Using natural language processing for automated classification of disease and to identify misclassified ICD codes in cardiac disease.

Aims: ICD codes are used for classification of hospitalizations. The codes are used for administrative, financial, and research purposes. It is known, however, that errors occur. Natural language processing (NLP) offers promising solutions for optimizing the process. To investigate methods for automatic classification of disease in unstructured medical records using NLP and to compare these to conventional ICD coding. Methods and results: Two datasets were used: the open-source Medical Information Mart for Intensive Care (MIMIC)-III dataset (n = 55.177) and a dataset from a hospital in Belgium (n = 12.706). Automated searches using NLP algorithms were performed for the diagnoses 'atrial fibrillation (AF)' and 'heart failure (HF)'. Four methods were used: rule-based search, logistic regression, term frequency-inverse document frequency (TF-IDF), Extreme Gradient Boosting (XGBoost), and Bio-Bidirectional Encoder Representations from Transformers (BioBERT). All algorithms were developed on the MIMIC-III dataset. The best performing algorithm was then deployed on the Belgian dataset. After preprocessing a total of 1438 reports was retained in the Belgian dataset. XGBoost on TF-IDF matrix resulted in an accuracy of 0.94 and 0.92 for AF and HF, respectively. There were 211 mismatches between algorithm and ICD codes. One hundred and three were due to a difference in data availability or differing definitions. In the remaining 108 mismatches, 70% were due to incorrect labelling by the algorithm and 30% were due to erroneous ICD coding (2% of total hospitalizations). Conclusion: A newly developed NLP algorithm attained a high accuracy for classifying disease in medical records. XGBoost outperformed the deep learning technique BioBERT. NLP algorithms could be used to identify ICD-coding errors and optimize and support the ICD-coding process.

Multiomic analysis in fibroblasts of patients with inborn errors of cobalamin metabolism reveals concordance with clinical and metabolic variability.

BACKGROUND: The high variability in clinical and metabolic presentations of inborn errors of cobalamin (cbl) metabolism (IECM), such as the cblC/epicblC types with combined deficits in methylmalonyl-coA mutase (MUT) and methionine synthase (MS), are not well understood. They could be explained by the impaired expression/activity of enzymes from other metabolic pathways. METHODS: We performed metabolomic, genomic, proteomic, and post-translational modification (PTM) analyses in fibroblasts from three cblC cases and one epi-cblC case compared with three cblG cases with specific MS deficits and control fibroblasts. FINDINGS: CblC patients had metabolic profilings consistent with altered urea cycle, glycine, and energy mitochondrial metabolism. Metabolomic analysis showed partial disruption and increased glutamate/ketoglutarate anaplerotic pathway of the tricarboxylic acid cycle (TCA), in patient fibroblasts. RNA-seq analysis showed decreased expression of MT-TT (mitochondrial tRNA threonine), MT-TP (mitochondrial tRNA proline), OXCT1 (succinyl CoA:3-oxoacid CoA transferase deficiency), and MT-CO1 (cytochrome C oxidase subunit 1). Proteomic changes were observed for key mitochondrial enzymes, including NADH:ubiquinone oxidoreductase subunit A8 (NDUFA8), carnitine palmitoyltransferase 2 (CPT2), and ubiquinol-cytochrome C reductase, complex III subunit X (UQCR10). Propionaldehyde addition in ornithine aminotransferase was the predominant PTM in cblC cells and could be related with the dramatic cellular increase in propionate and methylglyoxalate. It is consistent with the decreased concentration of ornithine reported in 3 cblC cases. Whether the changes detected after multi-omic analyses underlies clinical features in cblC and cblG types of IECM, such as peripheral and central neuropathy, cardiomyopathy, pulmonary hypertension, development delay, remains to be investigated. INTERPRETATION: The omics-related effects of IECM on other enzymes and metabolic pathways are consistent with the diversity and variability of their age-related metabolic and clinical manifestations. PTMs are expected to produce cumulative effects, which could explain the influence of age on neurological manifestations. FUNDING: French Agence Nationale de la Recherche (Projects PREDICTS and EpiGONE) and Inserm.

