The role of rapid diagnostics in managing Ebola epidemics

Rapid Decision Algorithm for Patient Triage during Ebola Outbreaks

The low specificity of Ebola virus disease clinical signs increases the risk for nosocomial transmission to patients and healthcare workers during outbreaks. Reducing this risk requires identifying patients with a high likelihood of Ebola virus infection. Analyses of retrospective data from patients suspected of having Ebola virus infection identified 13 strong predictors and time from disease onset as constituents of a prediction score for Ebola virus disease. We also noted 4 highly predictive variables that could distinguish patients at high risk for infection, independent of their scores. External validation of this algorithm on retrospective data revealed the probability of infection continuously increased with the score.

Systematic review and meta-analysis of antigen rapid diagnostic tests to detect Zaire ebolavirus

We conducted a systematic review and meta-analysis of studies and reports comparing the performance of antigen rapid diagnostic tests (Ag RDT) for diagnosing Ebola disease (EVD). We searched PubMed, EMBASE, and Web of Science for diagnostic studies published between 1976 and 2023, evaluating them with QUADAS-2. Using a bivariate random-effects model, we estimated the pooled sensitivity and specificity of Ag RDTs. Of 64 eligible full studies and reports, 16 met the inclusion criteria. Pooled sensitivity and specificity were 82.1% (95%CI: 75.2 - 88.0) and 97.0% (95%CI: 95.1-98.2), respectively. We conducted subgroup analysis on 4 Ag RDTs, 3 RT-PCR tests, and 4 sample types, showing varied performance. The high specificity and positive predictive value of Ag RDTs support their use to "rule-in" patients with EVD. However, high-sensitivity RDTs suitable for field settings and capable of detecting multiple ebolavirus species are needed.

Quantitative Assessment of Fungal Biomarkers in Clinical Samples via an Interface-Modulated Optical Fiber Biosensor

Invasive fungal infections pose a significant public health threat. The lack of precise and timely diagnosis is a primary factor contributing to the significant increase in patient mortality rates. Here, an interface-modulated biosensor utilizing an optical fiber for quantitative analysis of fungal biomarkers at the early stage of point-of-care testing (POCT), is reported. By integrating surface refractive index (RI) modulation and plasmon enhancement, the sensor to achieve high sensitivity in a directional response to the target analytes, is successfully optimized. As a result, a compact fiber-optic sensor with rapid response time, cost-effectiveness, exceptional sensitivity, stability, and specificity, is developed. This sensor can successfully identify the biomarkers of specific pathogens from blood or other tissue specimens in animal models. It quantifies clinical blood samples with precision and effectively discriminates between negative and positive cases, thereby providing timely alerts to potential patients. It significantly reduces the detection time of fungal infection to only 30 min. Additionally, this approach exhibits remarkable stability and achieves a limit of detection (LOD) three orders of magnitude lower than existing methods. It overcomes the limitations of existing detection methods, including a high rate of misdiagnosis, prolonged detection time, elevated costs, and the requirement for stringent laboratory conditions.

A Flexible, Quantitative Plasmonic-Fluor Lateral Flow Assay for the Rapid Detection of Orthoebolavirus zairense and Orthoebolavirus sudanense

Filoviruses comprise a family of single-stranded, negative-sense RNA viruses with a significant impact on human health. Given the risk for disease outbreaks, as highlighted by the recent outbreaks across Africa, there is an unmet need for flexible diagnostic technologies that can be deployed in resource-limited settings. Herein, we highlight the use of plasmonic-fluor lateral flow assays (PF-LFA) for the rapid, quantitative detection of an Ebolavirus-secreted glycoprotein, a marker for infection. Plasmonic fluors are a class of ultrabright reporter molecules that combine engineered nanorods with conventional fluorophores, resulting in improved analytical sensitivity. We have developed a PF-LFA for Orthoebolavirus zairense (EBOV) and Orthoebolavirus sudanense (SUDV) that provides estimated limits of detection as low as 0.446 and 0.641 ng/mL, respectively. Furthermore, our assay highlights a high degree of specificity between the two viral species while also maintaining a turnaround time as short as 30 min. To highlight the utility of our PF-LFA, we demonstrate the detection of EBOV infection in non-human primates. Our PF-LFA represents an enormous step forward in the development of a robust, field-deployable assay for filoviruses.

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.

Assessing potential insights of an imperfect testing strategy: Parameter estimation and practical identifiability using early COVID-19 data in India

A deterministic model with testing of infected individuals has been proposed to investigate the potential consequences of the impact of testing strategy. The model exhibits global dynamics concerning the disease-free and a unique endemic equilibrium depending on the basic reproduction number when the recruitment of infected individuals is zero; otherwise, the model does not have a disease-free equilibrium, and disease never dies out in the community. Model parameters have been estimated using the maximum likelihood method with respect to the data of early COVID-19 outbreak in India. The practical identifiability analysis shows that the model parameters are estimated uniquely. The consequences of the testing rate for the weekly new cases of early COVID-19 data in India tell that if the testing rate is increased by 20% and 30% from its baseline value, the weekly new cases at the peak are decreased by 37.63% and 52.90%; and it also delayed the peak time by four and fourteen weeks, respectively. Similar findings are obtained for the testing efficacy that if it is increased by 12.67% from its baseline value, the weekly new cases at the peak are decreased by 59.05% and delayed the peak by 15 weeks. Therefore, a higher testing rate and efficacy reduce the disease burden by tumbling the new cases, representing a real scenario. It is also obtained that the testing rate and efficacy reduce the epidemic's severity by increasing the final size of the susceptible population. The testing rate is found more significant if testing efficacy is high. Global sensitivity analysis using partial rank correlation coefficients (PRCCs) and Latin hypercube sampling (LHS) determine the key parameters that must be targeted to worsen/contain the epidemic.

Agnostic Sequencing for Detection of Viral Pathogens

The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.

The diagnostic accuracy of rapid diagnostic tests for Ebola virus disease: a systematic review

BACKGROUND

Ebola virus disease (EVD) is a dangerous condition that can cause an epidemic. Several rapid diagnostic tests (RDTs) have been developed to diagnose EVD. These RDTs promise to be quicker and easier to use than the current reference standard diagnostic test, PCR.

OBJECTIVES

To assess the diagnostic accuracy of RDTs for EVD.

METHODS

A systematic review of diagnostic accuracy studies.

DATA SOURCES

The following bibliographic databases were searched from inception to present: MEDLINE (Ovid), Embase, Global Health, Cochrane Central Register of Controlled Trials, WHO Global Index Medicus database, Web of Science, PROSPERO register of Systematic Reviews, and Clinical Trials.Gov.

STUDY ELIGIBILITY CRITERIA

Diagnostic accuracy studies.

PARTICIPANTS

Patients presenting to the Ebola treatment units with symptoms of EVD.

INTERVENTIONS

RDTs; reference standard, RT-PCR.

ASSESSMENT OF RISK OF BIAS

Quality Assessment of Diagnostic Accuracy Studies-2 tool.

METHODS OF DATA SYNTHESIS

Summary estimates of diagnostic accuracy study were produced for each device type. Subgroup analyses were performed for RDT type and specimen material. A sensitivity analysis was performed to assess the effect of trial design and bias.

