The Case for Improved Diagnostic Tools to Control Ebola Virus Disease in West Africa and How to Get There

Cost-effectiveness of incorporating Ebola prediction score tools and rapid diagnostic tests into a screening algorithm: A decision analytic model

BACKGROUND

No distinctive clinical signs of Ebola virus disease (EVD) have prompted the development of rapid screening tools or called for a new approach to screening suspected Ebola cases. New screening approaches require evidence of clinical benefit and economic efficiency. As of now, no evidence or defined algorithm exists.

OBJECTIVE

To evaluate, from a healthcare perspective, the efficiency of incorporating Ebola prediction scores and rapid diagnostic tests into the EVD screening algorithm during an outbreak.

METHODS

We collected data on rapid diagnostic tests (RDTs) and prediction scores' accuracy measurements, e.g., sensitivity and specificity, and the cost of case management and RDT screening in EVD suspect cases. The overall cost of healthcare services (PPE, procedure time, and standard-of-care (SOC) costs) per suspected patient and diagnostic confirmation of EVD were calculated. We also collected the EVD prevalence among suspects from the literature. We created an analytical decision model to assess the efficiency of eight screening strategies: 1) Screening suspect cases with the WHO case definition for Ebola suspects, 2) Screening suspect cases with the ECPS at -3 points of cut-off, 3) Screening suspect cases with the ECPS as a joint test, 4) Screening suspect cases with the ECPS as a conditional test, 5) Screening suspect cases with the WHO case definition, then QuickNavi™-Ebola RDT, 6) Screening suspect cases with the ECPS at -3 points of cut-off and QuickNavi™-Ebola RDT, 7) Screening suspect cases with the ECPS as a conditional test and QuickNavi™-Ebola RDT, and 8) Screening suspect cases with the ECPS as a joint test and QuickNavi™-Ebola RDT. We performed a cost-effectiveness analysis to identify an algorithm that minimizes the cost per patient correctly classified. We performed a one-way and probabilistic sensitivity analysis to test the robustness of our findings.

RESULTS

Our analysis found dual ECPS as a conditional test with the QuickNavi™-Ebola RDT algorithm to be the most cost-effective screening algorithm for EVD, with an effectiveness of 0.86. The cost-effectiveness ratio was 106.7 USD per patient correctly classified. The following algorithms, the ECPS as a conditional test with an effectiveness of 0.80 and an efficiency of 111.5 USD per patient correctly classified and the ECPS as a joint test with the QuickNavi™-Ebola RDT algorithm with an effectiveness of 0.81 and a cost-effectiveness ratio of 131.5 USD per patient correctly classified. These findings were sensitive to variations in the prevalence of EVD in suspected population and the sensitivity of the QuickNavi™-Ebola RDT.

CONCLUSIONS

Findings from this study showed that prediction scores and RDT could improve Ebola screening. The use of the ECPS as a conditional test algorithm and the dual ECPS as a conditional test and then the QuickNavi™-Ebola RDT algorithm are the best screening choices because they are more efficient and lower the number of confirmation tests and overall care costs during an EBOV epidemic.

Head-to-head comparison of diagnostic accuracy of four Ebola virus disease rapid diagnostic tests versus GeneXpert® in eastern Democratic Republic of the Congo outbreaks: a prospective observational study

BACKGROUND

Ebola virus disease (EVD) outbreaks have emerged in Central and West Africa. EVD diagnosis relies principally on RT-PCR testing with GeneXpert®, which has logistical and cost restrictions at the peripheral level of the health system. Rapid diagnostic tests (RDTs) would offer a valuable alternative at the point-of-care to reduce the turn-around time, if they show good performance characteristics. We evaluated the performance of four EVD RDTs against the reference standard GeneXpert® on stored EVD positive and negative blood samples collected between 2018 and 2021 from outbreaks in eastern Democratic Republic of the Congo (DRC).

METHODS

We conducted a prospective and observational study in the laboratory on QuickNavi-Ebola™, OraQuick® Ebola Rapid Antigen, Coris® EBOLA Ag K-SeT, and Standard® Q Ebola Zaïre Ag RDTs using left-over archived frozen EDTA whole blood samples. We randomly selected 450 positive and 450 negative samples from the EVD biorepositories in DRC, across a range of GeneXpert® cycle threshold values (Ct-values). RDT results were read by three persons and we considered an RDT result as "positive", when it was flagged as positive by at least two out of the three readers. We estimated the sensitivity and specificity through two independent generalized (logistic) linear mixed models (GLMM).

