusivity and exclusivity criteria, and has specimen stability characteristics consistent with the need for decentralized testing. The simplicity of the assay should enable testing in a wide variety of laboratory settings, including remote laboratories that are not capable of performing highly complex nucleic acid amplification tests, and during outbreaks where time to detection is critical.},
doi = {10.1371/journal.pone.0142216},
journal = {PLoS ONE},
number = 11,
volume = 10,
place = {United States},
year = {2015},
month = {11}
}