Ebola Virus Disease Diagnostics, Sierra Leone: Analysis of Real-time Reverse Transcription–Polymerase Chain Reaction Values for Clinical Blood and Oral Swab Specimens

Erickson, Bobbie R.; Sealy, Tara K.; Flietstra, Tim; Morgan, Laura; Kargbo, Brima; Matt-Lebby, Victor E.; Gibbons, Aridth; Chakrabarti, Ayan K.; Graziano, James; Presser, Lance; Flint, Mike; Bird, Brian H.; Brown, Shelley; Klena, John D.; Blau, Dianna M.; Brault, Aaron C.; Belser, Jessica A.; Salzer, Johanna S.; Schuh, Amy J.; Lo, Michael K.; Zivcec, Marko; Priestley, Rachael A.; Pyle, Meredith; Goodman, Christin H.; Bearden, Scott W.; Amman, Brian R.; Basile, Alison Jane; Bergeron, Éric; Bowen, Michael D.; Dodd, Kimberly A.; Freeman, Molly M.; McMullan, Laura K.; Paddock, Christopher D.; Russell, Brandy J.; Sanchez, Angela J.; Towner, Jonathan S.; Wang, David; Zemtsova, Galina E.; Stoddard, Robyn A.; Turnsek, Maryann; Guerrero, Lisa Wiggleton; Emery, Shannon; Stovall, Janae L.; Kainulainen, Markus H.; Perniciaro, Jamie L.; Mijatovic-Rustempasic, Slavica; Shakirova, Gulchekhra; Winter, Jörn; Sexton, Christopher; Liu, Feng; Slater, Kimetha S.; Anderson, R Oy M.; Andersen, Lauren E.; Chiang, Cheng‐Feng; Tzeng, Wen-Pin; Crowe, Samuel J.; Maenner, Matthew J.; Spiropoulou, Christina F.; Nichol, Stuart T.; Ströher, Ute

doi:10.1093/infdis/jiw296

Cited by 23 publications

(28 citation statements)

References 9 publications

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“…The assays are highly sensitive, 19,22 and the detection of viral RNA does not necessarily indicate that infectious virus is present in blood or semen. 21,25,26 …”

Section: Discussionmentioning

confidence: 99%

“…19–21 A specimen was considered to be positive if the NP and VP40 gene targets were both detected within 40 cycles of replication, and the results were considered to be indeterminate if one of the NP or VP40 gene targets was detected but not both.…”

Section: Methodsmentioning

confidence: 99%

“…The value was determined by means of the assay from the Centers for Disease Control and Prevention, which was a quantitative RT-PCR assay that used Ebola virus–specific gene targets (NP and VP40) and the human β 2 -microglobulin ( B2M ) gene, as described previously. 19–21 The findings were considered to be positive if the VP40 and the NP gene targets were both detected within 40 cycles of replication. Higher cycle-threshold values indicate lower RNA levels.…”

Section: Figurementioning

confidence: 99%

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Ebola RNA Persistence in Semen of Ebola Virus Disease Survivors — Final Report

Deen¹,

et al. 2017

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BACKGROUND Ebola virus has been detected in the semen of men after their recovery from Ebola virus disease (EVD). We report the presence of Ebola virus RNA in semen in a cohort of survivors of EVD in Sierra Leone. METHODS We enrolled a convenience sample of 220 adult male survivors of EVD in Sierra Leone, at various times after discharge from an Ebola treatment unit (ETU), in two phases (100 participants were in phase 1, and 120 in phase 2). Semen specimens obtained at baseline were tested by means of a quantitative reverse-transcriptase–polymerase-chain-reaction (RT-PCR) assay with the use of the target sequences of NP and VP40 (in phase 1) or NP and GP (in phase 2). This study did not evaluate directly the risk of sexual transmission of EVD. RESULTS Of 210 participants who provided an initial semen specimen for analysis, 57 (27%) had positive results on quantitative RT-PCR. Ebola virus RNA was detected in the semen of all 7 men with a specimen obtained within 3 months after ETU discharge, in 26 of 42 (62%) with a specimen obtained at 4 to 6 months, in 15 of 60 (25%) with a specimen obtained at 7 to 9 months, in 4 of 26 (15%) with a specimen obtained at 10 to 12 months, in 4 of 38 (11%) with a specimen obtained at 13 to 15 months, in 1 of 25 (4%) with a specimen obtained at 16 to 18 months, and in no men with a specimen obtained at 19 months or later. Among the 46 participants with a positive result in phase 1, the median baseline cycle-threshold values (higher values indicate lower RNA values) for the NP and VP40 targets were lower within 3 months after ETU discharge (32.4 and 31.3, respectively; in 7 men) than at 4 to 6 months (34.3 and 33.1; in 25), at 7 to 9 months (37.4 and 36.6; in 13), and at 10 to 12 months (37.7 and 36.9; in 1). In phase 2, a total of 11 participants had positive results for NP and GP targets (samples obtained at 4.1 to 15.7 months after ETU discharge); cycle-threshold values ranged from 32.7 to 38.0 for NP and from 31.1 to 37.7 for GP. CONCLUSIONS These data showed the long-term presence of Ebola virus RNA in semen and declining persistence with increasing time after ETU discharge. (Funded by the World Health Organization and others.)