FINDINGS

476 (53%) of 900 samples had a positive GeneXpert Ebola result when retested. The QuickNavi-Ebola™ showed a sensitivity of 56.8% (95% CI 53.6-60.0) and a specificity of 97.5% (95% CI 96.2-98.4), the OraQuick® Ebola Rapid Antigen test displayed 61.6% (95% CI 57.0-65.9) sensitivity and 98.1% (95% CI 96.2-99.1) specificity, the Coris® EBOLA Ag K-SeT showed 25.0% (95% CI 22.3-27.9) sensitivity and 95.9% (95% CI 94.2-97.1) specificity, and the Standard® Q Ebola Zaïre Ag displayed 21.6% (95% CI 18.1-25.7) sensitivity and 99.1% (95% CI 97.4-99.7) specificity.

INTERPRETATION

None of the RDTs evaluated approached the "desired or acceptable levels" for sensitivity set out in the WHO target product profile, while all of the tests met the "desired level" for specificity. Nevertheless, the QuickNavi-Ebola™ and OraQuick® Ebola Rapid Antigen Test demonstrated the most favorable profiles, and may be used as frontline tests for triage of suspected-cases while waiting for RT-qPCR confirmatory testing.

FUNDING

Institute of Tropical Medicine Antwerp/EDCTP PEAU-EBOV-RDC project.

Field performance of three Ebola rapid diagnostic tests used during the 2018-20 outbreak in the eastern Democratic Republic of the Congo: a retrospective, multicentre observational study

BACKGROUND

The Democratic Republic of the Congo has confronted 13 outbreaks of Ebola virus disease since 1976. Rapid diagnostic tests (RDTs) detecting viral antigens have been developed to circumvent difficulties encountered with RT-PCR for diagnosis in remote low-resource settings, but there is still uncertainty about their performance characteristics and usability during outbreaks. We aimed to assess the field performance of three antigen detection RDTs compared with the gold-standard Cepheid GeneXpert Ebola assay results.

METHODS

We conducted a retrospective, multicentre observational study using complete and de-identified databases of five mobile laboratories (managed by the Institut National de Recherche Biomédicale) to assess the performance of three Ebola virus disease RDTs (QuickNavi-Ebola, OraQuick Ebola Rapid Antigen Test, and Coris EBOLA Ag K-SeT rapid test) run on blood samples of patients with suspected Ebola virus disease in direct comparison with the Cepheid GeneXpert Ebola assay reference test during the 2018-20 outbreak in the eastern Democratic Republic of the Congo. We estimated the sensitivity and specificity of each test through generalised linear mixed models against the GeneXpert Ebola assay reference test and corrected for cycle threshold value and random site effects.

FINDINGS

719 (7·9%) of 9157 samples had a positive GeneXpert Ebola assay result. The QuickNavi-Ebola RDT had a sensitivity of 87·4% (95% CI 63·6-96·8) around the mean cycle threshold value and a specificity of 99·6% (99·3-99·8). The OraQuick Ebola Rapid Antigen Test had a sensitivity of 57·4% (95% CI 38·8-75·8) and specificity of 98·3% (97·5-99·0), and the Coris EBOLA Ag K-SeT rapid test had a sensitivity of 38·9% (23·0-63·6) against the GeneXpert Ebola assay reference and specificity of 97·4% (85·3-99·6). The QuickNavi-Ebola RDT showed a robust performance with good sensitivity, particularly with increasing viral loads (ie, low cycle threshold values), and specificity.

INTERPRETATION

The three RDTs evaluated did not achieve the desired sensitivity and specificity of the WHO target product profile. Although the RDTs cannot triage and rule out Ebola virus infection among clinical suspects, they can still help to sort people with suspected Ebola virus disease into high-risk and low-risk groups while waiting for GeneXpert Ebola assay reference testing.

FUNDING

None.

TRANSLATION

For the French translation of the abstract see Supplementary Materials section.

Recent advances and clinical application in point-of-care testing of SARS-CoV-2

The novel coronavirus 2019 (COVID-19) caused by SARS-CoV-2 spread rapidly worldwide, posing a severe threat to public life and health. It is significant to realize rapid testing and timely control of epidemic situations under the condition of limited resources. However, laboratory-based standardized nucleic acid detection methods have a long turnaround time and high cost, so it is urgent to develop convenient methods for detecting COVID-19. This paper summarizes the point-of-care testing (POCT) developed for novel coronavirus from three aspects: nucleic acid extraction, nucleic acid amplification, and detection methods. This paper introduces a commercial real-time detection system that integrates the abovementioned three steps and the matters needing attention in use. The primary purpose of this review is to provide a reference for emergency response and rapid deployment of COVID-19 and some other emerging infectious diseases.