RESULTS

We included 15 diagnostic accuracy studies. The summary estimate of sensitivity for lateral flow assays was 86.1% (95% CI, 86-86.2%), with specificity of 97% (95% CI, 96.1-97.9%). The summary estimate for rapid PCR devices was sensitivity of 96.2% (95% CI, 95.3-97.9%), with a specificity of 96.8% (95% CI, 95.3-97.9%). Pre-specified subgroup analyses demonstrated that RDTs were effective on a range of specimen material. Overall, the risk of bias throughout the included studies was low, but it was high in patient selection and uncertain in the flow and timing domains.

CONCLUSIONS

RDTs possess both high sensitivity and specificity compared with RT-PCR among symptomatic patients presenting to the Ebola treatment units. Our findings support the use of RDTs as a 'rule in' test to expedite treatment and vaccination.

Fast and Sensitive Detection of SARS-CoV-2 Nucleic Acid Using a Rapid Detection System Free of RNA Extraction

Objectives

To establish and evaluate the analytical and clinical performance of the Flash20 SARS-CoV-2 nucleic acid rapid detection system free of RNA extraction.

Methods

The limit of detection (LoD) was determined using a negative nasopharyngeal swab matrix spiked with different concentrations of SARS-CoV-2 virus; a total of 734,337 reference sequences of viral genomes from GenBank were used for the in-silico analysis to assess the inclusivity of the assay. The specificity of the system was evaluated by testing 27 medically relevant organisms. A total of 115 clinical specimens were collected and tested on the Flash20 SARS-CoV-2 detection system and with an FDA-approved comparator test to assess the clinical performance of the system.

Results

The LoD of the Flash20 SARS-CoV-2 detection system is 250 copies/mL with a positive rate ≥90% (n = 20); alignments results showed that over 99% identity of the primer and probe of the Flash20 SARS-CoV-2 nucleic acid rapid detection system to the available SARS-CoV-2 sequences; the omicron samples tested 100% positive. None of the 27 organisms showed cross-reactivity with the Flash20 SARS-CoV-2 nucleic acid rapid detection system. Among all the 215 clinical samples, the Flash20 SARS-CoV-2 nucleic acid rapid detection system exhibits a high sensitivity of 99.24% (131/132) and 100% (83/83) specificity.

Conclusion

The nucleic acid rapid detection system provides sensitive and accurate detection of SARS-CoV-2 free of RNA extraction. The high sensitivity and short time to results of approximately 35 minutes may impact earlier infection control and disease management.

Diagnostics of Ebola virus

Ebola is a highly pathogenic virus, which in humans reaches a mortality rate above 50%. Due to a lack of laboratories in territories where Ebola viruses are endemic and the limited number of surveillance programmes, tests for the confirmation of suspected cases of Ebola are often performed in Reference Laboratories. While this provides guarantees regarding the accuracy of results, the shipment of samples to a centralized facility where the diagnostic test can be performed and the time required to achieve the results takes several days, which increases costs and entails delays in the isolation of positive subjects and therapeutic intervention with negative consequences both for patients and the community. Molecular tests have been the most frequently used tool in Ebola diagnosis in recent outbreaks. One of the most commonly used molecular tests is the Real-Star Altona, which targets a conserved area of the L gene. This assay showed different sensitivities depending on the Ebola virus: 471 copies/mL (EBOV) and 2871 copies/ml (SUDAN virus). The Cepheid system also showed good sensitivity (232 copies/mL). The LAMP platform is very promising because, being an isothermal reaction, it does not require high-precision instrumentation and can be considered a Point of Care (PoC) tool. Its analytical sensitivity is 1 copy/reaction. However, since data from real life studies are not yet available, it is premature to give any indications on its feasibility. Moreover, in November 2014, the WHO recommended the development of rapid diagnostic tests (RDT) according to ASSURED criteria. Several RDT assays have since been produced, most of which are rapid tests based on the search for antibody anti-Ebola viral proteins with immunochromatographic methods. Several viral antigens are used for this purpose: VP40, NP and GP. These assays show different sensitivities according to the protein used: VP40 57.4-93.1%, GP 53-88.9% and 85% for NP compared to reference molecular assays. From these results, it can be deduced that no RDT reaches the 99% sensitivity recommended by the WHO and therefore any RDT negative results in suspected cases should be confirmed with a molecular test.

Communicable diseases in humanitarian operations and disasters

Military organisations have battled communicable disease for millennia. They have pioneered disease prevention from the Crusades to the World Wars and continue to do so today. Predeployment vaccinations and chemoprophylaxis are effective in preventing communicable disease, as is reliable vector destruction and bite prevention, especially in the era of multidrug resistant organisms. These measures are unlikely to be fully possible in disasters, but reactive vaccination and efforts to reduce exposure to communicable disease should be a priority. Communicable diseases can be challenging to diagnose-the UK Defence Medical Services have become familiar with tools such as multiplex PCR and mass spectrometry. These have the potential to accurately identify organisms and sensitivity patterns in austere environments. Management of communicable diseases depends on accurate diagnosis and has a largely well-established evidence base but can be limited by a lack of resources and skills in an austere setting, therefore telemedicine can assist diagnosis and treatment of infections by projecting specialist skill. Systems such as EpiNATO2 are useful in monitoring diseases and identifying trends in order to establish control measures. Many of these tools and techniques are effective in austere environments and offer learning opportunities for those providing care in similar settings. Further research is ongoing into diagnostic tools as well as remote management.

Enhanced Enzymatically Amplified Metallization on Nanostructured Surfaces for Multiplexed Point-of-Care Electrical Detection of COVID-19 Biomarkers

Inexpensive yet sensitive and specific biomarker detection is a critical bottleneck in diagnostics, monitoring, and surveillance of infectious diseases such as COVID-19. Multiplexed detection of several biomarkers can achieve wider diagnostic applicability, accuracy, and ease-of-use, while reducing cost. Current biomarker detection methods often use enzyme-linked immunosorbent assays (ELISA) with optical detection which offers high sensitivity and specificity. However, this is complex, expensive, and limited to detecting only a single analyte at a time. Here, it is found that biomarker-bound enzyme-labeled probes act synergistically with nanostructured catalytic surfaces and can be used to selectively reduce a soluble silver substrate to generate highly dense and conductive, localized surface silver metallization on microelectrode arrays. This enables a sensitive and quantitative, simple, direct electronic readout of biomarker binding without the use of any intermediate optics. Furthermore, the localized and dry-phase stable nature of the metallization enables multiplexed electronic measurement of several biomarkers from a single drop (<10 µL) of sample on a microchip.This method is applied for the multiplexed point-of-care (POC) quantitative detection of multiple COVID-19 antigen-specific antibodies. Combining a simple microchip and an inexpensive, cellphone-interfaced, portable reader, the detection and discrimination of biomarkers of prior infection versus vaccination is demonstrated.

Rapid diagnostic tests versus RT-PCR for Ebola virus infections: a systematic review and meta-analysis

Objective

To evaluate the clinical accuracy of rapid diagnostic tests for the detection of Ebola virus.

