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...
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| Veröffentlicht in: | PloS one 2015-11, Vol.10 (11), p.e0142216-e0142216 |
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| creator | 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 |
| description | 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.
This 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 summary, 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_str_mv | 10.1371/journal.pone.0142216 |
| format | Article |
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This 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 summary, 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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0142216</identifier><identifier>PMID: 26562786</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>60 APPLIED LIFE SCIENCES ; Acids ; Amplification ; Animals ; Antigens ; Assaying ; Automation ; Biological and medical sciences ; Blood ; Cercopithecus aethiops ; Deactivation ; Dynamic stability ; Ebola virus ; Ebolavirus ; Ebolavirus - genetics ; Ebolavirus - physiology ; Epidemics ; Gene sequencing ; Genes, Viral - genetics ; Genomes ; Glycoproteins ; Hemorrhagic Fever, Ebola - blood ; Hemorrhagic Fever, Ebola - diagnosis ; Hemorrhagic Fever, Ebola - virology ; Host-Pathogen Interactions ; Humans ; Inactivation ; Infectious diseases ; Laboratories ; Mass Screening - methods ; Mathematical analysis ; Medicine ; Nucleic Acid Amplification Techniques - methods ; Nucleic acids ; Outbreaks ; Pathogens ; Pathology ; Public health ; Remote monitoring ; Reproducibility of Results ; reverse transcriptase-polymerase chain reaction ; Ribonucleic acid ; RNA ; RNA polymerase ; RNA viruses ; RNA, Viral - blood ; RNA, Viral - genetics ; Sensitivity ; Sensitivity analysis ; Sensitivity and Specificity ; Stability analysis ; Stability criteria ; Time Factors ; Vero Cells ; Viral diseases ; viral genomics ; viral nucleic acid ; viral replication ; Virus Inactivation ; Viruses</subject><ispartof>PloS one, 2015-11, Vol.10 (11), p.e0142216-e0142216</ispartof><rights>This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. 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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.
This 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 summary, 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.</description><subject>60 APPLIED LIFE SCIENCES</subject><subject>Acids</subject><subject>Amplification</subject><subject>Animals</subject><subject>Antigens</subject><subject>Assaying</subject><subject>Automation</subject><subject>Biological and medical sciences</subject><subject>Blood</subject><subject>Cercopithecus aethiops</subject><subject>Deactivation</subject><subject>Dynamic stability</subject><subject>Ebola virus</subject><subject>Ebolavirus</subject><subject>Ebolavirus - genetics</subject><subject>Ebolavirus - physiology</subject><subject>Epidemics</subject><subject>Gene sequencing</subject><subject>Genes, Viral - genetics</subject><subject>Genomes</subject><subject>Glycoproteins</subject><subject>Hemorrhagic Fever, 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Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pinsky, Benjamin A</au><au>Sahoo, Malaya K</au><au>Sandlund, Johanna</au><au>Kleman, Marika</au><au>Kulkarni, Medha</au><au>Grufman, Per</au><au>Nygren, Malin</au><au>Kwiatkowski, Robert</au><au>Baron, Ellen Jo</au><au>Tenover, Fred</au><au>Denison, Blake</au><au>Higuchi, Russell</au><au>Van Atta, Reuel</au><au>Beer, Neil Reginald</au><au>Carrillo, Alda Celena</au><au>Naraghi-Arani, Pejman</au><au>Mire, Chad E</au><au>Ranadheera, Charlene</au><au>Grolla, Allen</au><au>Lagerqvist, Nina</au><au>Persing, David H</au><aucorp>Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-11-12</date><risdate>2015</risdate><volume>10</volume><issue>11</issue><spage>e0142216</spage><epage>e0142216</epage><pages>e0142216-e0142216</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>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.
This 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 summary, 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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26562786</pmid><doi>10.1371/journal.pone.0142216</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2015-11, Vol.10 (11), p.e0142216-e0142216 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1733201265 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | 60 APPLIED LIFE SCIENCES Acids Amplification Animals Antigens Assaying Automation Biological and medical sciences Blood Cercopithecus aethiops Deactivation Dynamic stability Ebola virus Ebolavirus Ebolavirus - genetics Ebolavirus - physiology Epidemics Gene sequencing Genes, Viral - genetics Genomes Glycoproteins Hemorrhagic Fever, Ebola - blood Hemorrhagic Fever, Ebola - diagnosis Hemorrhagic Fever, Ebola - virology Host-Pathogen Interactions Humans Inactivation Infectious diseases Laboratories Mass Screening - methods Mathematical analysis Medicine Nucleic Acid Amplification Techniques - methods Nucleic acids Outbreaks Pathogens Pathology Public health Remote monitoring Reproducibility of Results reverse transcriptase-polymerase chain reaction Ribonucleic acid RNA RNA polymerase RNA viruses RNA, Viral - blood RNA, Viral - genetics Sensitivity Sensitivity analysis Sensitivity and Specificity Stability analysis Stability criteria Time Factors Vero Cells Viral diseases viral genomics viral nucleic acid viral replication Virus Inactivation Viruses |
| title | Analytical Performance Characteristics of the Cepheid GeneXpert Ebola Assay for the Detection of Ebola Virus |
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