Application experience of a rapid nucleic acid detection system for COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is raging worldwide. The COVID-19 outbreak caused severe threats to the life and health of all humans caused by SARS-CoV-2. Clinically, there is an urgent need for an in vitro diagnostic product to detect SARS-CoV-2 nucleic acid quickly. Under this background, commercial SARS-CoV-2 nucleic acid POCT products came into being. However, how to choose these products and how to use these products in a standardized way have brought new puzzles to clinical laboratories. This paper focuses on evaluating the performance of these commercial SARS-CoV-2 nucleic acid POCT products and helps the laboratory make the correct choice. At the same time, to standardize the use of this kind of product, this paper also puts forward corresponding suggestions from six elements of total quality management, namely, human, machine, material, method, environment, and measurement. In addition, this paper also puts forward some ideas on the future development direction of POCT products.

Deskilled and Rapid Drug-Resistant Gene Detection by Centrifugal Force-Assisted Thermal Convection PCR Device

Here we report the improved Cyclo olefin polymer (COP) microfluidic chip and polymerase chain reaction (PCR) amplification system for point-of-care testing (POCT) in rapid detection of Carbapenem-resistant Enterobacteriaceae (CRE). The PCR solution and thermal cycling is controlled by the relative gravitational acceleration (7G) only and is expected to pose minimal problem in operation by non-expert users. Detection is based on identifying the presence of carbapenemase encoding gene through the corresponding fluorescence signal after amplification. For preliminary tests, the device has been demonstrated to detect bla_IMP-6 from patients stool samples. From the prepared samples, 96.4 fg/µL was detected with good certainty within 15 min (~106 thermocycles,) which is significantly faster than the conventional culture plate method. Moreover, the device is expected to detect other target genes in parallel as determination of the presence of bla_NDM-1 and bla_OXA-23 from control samples has also been demonstrated. With the rising threat of drug-resistant bacteria in global healthcare, this technology can greatly aid the health sector by enabling the appropriate use of antibiotics, accelerating the treatment of carriers, and suppressing the spread.

Comparative performance study of three Ebola rapid diagnostic tests in Guinea

Background

The 2014/15 Ebola outbreak in West Africa resulted in 11,000 deaths and massive strain on local health systems, and the ongoing outbreak in Democratic Republic of Congo has afflicted more than 3000 people. Accurate, rapid Ebola diagnostics suitable for field deployment would enable prompt identification and effective response to future outbreaks, yet remain largely unavailable. The purpose of this study was to assess the accuracy of three novel rapid diagnostic tests (RDTs): an Ebola, an Ebola-Malaria, and a Fever Panel test that includes Ebola, all from a single manufacturer.

Methods

We evaluated the three RDTs in 109 Ebola-positive and 96 Ebola-negative stored serum samples collected during the outbreak in Guinea in 2014/15, and tested by real-time polymerase chain reaction (RT-PCR). Sensitivity, specificity, and overall percent agreement were calculated for each RDT using RT-PCR as a reference standard, stratified by Ct value ranges.

Results

All tests performed with high accuracy on samples with low Ct value (high viral load). The Fever Panel test performed with the highest accuracy, with a sensitivity of 89.9% and specificity of 90.6%. The Ebola and Ebola-Malaria tests performed comparably to each other: sensitivity was 77.1 and 78% respectively, and specificity was 91.7% for the Ebola test and 95.8% for the Ebola-Malaria test.

Conclusions

This study evaluated the accuracy of three novel rapid diagnostic tests for Ebola. The tests may have significant public health relevance, particularly the Fever Panel test, which detects seven pathogens including Ebola. Given limitations to the study resulting from uncertain sample quality, further evaluation is warranted. All tests performed with highest accuracy on samples with low Ct value (high viral load), and the data presented here suggests that these RDTs may be useful for point-of-care diagnosis of cases in the context of an outbreak. Restrictions to their use in non-severe Ebola cases or for longitudinal monitoring, when viral loads are lower, may be appropriate. Highlighting the challenge in developing and evaluating Ebola RDTs, there were concerns regarding sample integrity and reference testing, and there is a need for additional research to validate these assays.