Methods

We searched MEDLINE®, Embase® and Web of Science for articles published between 1976 and October 2021 reporting on clinical studies assessing the performance of Ebola virus rapid diagnostic tests compared with reverse transcription polymerase chain reaction (RT-PCR). We assessed study quality using the QUADAS-2 criteria. To estimate the pooled sensitivity and specificity of these rapid diagnostic tests, we used a bivariate random-effects meta-analysis.

Findings

Our search identified 113 unique studies, of which nine met the inclusion criteria. The studies were conducted in the Democratic Republic of the Congo, Guinea, Liberia and Sierra Leone and they evaluated 12 rapid diagnostic tests. We included eight studies in the meta-analysis. The pooled sensitivity and specificity of the rapid tests were 86% (95% confidence interval, CI: 80-91) and 95% (95% CI: 91-97), respectively. However, pooled sensitivity decreased to 83% (95% CI: 77-88) after removing outliers. Pooled sensitivity increased to 90% (95% CI: 82-94) when analysis was restricted to studies using the RT-PCR from altona Diagnostics as gold standard. Pooled sensitivity increased to 99% (95% CI: 67-100) when the analysis was restricted to studies using whole or capillary blood specimens.

Conclusion

The included rapid diagnostic tests did not detect all the Ebola virus disease cases. While the sensitivity and specificity of these tests are moderate, they are still valuable tools, especially useful for triage and detecting Ebola virus in remote areas.

Effect of mismatch between types of viral nucleic acid and intended targets of extraction kits on polymerase chain reaction-based testing

Lab personnel generally select an extraction kit based on the nucleic acid (NA) type of the target. This study investigated the effect of mismatch between the NA type of the target and the intended target NA of the extraction kit on the polymerase chain reaction outcome. DNA, RNA and total NA extraction kits manufactured by the same company were used to isolate NA from serial dilutions of four viruses representing different genome types. All extracts were tested for the viruses by either conventional or real-time polymerase chain reactions with and without reverse transcription. While the DNA kit specifically isolated DNA from samples, the RNA kit extracted both DNA and RNA as efficiently as the total NA kit, suggesting that RNA kits can be an economical alternative.

Modelling the Role of Human Behaviour in Ebola Virus Disease (EVD) Transmission Dynamics

The role of human behaviour in the dynamics of infectious diseases cannot be underestimated. A clear understanding of how human behaviour influences the spread of infectious diseases is critical in establishing and designing control measures. To study the role that human behaviour plays in Ebola disease dynamics, in this paper, we design an Ebola virus disease model with disease transmission dynamics based on a new exponential nonlinear incidence function. This new incidence function that captures the reduction in disease transmission due to human behaviour innovatively considers the efficacy and the speed of behaviour change. The model's steady states are determined and suitable Lyapunov functions are built. The proofs of the global stability of equilibrium points are presented. To demonstrate the utility of the model, we fit the model to Ebola virus disease data from Liberia and Sierra Leone. The results which are comparable to existing findings from the outbreak of 2014 − 2016 show a better fit when the efficacy and the speed of behaviour change are higher. A rapid and efficacious behaviour change as a control measure to rapidly control an Ebola virus disease epidemic is advocated. Consequently, this model has implications for the management and control of future Ebola virus disease outbreaks.

Patient delay in a coronavirus disease 2019 (COVID-19) outbreak in Tianjin, China from January to February 2020

Background

Patient delay of COVID-19 patients occurs frequently, which poses a challenge to the overall epidemic situation. In this study, we aimed to evaluate the extent of patient delay, explore its factors, and investigate the effects of patient interval on epidemic situation.

Methods

A retrospective cohort study was conducted with 136 COVID-19 patients in Tianjin, China. Factors associated with patient delay were explored using logistic regression models. The relationship was investigated by spearman correlation analysis and mean absolute error between patient interval of lagging days and epidemic situation.

Results

The factors associated with patient delay of COVID-19 patients were mainly the imported cases, the first presentation to a tertiary hospital, close contacts and spatial accessibility to fever clinic. The longer the patient intervals of lagging days, the greater the number of new-onset and confirmed cases in 3–4 and 5–7 days after the first day symptoms, respectively.

Conclusion

Identification and quarantine of close contacts, promoting the spatial accessibility to fever clinics and creating public awareness are crucial to shortening patient delays to flat the curve for COVID-19.

Rapid Diagnostics for Hepatitis B and C Viruses in Low- and Middle-Income Countries

The global health challenge posed by hepatitis B virus (HBV) and hepatitis C virus (HCV) persists, especially in low-and-middle-income countries (LMICs), where underdiagnosis of these viral infections remains a barrier to the elimination target of 2030. HBV and HCV infections are responsible for most liver-related mortality worldwide. Infected individuals are often unaware of their condition and as a result, continue to transmit these viruses. Although conventional diagnostic tests exist, in LMIC they are largely inaccessible due to high costs or a lack of trained personnel, resulting in poor linkage to care and increased infections. Timely and accurate diagnosis is needed to achieve elimination of hepatitis B and C by the year 2030 as set out by the World Health Organization Global Health Sector Strategy. In this review rapid diagnostic tests allowing for quick and cost-effective screening and diagnosis of HBV and HCV, are discussed, as are their features, including suitability, reliability, and applicability in LMIC, particularly those within Africa.

Comparison and Evaluation of Real-Time Taqman PCR for Detection and Quantification of Ebolavirus

Given that ebolavirus causes severe and frequently lethal disease, its rapid and accurate detection using available and validated methods is essential for controlling infection. Real-time reverse-transcription PCR (RT-PCR) has proven to be an invaluable tool for ebolaviruses diagnostics. Many assays with different targets have been developed, but they have not been externally compared or validated, and limits of detection are not uniformly reported. Here we compared and evaluated the sensitivity, reproducibility and specificity of 23 in-house assays under the same conditions. Our results showed that these assays were highly gene- and species- specific when evaluated using in vitro RNA transcripts and viral RNA, and the potential limits of detection were uniformly reported ranging from 102 to 106 in vitro synthesized RNA transcripts copies perμL and 1-100 TCID50/mL. The comparison of these assays indicated that those targeting the more conservative NP gene could be the better option for EVD case definition and quantitative measurement because of its higher sensitivity for the same species. Our analysis could contribute to the standardization of ebolavirus detection and quantification assays, which can offer a better understanding of the meaning of results across laboratories and time points, as well as make them easy to implement, especially under outbreak conditions.

Economic Benefits of Diagnostic Testing in Livestock: Anaplasmosis in Cattle

Anaplasmosis is a costly livestock disease that persists across the United States and the world. While the traditional control options of feed additives, vaccination, and post-infection antibiotic treatments exist, the highly infectious, often asymptomatic onset of anaplasmosis in cattle makes the optimal combination of disease control measures uncertain. Reducing the infection uncertainty through early detection may help producer management decisions and reduce the economic impact of anaplasmosis. To address this, we calculate the costs of applying a range of anaplasmosis control decisions for a representative cow-calf producer in the United States and extend existing analyses to incorporate early detection through diagnostic testing. We use parameters from extant literature, including for mortality, morbidity, and treatment costs to populate a stochastic, dynamic model. Updating the cost estimates finds that production losses account for the majority of anaplasmosis costs, following previous empirical estimates. Using these estimates in our decision model, the outcomes suggest that diagnostic testing with preventative treatments is the optimal herd management strategy. By further framing our findings in the context of three anaplasmosis infection regions in the United States (endemic, disease free, non-endemic buffer), we show that additional considerations exist, which can make sub-optimal control strategies competitive. Our analysis provides an initial exploration of the economic feasibility of diagnostic testing, while helping to assess the burden of anaplasmosis more accurately.