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“…The assays are highly sensitive, 19,22 and the detection of viral RNA does not necessarily indicate that infectious virus is present in blood or semen. 21,25,26 …”

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

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Ebola RNA Persistence in Semen of Ebola Virus Disease Survivors — Final Report

Deen¹,

et al. 2017

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“…Of note, antibody responses may not reliably develop or may be delayed in acutely symptomatic patients with EVD. Thus, PCR-based testing is optimal in the acutely ill patient (from blood samples) and also for detection of EBOV RNA in amniotic fluid, breast milk, ocular fluid, saliva, seminal fluid, stool, sweat, tears, urine and vaginal fluid even after blood samples begin to test negative 36,40,57,134,161,162 .…”

Section: Diagnosis Of Acute Evdmentioning

confidence: 99%

Ebola virus disease

Jacob

Crozier

Fischer

et al. 2020

Nat Rev Dis Primers

374

345

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To date, 12 distinct filoviruses have been described 1. The seven filoviruses that have been found in humans belong either to the genus Ebolavirus (Bundibugyo virus (BDBV), Ebola virus (EBOV), Reston virus (RESTV), Sudan virus (SUDV) and Taï Forest virus (TAFV); Fig. 1) or to the genus Marburgvirus (Marburg virus (MARV) and Ravn virus (RAVV)) 2. The WHO International Classification of Diseases Revision 11 (ICD-11) of 2018 recognizes two major subcategories of filovirus disease (FVD): Ebola disease caused by BDBV, EBOV, SUDV or TAFV, and Marburg disease caused by MARV or RAVV. Ebola virus disease (EVD) is defined as a disease only caused by EBOV. This subcategorization of FVD is largely based on the increasing evidence of molecular differences between ebolaviruses and marburgviruses, differences that may influence virus-host reservoir tropism, pathogenesis and disease phenotype in accidental primate hosts 2. Since the discovery of filoviruses in 1967 (reF. 3), 43 FVD outbreaks (excluding at least five laboratoryacquired infections) have been recorded in or exported from Africa 4. The epidemiological definition of outbreak is one or more cases above the known endemic prevalence. For example, the single case of TAFV infection recorded in a setting in which FVD had never been reported before (Côte d'Ivoire) 5 is still considered an outbreak. All FVD outbreaks, with the exception of that caused by TAFV, were characterized by extremely high case-fatality rates (CFRs, also known as lethality). Until 2013, the most extensive outbreak, caused by SUDV, involved 425 cases and 224 deaths (CFR 52.7%) 6. The overall limited numbers of FVD cases (1967-2013: 2,886 cases including 1,982 deaths 4), the typical remote and rural locations of outbreaks and the often delayed announcement of new outbreaks to the international community 7 have prevented the systematic study of clinical FVD in humans. Thus, the commonly used description of FVD was derived either from observation of small groups of patients in care settings that were not well-equipped for diagnosis, treatment and disease characterization, or from observations of even smaller samples, such as individuals who were transferred from Equatorial Africa to Europe and the USA or who fell sick in Europe or the USA after contracting the virus elsewhere. Pathological characterization of FVD via autopsies has been rare 7,8. In the absence of extensive human clinical data, FVD could only be defined further via the use of experimental animal infections 9,10 .

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“…Ideally, the methods employed will be selected or designed both to allow for the detection of emerging zoonoses during the acute phase of infection, while the patient or animal remains acutely infected with active pathogen replication or shedding, and to monitor for antibody development and persistence after recovery, when the potential pathogen may no longer be present and available to cause disease in the monitored patient or other individuals (Figure 1). For many known highconsequence viral pathogens, the acute phase of infection is only a few days long and typically ranges from 2 to 21 days postinfection (88,89), thus limiting the time that molecular diagnostic techniques targeting the pathogen genomic material, such as polymerase chain reaction (PCR) and its derivatives, may be diagnostically useful. The advent of highly sensitive and specific molecular techniques that can directly detect a pathogen's genome based on NAAT technologies, such as PCR amplification of RNA (after reverse transcription) and DNA, has revolutionized pathogen discovery.…”

Section: Integrated Laboratory Testing To Span the Diagnostic Spectrummentioning

confidence: 99%

Detection of Emerging Zoonotic Pathogens: An Integrated One Health Approach

Bird

Mazet

2018

Annu. Rev. Anim. Biosci.

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The emergence of novel zoonotic pathogens is one of the greatest challenges to global health security. The advent of increasingly sophisticated diagnostics tools has revolutionized our capacity to detect and respond to these health threats more rapidly than ever before. Yet, no matter how sophisticated these tools become, the initial identification of emerging infectious diseases begins at the local community level. It is here that the initial human or animal case resides, and it is here that early pathogen detection would have maximum benefit. Unfortunately, many areas at highest risk of zoonotic disease emergence lack sufficient infrastructure capacity to support robust laboratory diagnostic systems. Multiple factors are essential for pathogen detection networks, including an understanding of the complex sociological and ecological factors influencing disease transmission risk, community engagement, surveillance along high-risk human-animal interfaces, and a skilled laboratory workforce. Here we discuss factors relevant to the emerging disease paradigm, recent technical advances in diagnostic methods, and strategies for comprehensive and sustainable approaches to rapid zoonotic disease detection.

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Ebola Virus Disease Diagnostics, Sierra Leone: Analysis of Real-time Reverse Transcription–Polymerase Chain Reaction Values for Clinical Blood and Oral Swab Specimens

Cited by 23 publications

References 9 publications

Ebola RNA Persistence in Semen of Ebola Virus Disease Survivors — Final Report

Ebola RNA Persistence in Semen of Ebola Virus Disease Survivors — Final Report

Ebola virus disease

Detection of Emerging Zoonotic Pathogens: An Integrated One Health Approach

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