Redefining typhoid diagnosis: what would an improved test need to look like?

INTRODUCTION

Typhoid fever is one of the most common bacterial causes of acute febrile illness in the developing world, with an estimated 10.9 million new cases and 116.8 thousand deaths in 2017. Typhoid point-of-care (POC) diagnostic tests are widely used but have poor sensitivity and specificity, resulting in antibiotic overuse that has led to the emergence and spread of multidrug-resistant strains. With recent advances in typhoid surveillance and detection, this is the ideal time to produce a target product profile (TPP) that guides product development and ensure that a next-generation test meets the needs of users in the resource-limited settings where typhoid is endemic.

METHODS

A structured literature review was conducted to develop a draft TPP for a next-generation typhoid diagnostic test with minimal and optimal desired characteristics for 36 test parameters. The TPP was refined using feedback collected from a Delphi survey of key stakeholders in clinical medicine, microbiology, diagnostics and public and global health.

RESULTS

A next-generation typhoid diagnostic test should improve patient management through the diagnosis and treatment of infection with acute Salmonella enterica serovars Typhi or Paratyphi with a sensitivity ≥90% and specificity ≥95%. The test would ideally be used at the lowest level of the healthcare system in settings without a reliable power or water supply and provide results in <15 min at a cost of

CONCLUSION

This report outlines the first comprehensive TPP for typhoid fever and is intended to guide the development of a next-generation typhoid diagnostic test. An accurate POC test will reduce the morbidity and mortality of typhoid fever through rapid diagnosis and treatment and will have the greatest impact in reducing antimicrobial resistance if it is combined with diagnostics for other causes of acute febrile illness in a treatment algorithm.

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Key Words

• Other diagnostic or tool
• Public Health
• diagnostics and tools
• typhoid and paratyphoid fevers

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MESH Headings Collapse

Grants

• Department for International Development

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Affiliation(s)

Richard G Mather Malaria and Fever Program, Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
Heidi Hopkins Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
Christopher M Parry Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
Sabine Dittrich Malaria and Fever Program, Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland Nuffield Department of Medicine, University of Oxford, Oxford, UK

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A comprehensive district-level laboratory intervention after the Ebola epidemic in Sierra Leone

Background

The 2014–2016 Ebola outbreak exposed the poor laboratory systems in Sierra Leone. Immense needs were recognised across all areas, from facilities, diagnostic capacity, supplies, trained personnel to quality assurance mechanisms.

Objective

We aimed to describe the first year of a comprehensive intervention, which started in 2015, in a public hospital’s general laboratory serving a population of over 500 000 in a rural district.

Methods

The intervention focused on (1) supporting local authorities and healthcare workers in policy implementation and developing procedures to enhance access to services, (2) addressing gaps by investing in infrastructure, supplies, and equipment, (3) development of quality assurance mechanisms via mentorship, bench-side training, and the introduction of quality control and information systems. All work was performed alongside counterparts from the Ministry of Health and Sanitation.

Results

We observed a strong increase in patient visits and inpatient and outpatient testing volumes. Novel techniques and procedures were taken up well by staff, leading to improved and expanded service and safety, laying foundations for further improvements.

Conclusion

This comprehensive approach was successful and the results suggest an increase in trust from patients and healthcare workers.

Development of Mobile Laboratory for Viral Hemorrhagic Fever Detection in Africa

Background

A mobile laboratory transportable on commercial flights was developed to enable local response to viral hemorrhagic fever outbreaks.

Methods

The development progressed from use of mobile real-time reverse-transcription polymerase chain reaction to mobile real-time recombinase polymerase amplification. In this study, we describe various stages of the mobile laboratory development.

Results

A brief overview of mobile laboratory deployments, which culminated in the first on-site detection of Ebola virus disease (EVD) in March 2014, and their successful use in a campaign to roll back EVD cases in Conakry in the West Africa Ebola virus outbreak are described.

Conclusions

The developed mobile laboratory successfully enabled local teams to perform rapid disgnostic testing for viral hemorrhagic fever.