Ultrasensitive point-of-care immunoassay for secreted glycoprotein detects Ebola infection earlier than PCR

Ebola virus (EBOV) hemorrhagic fever outbreaks have been challenging to deter due to the lack of health care infrastructure in disease-endemic countries and a corresponding inability to diagnose and contain the disease at an early stage. EBOV vaccines and therapies have improved disease outcomes, but the advent of an affordable, easily accessed, mass-produced rapid diagnostic test (RDT) that matches the performance of more resource-intensive polymerase chain reaction (PCR) assays would be invaluable in containing future outbreaks. Here, we developed and demonstrated the performance of a new ultrasensitive point-of-care immunoassay, the EBOV D4 assay, which targets the secreted glycoprotein of EBOV. The EBOV D4 assay is 1000-fold more sensitive than the U.S. Food and Drug Administration-approved RDTs and detected EBOV infection earlier than PCR in a standard nonhuman primate model. The EBOV D4 assay is suitable for low-resource settings and may facilitate earlier detection, containment, and treatment during outbreaks of the disease.

Optofluidic Amplification-free Multiplex Detection of Viral Hemorrhagic Fevers

Infectious disease outbreaks such as Ebola and other Viral Hemorrhagic Fevers (VHF) require low-complexity, specific, and differentiated diagnostics as illustrated by the recent outbreak in the Democratic Republic of Congo. Here, we describe amplification-free spectrally multiplex detection of four different VHF total RNA samples using multi-spot excitation on a multimode interference waveguide platform along with combinatorial fluorescence labeling of target nucleic acids. In these experiments, we observed an average of 8-fold greater fluorescence signal amplitudes for the Ebola total RNA sample compared to three other total RNA samples: Lake Victoria Marburg Virus, Ravn Marburg Virus, and Crimean-Congo Hemorrhagic Fever. We have attributed this amplitude amplification to an increased amount of RNA during synthesis of soluble glycoprotein in infection. This hypothesis is confirmed by single molecule detection of the total RNA sample after heat-activated release from the carrier microbeads. From these experiments, we observed at least a 5.3x higher RNA mass loading on the Ebola carrier microbeads compared to the Lake Victoria Marburg carrier microbeads, which is consistent with the known production of soluble glycoprotein during infection.

The Use of Near-Infrared Light-Emitting Fluorescent Nanodiamond Particles to Detect Ebola Virus Glycoprotein: Technology Development and Proof of Principle

Background

There is a dire need for rapid diagnostic tests of high sensitivity, efficiency, and point-of-test reporting capability to mitigate lethal viral epidemic outbreaks.

Purpose

To develop a new operating system within the lateral flow assay (LFA) format for Ebola virus (EBOV), based on fluorescent nanodiamond particles (FNDP) nitrogen vacancy (NV) emitting near-infrared (NIR) light. Specifically, we aimed to detail technical issues and the feasibility of mobilizing FNDP-NV on nitrocellulose membranes (NCM) and capturing them at test and control lines.

Methods

FNDP-NV-200nm, 400nm or 800nm were linked to anti-EBOV glycoprotein (GP) monoclonal antibodies (mAb) and tested for LFA performance by monitoring NIR emissions using an in vivo imaging system or optoelectronic device (OED). Anti-EBOV recombinant glycoprotein (GP) humanized mAb c13C6 was linked to FNDP-NV-200nm for the mobile phase; and a second anti-GP mouse mAb, 6D8, was printed on NCM at the test line. Goat anti-human IgG (GAH-IgG) served as a nonspecific antibody for conjugated FNDP-NV-200nm at the control line.

Results

FNDP-NV-200nm-c13C6 specifically and dose-dependently bound to recombinant EBOV GP in vitro and was effectively captured in a sandwich configuration at the test line by mAb 6D8. FNDP-NV-200nm-c13C6 was captured on the control line by GAH-IgG. The OED quantitative analysis of NIR (obtained in less than 1 minute) was further validated by an in vivo imaging system.

Conclusion

FNDP-NV-200nm performance as a reporter for EBOV GP rapid diagnostic tests suggests an opportunity to replace contemporary visual tests for EBOV GP and other highly lethal viral pathogens. Mobile, battery-operated OED adds portability, quantitative data, rapid data collection, and point-of-test reporting capability. Further development of FNDP-NV-200nm within a LFA format is justified.

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.

Detecting the Coronavirus (COVID-19)

The COVID-19 pandemic has created huge damage to society and brought panic around the world. Such panic can be ascribed to the seemingly deceptive features of COVID-19: Compared to other deadly viral outbreaks, it has medium transmission and mortality rates. As a result, the severity of the causative coronavirus, SARS-CoV-2, was deeply underestimated by society at the beginning of the COVID-19 outbreak. Based on this, in this review, we define the viruses with features similar to those of SARS-CoV-2 as the Panic Zone viruses. To contain those viruses, accurate and fast diagnosis followed by effective isolation and treatment of patients are pivotal at the early stage of virus breakouts. This is especially true when there is no cure or vaccine available for a transmissible disease, which is the case for the current COVID-19 pandemic. As of July 2020, more than 100 kits for COVID-19 diagnosis on the market have been surveyed in this review, while emerging sensing techniques for SARS-CoV-2 are also discussed. It is of critical importance to rationally use these kits for efficient management and control of the Panic Zone viruses. Therefore, we discuss guidelines to select diagnostic kits at different outbreak stages of the Panic Zone viruses, SARS-CoV-2 in particular. While it is of utmost importance to use nucleic acid based detection kits with low false negativity (high sensitivity) at the early stage of an outbreak, the low false positivity (high specificity) gains importance at later stages of the outbreak. When society is set to reopen from the lockdown stage of the COVID-19 pandemic, it becomes critical to have immunoassay based kits with high specificity to identify people who can safely return to society after their recovery from SARS-CoV-2 infections. Finally, since a massive attack from a viral pandemic requires a massive defense from the whole society, we urge both government and the private sector to research and develop affordable and reliable point-of-care testing (POCT) kits, which can be used massively by the general public (and therefore called massive POCT) to contain Panic Zone viruses in the future.