Symptom- and Laboratory-Based Ebola Risk Scores to Differentiate Likely Ebola Infections

Rapidly identifying likely Ebola patients is difficult because of a broad case definition, overlap of symptoms with common illnesses, and lack of rapid diagnostics. However, rapid identification is critical for care and containment of contagion. We analyzed retrospective data from 252 Ebola-positive and 172 Ebola-negative patients at a Sierra Leone Ebola treatment center to develop easy-to-use risk scores, based on symptoms and laboratory tests (if available), to stratify triaged patients by their likelihood of having Ebola infection. Headache, diarrhea, difficulty breathing, nausea/vomiting, loss of appetite, and conjunctivitis comprised the symptom-based score. The laboratory-based score also included creatinine, creatine kinase, alanine aminotransferase, and total bilirubin. This risk score correctly identified 92% of Ebola-positive patients as high risk for infection; both scores correctly classified >70% of Ebola-negative patients as low or medium risk. Clinicians can use these risk scores to gauge the likelihood of triaged patients having Ebola while awaiting laboratory confirmation.

The current landscape of nucleic acid tests for filovirus detection

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Filoviruses can cause severe hemorrhagic fever in humans and non-human primates.

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There is an urgent need for rapid diagnosis of filoviruses during outbreaks.

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Filovirus diagnostics have advanced since the 2014–2016 Ebolavirus outbreak.

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NATs are the gold standard for filovirus detection.

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NAT-based diagnostic speed, portability and multiplexing have all improved.

Nucleic acid testing (NAT) for pathogenic filoviruses plays a key role in surveillance and to control the spread of infection. As they share clinical features with other pathogens, the initial spread of these viruses can be misdiagnosed. Tests that can identify a pathogen in the initial stages of infection are essential to control outbreaks. Since the Ebola virus disease (EVD) outbreak in 2014–2016 several tests have been developed that are faster than previous tests and more suited for field use. Furthermore, the ability to test for a range of pathogens simultaneously has been expanded to improve clinical pathway management of febrile syndromes. This review provides an overview of these novel diagnostic tests.

Establishing Ebola Virus Disease (EVD) diagnostics using GeneXpert technology at a mobile laboratory in Liberia: Impact on outbreak response, case management and laboratory systems strengthening

The 2014-16 Ebola Virus Disease (EVD) outbreak in West Africa highlighted the necessity for readily available, accurate and rapid diagnostics. The magnitude of the outbreak and the re-emergence of clusters of EVD cases following the declaration of interrupted transmission in Liberia, reinforced the need for sustained diagnostics to support surveillance and emergency preparedness. We describe implementation of the Xpert Ebola Assay, a rapid molecular diagnostic test run on the GeneXpert platform, at a mobile laboratory in Liberia and the subsequent impact on EVD outbreak response, case management and laboratory system strengthening. During the period of operation, site coordination, management and operational capacity was supported through a successful collaboration between Ministry of Health (MoH), World Health Organization (WHO) and international partners. A team of Liberian laboratory technicians were trained to conduct EVD diagnostics and the laboratory had capacity to test 64-100 blood specimens per day. Establishment of the laboratory significantly increased the daily testing capacity for EVD in Liberia, from 180 to 250 specimens at a time when the effectiveness of the surveillance system was threatened by insufficient diagnostic capacity. During the 18 months of operation, the laboratory tested a total of 9,063 blood specimens, including 21 EVD positives from six confirmed cases during two outbreaks. Following clearance of the significant backlog of untested EVD specimens in November 2015, a new cluster of EVD cases was detected at the laboratory. Collaboration between surveillance and laboratory coordination teams during this and a later outbreak in March 2016, facilitated timely and targeted response interventions. Specimens taken from cases during both outbreaks were analysed at the laboratory with results informing clinical management of patients and discharge decisions. The GeneXpert platform is easy to use, has relatively low running costs and can be integrated into other national diagnostic algorithms. The technology has on average a 2-hour sample-to-result time and allows for single specimen testing to overcome potential delays of batching. This model of a mobile laboratory equipped with Xpert Ebola test, staffed by local laboratory technicians, could serve to strengthen outbreak preparedness and response for future outbreaks of EVD in Liberia and the region.

Prevention of common healthcare-associated infections in humanitarian hospitals

PURPOSE OF REVIEW

Humanitarian medical organizations focus on vulnerable patients with increased risk for healthcare-associated infections (HAIs) and are obligated to minimize them in inpatient departments (IPDs). However, in doing so humanitarian groups face considerable obstacles. This report will focus on approaches to reducing common HAIs that the authors have found to be helpful in humanitarian settings.

RECENT FINDINGS

HAIs are common in humanitarian contexts but there are few interventions or guidelines adapted for use in poor and conflict-affected settings to improve prevention and guide surveillance. Based on existing recommendations and studies, it appears prudent that all humanitarian IPDs introduce a basic infection prevention infrastructure, assure high adherence to hand hygiene with wide accessibility to alcohol-based hand rub, and develop pragmatic surveillance based on clinically evident nosocomial infection. Although microbiology remains out of reach for most humanitarian hospitals, rapid tests offer the possibility of improving the diagnosis of HAIs in humanitarian hospitals in the decade ahead.

SUMMARY

There is a dearth of new studies that can direct efforts to prevent HAIs in IPDs in poor and conflict-affected areas and there is a need for practical, field-adapted guidelines from professional societies, and international bodies to guide infection prevention efforts in humanitarian environments.

Strategies in Ebola virus disease (EVD) diagnostics at the point of care

Ebola virus disease (EVD) is a devastating, highly infectious illness with a high mortality rate. The disease is endemic to regions of Central and West Africa, where there is limited laboratory infrastructure and trained staff. The recent 2014 West African EVD outbreak has been unprecedented in case numbers and fatalities, and has proven that such regional outbreaks can become a potential threat to global public health, as it became the source for the subsequent transmission events in Spain and the USA. The urgent need for rapid and affordable means of detecting Ebola is crucial to control the spread of EVD and prevent devastating fatalities. Current diagnostic techniques include molecular diagnostics and other serological and antigen detection assays; which can be time-consuming, laboratory-based, often require trained personnel and specialized equipment. In this review, we discuss the various Ebola detection techniques currently in use, and highlight the potential future directions pertinent to the development and adoption of novel point-of-care diagnostic tools. Finally, a case is made for the need to develop novel microfluidic technologies and versatile rapid detection platforms for early detection of EVD.

Emerging Zoonotic and Vector-Borne Viral Diseases

Many vector-borne and zoonotic diseases are considered to be emerging; since they are either newly reported to cause human disease, or are causing disease in geographical locations or species not previously documented. In the past 15 years, significant outbreaks of Severe Acute Respiratory Syndrome (or SARS) and Middle Eastern Respiratory Syndrome (or MERS), Nipah and Hendra, Ebola virus disease and Zika fever and others have been reported. In this chapter the clinical characteristics, epidemiological aspects, treatment and prevention and information related to the laboratory investigation of important zoonotic and vector-borne diseases that have emerged in the past 10 years, and how this affects children, will be discussed. Furthermore rabies, considered a neglected viral disease with the majority of victims in Africa being children, will also be addressed.

Molecular Diagnostic Field Test for Point-of-Care Detection of Ebola Virus Directly From Blood

A molecular diagnostic method for robust detection of Ebola virus (EBOV) at the point of care (POC) directly from blood samples is described. This assay is based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) of the glycoprotein gene of EBOV. Complete reaction formulations were lyophilized in 0.2-mL polymerase chain reaction tubes. RT-LAMP reactions were performed on a battery-operated isothermal instrument. Limit of detection of this RT-LAMP assay was 2.8 × 10² plaque-forming units (PFU)/test and 1 × 10³ PFU/test within 40 minutes for EBOV-Kikwit and EBOV-Makona, respectively. This assay was found to be specific for the detection of EBOV, as no nonspecific amplification was detected in blood samples spiked with closely related viruses and other pathogens. These results showed that this diagnostic test can be used at the point of care for rapid and specific detection of EBOV directly from blood with high sensitivity within 40 minutes.

Prevention of sexual transmission of Ebola in Liberia through a national semen testing and counselling programme for survivors: an analysis of Ebola virus RNA results and behavioural data

BACKGROUND

Ebola virus has been detected in semen of Ebola virus disease survivors after recovery. Liberia's Men's Health Screening Program (MHSP) offers Ebola virus disease survivors semen testing for Ebola virus. We present preliminary results and behavioural outcomes from the first national semen testing programme for Ebola virus.

METHODS

The MHSP operates out of three locations in Liberia: Redemption Hospital in Montserrado County, Phebe Hospital in Bong County, and Tellewoyan Hospital in Lofa County. Men aged 15 years and older who had an Ebola treatment unit discharge certificate are eligible for inclusion. Participants' semen samples were tested for Ebola virus RNA by real-time RT-PCR and participants received counselling on safe sexual practices. Participants graduated after receiving two consecutive negative semen tests. Counsellors collected information on sociodemographics and sexual behaviours using questionnaires administered at enrolment, follow up, and graduation visits. Because the programme is ongoing, data analysis was restricted to data obtained from July 7, 2015, to May 6, 2016.