Six decades of lateral flow immunoassay: from determining metabolic markers to diagnosing COVID-19

Technologies based on lateral flow immunoassay (LFIA), known in some countries of the world as immunochromatographic tests, have been successfully used for the last six decades in diagnostics of many diseases and conditions as they allow rapid detection of molecular ligands in biosubstrates. The popularity of these diagnostic platforms is constantly increasing in healthcare facilities, particularly those facing limited budgets and time, as well as in household use for individual health monitoring. The advantages of these low-cost devices over modern laboratory-based analyzers come from their availability, opportunity of rapid detection, and ease of use. The attractiveness of these portable diagnostic tools is associated primarily with their high analytical sensitivity and specificity, as well as with the easy visual readout of results. These qualities explain the growing popularity of LFIA in developing countries, when applied at small hospitals, in emergency situations where screening and monitoring health condition is crucially important, and as well as for self-testing of patients. These tools have passed the test of time, and now LFIA test systems are fully consistent with the world's modern concept of ‘point-of-care testing’, finding a wide range of applications not only in human medicine, but also in ecology, veterinary medicine, and agriculture. The extensive opportunities provided by LFIA contribute to the continuous development and improvement of this technology and to the creation of new-generation formats. This review will highlight the modern principles of design of the most widely used formats of test-systems for clinical laboratory diagnostics, summarize the main advantages and disadvantages of the method, as well as the current achievements and prospects of the LFIA technology. The latest innovations are aimed at improving the analytical performance of LFIA platforms for the diagnosis of bacterial and viral infections, including COVID-19.

Ebola virus disease

Ebola virus disease (EVD) is a severe and frequently lethal disease caused by Ebola virus (EBOV). EVD outbreaks typically start from a single case of probable zoonotic transmission, followed by human-to-human transmission via direct contact or contact with infected bodily fluids or contaminated fomites. EVD has a high case-fatality rate; it is characterized by fever, gastrointestinal signs and multiple organ dysfunction syndrome. Diagnosis requires a combination of case definition and laboratory tests, typically real-time reverse transcription PCR to detect viral RNA or rapid diagnostic tests based on immunoassays to detect EBOV antigens. Recent advances in medical countermeasure research resulted in the recent approval of an EBOV-targeted vaccine by European and US regulatory agencies. The results of a randomized clinical trial of investigational therapeutics for EVD demonstrated survival benefits from two monoclonal antibody products targeting the EBOV membrane glycoprotein. New observations emerging from the unprecedented 2013-2016 Western African EVD outbreak (the largest in history) and the ongoing EVD outbreak in the Democratic Republic of the Congo have substantially improved the understanding of EVD and viral persistence in survivors of EVD, resulting in new strategies toward prevention of infection and optimization of clinical management, acute illness outcomes and attendance to the clinical care needs of patients.

Characterization and analytical validation of a new antigenic rapid diagnostic test for Ebola virus disease detection

Hemorrhagic fever outbreaks are difficult to diagnose and control in part because of a lack of low-cost and easily accessible diagnostic structures in countries where etiologic agents are present. Furthermore, initial clinical symptoms are common and shared with other endemic diseases such as malaria or typhoid fever. Current molecular diagnostic methods such as polymerase chain reaction require trained personnel and laboratory infrastructure, hindering diagnostics at the point of need, particularly in outbreak settings. Therefore, rapid diagnostic tests such as lateral flow can be broadly deployed and are typically well-suited to rapidly diagnose hemorrhagic fever viruses, such as Ebola virus. Early detection and control of Ebola outbreaks require simple, easy-to-use assays that can detect very low amount of virus in blood. Here, we developed and characterized an immunoassay test based on immunochromatography coupled to silver amplification technology to detect the secreted glycoprotein of EBOV. The glycoprotein is among the first viral proteins to be detected in blood. This strategy aims at identifying infected patients early following onset of symptoms by detecting low amount of sGP protein in blood samples. The limit of detection achieved by this sGP-targeted kit is 2.2 x 10⁴ genome copies/ml in plasma as assayed in a monkey analytical cohort. Clinical performance evaluation showed a specificity of 100% and a sensitivity of 85.7% when evaluated with plasma samples from healthy controls and patients infected with Zaire Ebola virus from Macenta, Guinea. This rapid and accurate diagnostic test could therefore be used in endemic countries for early detection of infected individuals in point of care settings. Moreover, it could also support efficient clinical triage in hospitals or clinical centers and thus reducing transmission rates to prevent and better manage future severe outbreaks.

Ebola virus disease is a severe disease caused by Ebola virus, a member of the filovirus family, which occurs in humans and other primates. Ebola is believed to be zoonotic, however the natural reservoir is unknown. Overlapping symptoms with other endemic diseases, such as malaria and cholera, make accurate diagnostic challenging. Outbreaks of Ebola have been widespread as the consequence of the absence of available rapid, sensitive, specific, robust, and affordable licensed diagnostic test in remote areas, where outbreaks usually start. Here we have established and validated a rapid diagnostic test, which is fast, sensitive, specific, efficient, affordable, and user-friendly. Its analytical characteristics make it suitable for clinical management during Ebola virus outbreaks in remote areas. Of interest, this rapid diagnostic test detects the presence of an early viral antigen, the secreted glycoprotein, found in blood of patients shortly after infection, suggesting that it could be used to identify infected patients shortly after onset of symptoms.

Bi-stability of SUDR+K model of epidemics and test kits applied to COVID-19

Motivated by the many diverse responses of different countries to the COVID-19 emergency, here we develop a toy model of the dependence of the epidemics spreading on the availability of tests for disease. Our model, that we call SUDR+K, grounds on the usual SIR model, with the difference of splitting the total fraction of infected individuals in two components: patients that are still undetected and patients that have been already detected through tests. Moreover, we assume that available tests increase at a constant rate from the beginning of epidemics but are consumed to detect infected individuals. Strikingly, we find a bi-stable behavior between a phase with a giant fraction of infected and a phase with a very small fraction. We show that the separation between these two regimes is governed by a match between the rate of testing and a rate of infection spread at given time. We also show that the existence of two phases does not depend on the mathematical choice of the form of the term describing the rate at which undetected individuals are tested and detected. Presented research implies that a vigorous early testing activity, before the epidemics enters its giant phase, can potentially keep epidemics under control, and that even a very small change of the testing rate around the bi-stable point can determine a fluctuation of the size of the whole epidemics of various orders of magnitude. For the real application of realistic model to ongoing epidemics, we would gladly collaborate with field epidemiologists in order to develop quantitative models of testing process.

Presentation and Treatment Outcomes of Liberian Children Age 5 Years and Under Diagnosed With Severe Malaria

Malaria is endemic in Liberia with a prevalence rate of up to 60% in some regions, and it has been a major cause of death in children under 5 years of age. Prior to the recent Ebola epidemic, we undertook a prospective, hospital-based pilot study at the National Referral Hospital in Monrovia, to characterize the presentation, accuracy of diagnosis, and treatment outcomes of children presenting for treatment of malaria. From June 2013 to May 2014, we recruited children 5 years and under who presented to the JFK Medical Center with suspected malaria. We collected both clinical and laboratory data on admission and on discharge. We enrolled 477 patients with an average age of 1.6 years. Demographic factors associated with testing negative for malaria included regular bed net use and prior treatment for malaria. The most common presenting symptoms of severe malaria in this population were headache and seizures. Of 246 patients admitted and treated for severe malaria, 33% tested negative by rapid diagnostic test and blood smear for malaria. The case fatality rate was higher for the patients who tested negative for malaria (4.9%) versus those who tested positive (0.6%). Three children who tested negative for malaria showed evidence of undiagnosed Salmonella typhi infection. These results suggest that malaria may be overdiagnosed and that the diagnoses of other infectious diseases, which present in a similar fashion, may be neglected. These findings underscore the need to develop rapid diagnostic tests to screen for alternative causes of febrile illness.

A Rational Explanation of Limited FMD Vaccine Uptake in Endemic Regions

Vaccination for foot-and-mouth (FMD) disease remains low in parts of Africa despite the existence of vaccines. In East Africa, the presence of multiple virus serotypes and sub-types makes matching a vaccine with the circulating virus type in the field, or providing a high potency vaccine, a challenge. In this paper we use game theory to show that the resulting vaccine uncertainty associated with these vaccination conditions in an endemic setting help explain the low vaccine uptake. We evaluate vaccination for FMD in the context of East Africa due to FMD being endemic in the region, the diversity of FMD virus types, and barriers to implementing other disease control measures, such as controlled movements. We incorporate these conditions into a vaccination game setting and compare the payoffs to those of a traditional vaccination game for seasonal influenza and commercial livestock vaccination in a developed country context. In showing that vaccination provides households with a lower payoff than not vaccinating, our simple game theoretical explanation supports existing evidence calling for improved vaccine quality and efforts to enhance surveillance to provide early information on disease status.

An overview of RNA virus-encoded microRNAs

MicroRNAs (miRNAs) are a number of small non-coding RNAs playing a regulatory part in gene expression. Many virus-encoded miRNAs have been found, which manifests that viruses as well apply the basic pattern of gene regulation, however, mostly in viruses transcribed from double-stranded DNA genomes. It is still in dispute if RNA viruses could encode miRNAs because the excision of miRNA might result in the cleavage of viral RNA genome. We will focus on the miRNAs encoded by RNA virus and discuss their potential role in viral replication cycle and host cells.

Lassa fever diagnostics: past, present, and future

Lassa fever is a unique viral hemorrhagic fever that is endemic in parts of West Africa, primarily Sierra Leone, Guinea, Liberia, and Nigeria. The disease is caused by the Lassa virus, an Old World arenavirus that has as primary reservoir host the multimammate rodent Mastomys nataliensis, which lives in association with humans. Recent estimates suggest LF causes two million cases and 5000-10000 deaths annually, mainly in West Africa. Clinical diagnosis and laboratory confirmation have always been major challenges for effective management and control of the disease in afflicted areas of West Africa. Recent advancements in molecular biology, recombinant DNA technology, and genomics sequencing has facilitated major advancement in development of better diagnostic and surveillance tools for Lassa fever virus. These include, the multiplex, magnetic bead-based immunodiagnostics for both Lassa virus antigens and antibodies; molecular probe-based quantitative real-time PCR for genomic signatures; rapid diagnostics tests that detects the most prevalent West African lineages; and the successful utilization of next-generation sequencing technology to diagnose and characterize Lassa virus in West Africa. These advances will continue to improve disease treatment, control, and prevention. In this review we will discuss progression of Lassa virus diagnostics from the past and into the future.

Outbreak analytics: a developing data science for informing the response to emerging pathogens

Despite continued efforts to improve health systems worldwide, emerging pathogen epidemics remain a major public health concern. Effective response to such outbreaks relies on timely intervention, ideally informed by all available sources of data. The collection, visualization and analysis of outbreak data are becoming increasingly complex, owing to the diversity in types of data, questions and available methods to address them. Recent advances have led to the rise of outbreak analytics, an emerging data science focused on the technological and methodological aspects of the outbreak data pipeline, from collection to analysis, modelling and reporting to inform outbreak response. In this article, we assess the current state of the field. After laying out the context of outbreak response, we critically review the most common analytics components, their inter-dependencies, data requirements and the type of information they can provide to inform operations in real time. We discuss some challenges and opportunities and conclude on the potential role of outbreak analytics for improving our understanding of, and response to outbreaks of emerging pathogens. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.

Ultrasensitive Ebola Virus Antigen Sensing via 3D Nanoantenna Arrays

Sensitive detection of pathogens is crucial for early disease diagnosis and quarantine, which is of tremendous need in controlling severe and fatal illness epidemics such as of Ebola virus (EBOV) disease. Serology assays can detect EBOV-specific antigens and antibodies cost-effectively without sophisticated equipment; however, they are less sensitive than reverse transcriptase polymerase chain reaction (RT-PCR) tests. Herein, a 3D plasmonic nanoantenna assay sensor is developed as an on-chip immunoassay platform for ultrasensitive detection of Ebola virus (EBOV) antigens. The EBOV sensor exhibits substantial fluorescence intensity enhancement in immunoassays compared to flat gold substrate. The nanoantenna-based biosensor successfully detects EBOV soluble glycoprotein (sGP) in human plasma down to 220 fg mL^-1 , a significant 240 000-fold sensitivity improvement compared to the 53 ng mL^-1 EBOV antigen detection limit of the existing rapid EBOV immunoassay. In a mock clinical trial, the sensor detects sGP-spiked human plasma samples at two times the limit of detection with 95.8% sensitivity. The results combined highlight the nanosensor's extraordinary capability of detecting EBOV antigen at ultralow concentration compared to existing immunoassay methods. It is a promising next-generation bioassay platform for early-stage disease diagnosis and pathogen detection for both public health and national security applications.

Recent advances in the development and evaluation of molecular diagnostics for Ebola virus disease

INTRODUCTION

The 2014-16 outbreak of ebola virus disease (EVD) in West Africa resulted in 11,308 deaths. During the outbreak only 60% of patients were laboratory confirmed and global health authorities have identified the need for accurate and readily deployable molecular diagnostics as an important component of the ideal response to future outbreaks, to quickly identify and isolate patients. Areas covered: Currently PCR-based techniques and rapid diagnostic tests (RDTs) that detect antigens specific to EVD infections dominate the diagnostic landscape, but recent advances in biosensor technologies have led to novel approaches for the development of EVD diagnostics. This review summarises the literature and available performance data of currently available molecular diagnostics for ebolavirus, identifies knowledge gaps and maps out future priorities for research in this field. Expert opinion: While there are now a plethora of diagnostic tests for EVD at various stages of development, there is an acute need for studies to compare their clinical performance, but the sporadic nature of EVD outbreaks makes this extremely challenging, demanding pragmatic new modalities of research funding and ethical/institutional approval, to enable responsive research in outbreak settings. Retrospective head-to-head diagnostic comparisons could also be implemented using biobanked specimens, providing this can be done safely.

Comparative performance of four rapid Ebola antigen-detection lateral flow immunoassays during the 2014-2016 Ebola epidemic in West Africa

Background

Without an effective vaccine, as was the case early in the 2014–2016 Ebola Outbreak in West Africa, disease control depends entirely on interrupting transmission through early disease detection and prompt patient isolation. Lateral Flow Immunoassays (LFI) are a potential supplement to centralized reference laboratory testing for the early diagnosis of Ebola Virus Disease (EVD).