FINDINGS

As of May 6, 2016, 466 Ebola virus disease survivors had enrolled in the programme; real-time RT-PCR results were available from 429 participants. 38 participants (9%) produced at least one semen specimen that tested positive for Ebola virus RNA. Of these, 24 (63%) provided semen specimens that tested positive 12 months or longer after Ebola virus disease recovery. The longest interval between discharge from an Ebola treatment unit and collection of a positive semen sample was 565 days. Among participants who enrolled and provided specimens more than 90 days since their Ebola treatment unit discharge, men older than 40 years were more likely to have a semen sample test positive than were men aged 40 years or younger (p=0·0004). 84 (74%) of 113 participants who reported not using a condom at enrolment reported using condoms at their first follow-up visit (p<0·0001). 176 (46%) of 385 participants who reported being sexually active at enrolment reported abstinence at their follow-up visit (p<0·0001).

INTERPRETATION

Duration of detection of Ebola virus RNA by real-time RT-PCR varies by individual and might be associated with age. By combining behavioural counselling and laboratory testing, the Men's Health Screening Program helps male Ebola virus disease survivors understand their individual risk and take appropriate measures to protect their sexual partners.

FUNDING

World Health Organization and the US Centers for Disease Control and Prevention.

Target Product Profile for a Diagnostic Assay to Differentiate between Bacterial and Non-Bacterial Infections and Reduce Antimicrobial Overuse in Resource-Limited Settings: An Expert Consensus

Acute fever is one of the most common presenting symptoms globally. In order to reduce the empiric use of antimicrobial drugs and improve outcomes, it is essential to improve diagnostic capabilities. In the absence of microbiology facilities in low-income settings, an assay to distinguish bacterial from non-bacterial causes would be a critical first step. To ensure that patient and market needs are met, the requirements of such a test should be specified in a target product profile (TPP). To identify minimal/optimal characteristics for a bacterial vs. non-bacterial fever test, experts from academia and international organizations with expertise in infectious diseases, diagnostic test development, laboratory medicine, global health, and health economics were convened. Proposed TPPs were reviewed by this working group, and consensus characteristics were defined. The working group defined non-severely ill, non-malaria infected children as the target population for the desired assay. To provide access to the most patients, the test should be deployable to community health centers and informal health settings, and staff should require <2 days of training to perform the assay. Further, given that the aim is to reduce inappropriate antimicrobial use as well as to deliver appropriate treatment for patients with bacterial infections, the group agreed on minimal diagnostic performance requirements of >90% and >80% for sensitivity and specificity, respectively. Other key characteristics, to account for the challenging environment at which the test is targeted, included: i) time-to-result <10 min (but maximally <2 hrs); ii) storage conditions at 0–40°C, ≤90% non-condensing humidity with a minimal shelf life of 12 months; iii) operational conditions of 5–40°C, ≤90% non-condensing humidity; and iv) minimal sample collection needs (50–100μL, capillary blood). This expert approach to define assay requirements for a bacterial vs. non-bacterial assay should guide product development, and enable targeted and timely efforts by industry partners and academic institutions.

Diagnostics in a digital age: an opportunity to strengthen health systems and improve health outcomes

Diagnostics play a critical role in clinical decision making, and in disease control and prevention. Rapid point-of-care (POC) tests for infectious diseases can improve access to diagnosis and patient management, but the quality of these tests vary, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. A new generation of POC molecular tests that are highly sensitive and specific, robust and easy to use are now available for deployment in low resource settings. Decentralisation of testing outside of the laboratory can put tremendous stress on the healthcare system and presents challenges for training and quality assurance. A feature of many of these POC molecular devices is that they are equipped with data transmission capacities. In a digital age, it is possible to link data from diagnostic laboratories and POC test readers and devices to provide data on testing coverage, disease trends and timely information for early warning of infectious disease outbreaks to inform design or optimisation of disease control and elimination programmes. Data connectivity also allows control programmes to monitor the quality of tests and testing, and optimise supply chain management; thus, increasing the efficiency of healthcare systems and improving patient outcomes.