The goal of this study was to assess the performance of commercially available simple and rapid antigen detection LFIs, submitted for review to the WHO via the Emergency Use Assessment and Listing procedure. The study was performed in an Ebola Treatment Centre laboratory involved in EVD testing in Sierra Leone.

In light of the current Ebola outbreak in May 2018 in the Democratic Republic of Congo, which highlights the lack of clarity in the global health community about appropriate Ebola diagnostics, our findings are increasingly critical.

Methods

A cross-sectional study was conducted to assess comparative performance of four LFIs for detecting EVD. LFIs were assessed against the same 328 plasma samples and 100 whole EDTA blood samples, using the altona RealStar Filovirus Screen real-time RT-PCR as the bench mark assay. The performance of the Public Health England (PHE) in-house Zaire ebolavirus-specific real time RT-PCR Trombley assay was concurrently assessed. Statistical analysis using generalized estimating equations was conducted to compare LFI performance.

Findings

Sensitivity and specificity varied between the LFIs, with specificity found to be significantly higher for whole EDTA blood samples compared to plasma samples in at least 2 LFIs (P≤0.003). Using the altona RT-PCR assay as the bench mark, sensitivities on plasma samples ranged from 79.53% (101/127, 95% CI: 71.46–86.17%) for the DEDIATEST EBOLA (SD Biosensor) to 98.43% (125/127, 95% CI: 94.43–99.81%) for the One step Ebola test (Intec). Specificities ranged from 80.20% (158/197, 95% CI: 74.07–88.60%) for plasma samples using the ReEBOV Antigen test Kit (Corgenix) to 100.00% (98/98, 95% CI: 96.31–100.00%) for whole blood samples using the DEDIATEST EBOLA (SD Biosensor) and SD Ebola Zaire Ag (SD Biosensor). Results also showed the Trombley RT-PCR assay had a lower limit of detection than the altona assay, with some LFIs having higher sensitivity than the altona assay when the Trombley assay was the bench mark.

Interpretation

All of the tested EVD LFIs may be considered suitable for use in an outbreak situation (i.e. rule out testing in communities), although they had variable performance characteristics, with none possessing both high sensitivity and specificity. The non-commercial Trombley Zaire ebolavirus RT-PCR assay warrants further investigation, as it appeared more sensitive than the current gold standard, the altona Filovirus Screen RT-PCR assay.

Development of a Pediatric Ebola Predictive Score, Sierra Leone1

We compared children who were positive for Ebola virus disease (EVD) with those who were negative to derive a pediatric EVD predictor (PEP) score. We collected data on all children <13 years of age admitted to 11 Ebola holding units in Sierra Leone during August 2014–March 2015 and performed multivariable logistic regression. Among 1,054 children, 309 (29%) were EVD positive and 697 (66%) EVD negative, with 48 (5%) missing. Contact history, conjunctivitis, and age were the strongest positive predictors for EVD. The PEP score had an area under receiver operating characteristics curve of 0.80. A PEP score of 7/10 was 92% specific and 44% sensitive; 3/10 was 30% specific, 94% sensitive. The PEP score could correctly classify 79%–90% of children and could be used to facilitate triage into risk categories, depending on the sensitivity or specificity required.

Ébola, abordaje clínico integral

Introducción. El virus del Ébola, antes llamado fiebre hemorrágica del Ébola, es una enfermedad altamente contagiosa con mortalidad entre 50% y 90%, para la cual existen prometedoras opciones de tratamiento que se encuentran en fase de evaluación y uso compasional.Objetivos. Revisar la mejor evidencia médica publicada y analizar el comportamiento de las epidemias por virus del Ébola, sus manifestaciones clínicas, sus complicaciones, los elementos más significativos para su diagnóstico y las nuevas opciones terapéuticas disponibles, para así aprender y aplicar estas experiencias en nuevos brotes.Materiales y métodos. Se realizó una búsqueda sistemática en las bases de datos PubMed, ProQuest, Embase, Redalyc, Ovid, Medline, DynaMed y ClinicalKey durante el periodo 2009-2017 en el contexto internacional, regional y local.Resultados. La revisión sistemática de artículos aportó un total de 51 430 registros, de los cuales 772 eran elegibles; de estos, 722 no eran relevantes, por lo que quedaron incluidos 50. A punto de partida se pudieron precisar los aspectos objeto de esta revisión.Conclusión. La enfermedad causada por el virus del Ébola, a pesar de su alta mortalidad, puede ser prevenida, diagnosticada oportunamente y tratada con efectividad, lo cual permite evaluar su impacto epidemiológico en las áreas endémicas y a nivel mundial. Existe un potencial arsenal terapéutico en fase de experimentación con resultados prometedores.

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

Genetic analyses have provided important insights into Ebola virus spread during the recent West African outbreak, but their implications for specific intervention scenarios remain unclear. Here, we address this issue using a collection of phylodynamic approaches. We show that long-distance dispersal events were not crucial for epidemic expansion and that preventing viral lineage movement to any given administrative area would, in most cases, have had little impact. However, major urban areas were critical in attracting and disseminating the virus: preventing viral lineage movement to all three capitals simultaneously would have contained epidemic size to one-third. We also show that announcements of border closures were followed by a significant but transient effect on international virus dispersal. By quantifying the hypothetical impact of different intervention strategies, as well as the impact of barriers on dispersal frequency, our study illustrates how phylodynamic analyses can help to address specific epidemiological and outbreak control questions.

During the last Ebola virus outbreak in West Africa, a large amount of viral genomic data was obtained. Here, Dellicour et al. use phylodynamic approaches to assess effect of intervention strategies such as border closures.

Criteria required for an acceptable point-of-care test for UTI detection: Obtaining consensus using the Delphi technique

BACKGROUND

Urinary Tract Infections (UTIs) are common bacterial infections, second only to respiratory tract infections and particularly prevalent within primary care. Conventional detection of UTIs is culture, however, return of results can take between 24 and 72 hours. The introduction of a point of care (POC) test would allow for more timely identification of UTIs, facilitating improved, targeted treatment. This study aimed to obtain consensus on the criteria required for a POC UTI test, to meet patient need within primary care.

METHODS

Criteria for consideration were compiled by the research team. These criteria were validated through a two-round Delphi process, utilising an expert panel of healthcare professionals from across Europe and United States of America. Using web-based questionnaires, panellists recorded their level of agreement with each criterion based on a 5-point Likert Scale, with space for comments. Using median response, interquartile range and comments provided, criteria were accepted/rejected/revised depending on pre-agreed cut-off scores.

RESULTS

The first round questionnaire presented thirty-three criteria to the panel, of which 22 were accepted. Consensus was not achieved for the remaining 11 criteria. Following response review, one criterion was removed, while after revision, the remaining 10 criteria entered the second round. Of these, four were subsequently accepted, resulting in 26 criteria considered appropriate for a POC test to detect urinary infections.

CONCLUSION

This study generated an approved set of criteria for a POC test to detect urinary infections. Criteria acceptance and comments provided by the healthcare professionals also supports the development of a multiplex point of care UTI test.

epicontacts: Handling, visualisation and analysis of epidemiological contacts

Epidemiological outbreak data is often captured in line list and contact format to facilitate contact tracing for outbreak control. epicontacts is an R package that provides a unique data structure for combining these data into a single object in order to facilitate more efficient visualisation and analysis. The package incorporates interactive visualisation functionality as well as network analysis techniques. Originally developed as part of the Hackout3 event, it is now developed, maintained and featured as part of the R Epidemics Consortium (RECON). The package is available for download from the Comprehensive R Archive Network (CRAN) and GitHub.

epicontacts: Handling, visualisation and analysis of epidemiological contacts

Epidemiological outbreak data is often captured in line list and contact format to facilitate contact tracing for outbreak control. epicontacts is an R package that provides a unique data structure for combining these data into a single object in order to facilitate more efficient visualisation and analysis. The package incorporates interactive visualisation functionality as well as network analysis techniques. Originally developed as part of the Hackout3 event, it is now developed, maintained and featured as part of the R Epidemics Consortium (RECON). The package is available for download from the Comprehensive R Archive Network (CRAN) and GitHub.

Virus-encoded miRNAs in Ebola virus disease

Ebola virus (EBOV) is a negative-strand RNA virus that replicates in the cytoplasm and causes an often-fatal hemorrhagic fever. EBOV, like other viruses, can reportedly encode its own microRNAs (miRNAs) to subvert host immune defenses. miRNAs are short noncoding RNAs that can regulate gene expression by hybridizing to multiple mRNAs, and viral miRNAs can enhance viral replication and infectivity by regulating host or viral genes. To date, only one EBOV miRNA has been examined in human infection. Here, we assayed mouse, rhesus macaque, cynomolgus macaque, and human samples infected with three EBOV variants for twelve computationally predicted viral miRNAs using RT-qPCR. Ten miRNAs aligned to EBOV variants and were detectable in the four species during disease with several viral miRNAs showing presymptomatic amplification in animal models. miRNA abundances in both the mouse and nonhuman primate models mirrored the human cohort, with miR-1-5p, miR-1-3p, and miR-T3-3p consistently at the highest levels. These striking similarities in the most abundant miRNAs during infection with different EBOV variants and hosts indicate that these miRNAs are potential valuable diagnostic markers and key effectors of EBOV pathogenesis.

Field validation of recombinant antigen immunoassays for diagnosis of Lassa fever

Lassa fever, a hemorrhagic fever caused by Lassa virus (LASV), is endemic in West Africa. It is difficult to distinguish febrile illnesses that are common in West Africa from Lassa fever based solely on a patient’s clinical presentation. The field performance of recombinant antigen-based Lassa fever immunoassays was compared to that of quantitative polymerase chain assays (qPCRs) using samples from subjects meeting the case definition of Lassa fever presenting to Kenema Government Hospital in Sierra Leone. The recombinant Lassa virus (ReLASV) enzyme-linked immunosorbant assay (ELISA) for detection of viral antigen in blood performed with 95% sensitivity and 97% specificity using a diagnostic standard that combined results of the immunoassays and qPCR. The ReLASV rapid diagnostic test (RDT), a lateral flow immunoassay based on paired monoclonal antibodies to the Josiah strain of LASV (lineage IV), performed with 90% sensitivity and 100% specificity. ReLASV immunoassays performed better than the most robust qPCR currently available, which had 82% sensitivity and 95% specificity. The performance characteristics of recombinant antigen-based Lassa virus immunoassays indicate that they can aid in the diagnosis of LASV Infection and inform the clinical management of Lassa fever patients.

A rapid bio-optical sensor for diagnosing Q fever in clinical specimens

Recent zoonotic outbreaks, such as Zika, Middle East respiratory syndrome and Ebola, have highlighted the need for rapid and accurate diagnostic assays that can be used to aid pathogen control. Q fever is a zoonotic disease caused by the transmission of Coxiella burnetii that can cause serious illness in humans through aerosols and is considered a potential bioterrorism agent. However, the existing assays are not suitable for the detection of this pathogen due to its low levels in real samples. We here describe a rapid bio-optical sensor for the accurate detection of Q fever and validate its clinical utility. By combining a bio-optical sensor, that transduces the presence of the target DNA based on binding-induced changes in the refractive index on the waveguide surface in a label-free and real-time manner, with isothermal DNA amplification, this new diagnostic tool offers a rapid (<20 min), 1-step DNA amplification/detection method. We confirmed the clinical sensitivity (>90%) of the bio-optical sensor by detecting C. burnetii in 11 formalin-fixed, paraffin-embedded liver biopsy samples from acute Q fever hepatitis patients and in 16 blood plasma samples from patients in which Q fever is the cause of fever of unknown origin.

Clinical bacteriology in low-resource settings: today's solutions

Low-resource settings are disproportionately burdened by infectious diseases and antimicrobial resistance. Good quality clinical bacteriology through a well functioning reference laboratory network is necessary for effective resistance control, but low-resource settings face infrastructural, technical, and behavioural challenges in the implementation of clinical bacteriology. In this Personal View, we explore what constitutes successful implementation of clinical bacteriology in low-resource settings and describe a framework for implementation that is suitable for general referral hospitals in low-income and middle-income countries with a moderate infrastructure. Most microbiological techniques and equipment are not developed for the specific needs of such settings. Pending the arrival of a new generation diagnostics for these settings, we suggest focus on improving, adapting, and implementing conventional, culture-based techniques. Priorities in low-resource settings include harmonised, quality assured, and tropicalised equipment, consumables, and techniques, and rationalised bacterial identification and testing for antimicrobial resistance. Diagnostics should be integrated into clinical care and patient management; clinically relevant specimens must be appropriately selected and prioritised. Open-access training materials and information management tools should be developed. Also important is the need for onsite validation and field adoption of diagnostics in low-resource settings, with considerable shortening of the time between development and implementation of diagnostics. We argue that the implementation of clinical bacteriology in low-resource settings improves patient management, provides valuable surveillance for local antibiotic treatment guidelines and national policies, and supports containment of antimicrobial resistance and the prevention and control of hospital-acquired infections.

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.

The contribution of biological, mathematical, clinical, engineering and social sciences to combatting the West African Ebola epidemic

The tragic West African Ebola epidemic claimed many lives, but would have been worse still if scientific insights from many disciplines had not been integrated to create a strong technical response. Epidemiology and modelling triggered the international response and guided where response efforts were directed; virology, engineering and clinical science helped reduce deaths and transmission in and from hospitals and treatment centres; social sciences were key to reducing deaths from funerals and in the community; diagnostic and operational research made the response more efficient; immunology and vaccine research contributed to the final stages of the epidemic and will help prevent future epidemics. These varied scientific contributions had to be integrated into a combined narrative, communicated to policymakers to inform decisions, and used by courageous local and international responders in the field in real time. Not every area of science was optimal, and in particular, clinical trials of simple interventions such as fluid management were slow to be adopted and sharing of data was initially poor. This Ebola epidemic demonstrated how science can respond to a major emergency, but also has lessons for better responses in future infectious emergencies.This article is part of the themed issue 'The 2013-2016 West African Ebola epidemic: data, decision-making and disease control'.