Development, Evaluation, and Integration of a Quantitative Reverse-Transcription Polymerase Chain Reaction Diagnostic Test for Ebola Virus on a Molecular Diagnostics Platform

BACKGROUND

The 2013-2016 Ebola epidemic in West Africa resulted in accelerated development of rapid diagnostic tests for emergency outbreak preparedness. We describe the development and evaluation of the Idylla™ prototype Ebola virus test, a fully automated sample-to-result molecular diagnostic test for rapid detection of Zaire ebolavirus (EBOV) and Sudan ebolavirus (SUDV).

METHODS

The Idylla™ prototype Ebola virus test can simultaneously detect EBOV and SUDV in 200 µL of whole blood. The sample is directly added to a disposable cartridge containing all reagents for sample preparation, RNA extraction, and amplification by reverse-transcription polymerase chain reaction analysis. The performance was evaluated with a variety of sample types, including synthetic constructs and whole blood samples from healthy volunteers spiked with viral RNA, inactivated virus, and infectious virus.

RESULTS

The 95% limits of detection for EBOV and SUDV were 465 plaque-forming units (PFU)/mL (1010 copies/mL) and 324 PFU/mL (8204 copies/mL), respectively. In silico and in vitro analyses demonstrated 100% correct reactivity for EBOV and SUDV and no cross-reactivity with relevant pathogens. The diagnostic sensitivity was 97.4% (for EBOV) and 91.7% (for SUDV), the specificity was 100%, and the diagnostic accuracy was 95.9%.

CONCLUSIONS

The Idylla™ prototype Ebola virus test is a fast, safe, easy-to-use, and near-patient test that meets the performance criteria to detect EBOV in patients with suspected Ebola.

Predicting and Evaluating the Epidemic Trend of Ebola Virus Disease in the 2014-2015 Outbreak and the Effects of Intervention Measures

We constructed dynamic Ebola virus disease (EVD) transmission models to predict epidemic trends and evaluate intervention measure efficacy following the 2014 EVD epidemic in West Africa. We estimated the effective vaccination rate for the population, with basic reproduction number (R0) as the intermediate variable. Periodic EVD fluctuation was analyzed by solving a Jacobian matrix of differential equations based on a SIR (susceptible, infective, and removed) model. A comprehensive compartment model was constructed to fit and predict EVD transmission patterns, and to evaluate the effects of control and prevention measures. Effective EVD vaccination rates were estimated to be 42% (31-50%), 45% (42-48%), and 51% (44-56%) among susceptible individuals in Guinea, Liberia and Sierra Leone, respectively. In the absence of control measures, there would be rapid mortality in these three countries, and an EVD epidemic would be likely recur in 2035, and then again 8~9 years later. Oscillation intervals would shorten and outbreak severity would decrease until the periodicity reached ~5.3 years. Measures that reduced the spread of EVD included: early diagnosis, treatment in isolation, isolating/monitoring close contacts, timely corpse removal, post-recovery condom use, and preventing or quarantining imported cases. EVD may re-emerge within two decades without control and prevention measures. Mass vaccination campaigns and control and prevention measures should be instituted to prevent future EVD epidemics.

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

BACKGROUND

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.

The role of rapid diagnostics in managing Ebola epidemics

Ebola emerged in West Africa around December 2013 and swept through Guinea, Sierra Leone and Liberia, giving rise to 27,748 confirmed, probable and suspected cases reported by 29 July 2015. Case diagnoses during the epidemic have relied on polymerase chain reaction-based tests. Owing to limited laboratory capacity and local transport infrastructure, the delays from sample collection to test results being available have often been 2 days or more. Point-of-care rapid diagnostic tests offer the potential to substantially reduce these delays. We review Ebola rapid diagnostic tests approved by the World Health Organization and those currently in development. Such rapid diagnostic tests could allow early triaging of patients, thereby reducing the potential for nosocomial transmission. In addition, despite the lower test accuracy, rapid diagnostic test-based diagnosis may be beneficial in some contexts because of the reduced time spent by uninfected individuals in health-care settings where they may be at increased risk of infection; this also frees up hospital beds. We use mathematical modelling to explore the potential benefits of diagnostic testing strategies involving rapid diagnostic tests alone and in combination with polymerase chain reaction testing. Our analysis indicates that the use of rapid diagnostic tests with sensitivity and specificity comparable with those currently under development always enhances control, whether evaluated at a health-care-unit or population level. If such tests had been available throughout the recent epidemic, we estimate, for Sierra Leone, that their use in combination with confirmatory polymerase chain-reaction testing might have reduced the scale of the epidemic by over a third.