Characterization of a Panel of Cross-Reactive Hantavirus Nucleocapsid Protein-Specific Monoclonal Antibodies.

Hantaviruses are emerging pathogens with a worldwide distribution that can cause life-threatening diseases in humans. Monoclonal antibodies (MAbs) against hantavirus nucleocapsid (N) proteins are important tools in virus diagnostics, epidemiological studies and basic research studies on virus replication and pathogenesis. Here, we extend the collection of previously generated MAbs raised against a segment of Puumala orthohantavirus (PUUV) N protein harbored on virus-like particles (VLPs) and MAbs against N proteins of Sin Nombre orthohantavirus/Andes orthohantavirus by generating nine novel MAbs against N proteins of Dobrava-Belgrade orthohantavirus (DOBV), Tula orthohantavirus (TULV), Thottapalayam thottimvirus (TPMV) and PUUV. In order to have a wide collection of well-described hantavirus-specific MAbs, the cross-reactivity of novel and previously generated MAbs was determined against N proteins of 15 rodent- and shrew-borne hantaviruses by different immunological methods. We found that all MAbs, excluding TPMV-specific MAbs, demonstrated different cross-reactivity patterns with N proteins of hantaviruses and recognized native viral antigens in infected mammalian cells. This well-characterized collection of cross-reactive hantavirus-specific MAbs has a potential application in various fields of hantavirus research, diagnostics and therapy.

Red deer reveal spatial risks of Crimean-Congo haemorrhagic fever virus infection.

Crimean-Congo haemorrhagic fever virus (CCHFV) continues to cause new human cases in Iberia while its spatial distribution and ecological determinants remain unknown. The virus remains active in a silent tick-animal cycle to which animals contribute maintaining the tick populations and the virus itself. Wild ungulates, in particular red deer, are essential hosts for Hyalomma ticks in Iberia, which are the principal competent vector of CCHFV. Red deer could be an excellent model to understand the ecological determinants of CCHFV as well as to predict infection risks for humans because it is large, gregarious, abundant and the principal host for Hyalomma lusitanicum. We designed a cross-sectional study, analysed the presence of CCHFV antibodies in 1444 deer from 82 populations, and statistically modelled exposure risk with host and environmental predictors. The best-fitted statistical model was projected for peninsular Spain to map infection risks. Fifty out of 82 deer populations were seropositive, with individual population prevalence as high as 88%. The highest prevalence of exposure to CCHFV occurred in the southwest of the Iberian Peninsula. Climate and ungulate abundance were the most influential predictors of the risk of exposure to the virus. The highest risk regions were those where H. lusitanicum is most abundant. Eight of the nine primary human cases occurred in or bordering these regions, demonstrating that the model predicts human infection risk accurately. A recent human case of CCHF occurred in northwestern Spain, a region that the model predicted as low risk, pointing out that it needs improvement to capture all determinants of the CCHFV infection risk. In this study, we have been able to identify the main ecological determinants of CCHFV, and we have also managed to create an accurate model to assess the risk of CCHFV infection.

E-mental health implementation in inpatient care: Exploring its potential and future challenges.

Background: There is a great evidence base today for the effectiveness of e-mental health, or the use of technology in mental healthcare. However, large-scale implementation in mental healthcare organisations is lacking, especially in inpatient specialized mental healthcare settings. Aim: The current study aimed to gain insights into the factors that promote or hinder the implementation of e-mental health applications on organisational, professional and patient levels in Belgium. Methods: Four Belgian psychiatric hospitals and psychiatric departments of general hospitals invited their professionals and patients to use Moodbuster, which is a modular web-based platform with a connected smartphone application for monitoring. The platform was used in addition to treatment as usual for three to four months. The professionals and patients completed pre- and post-implementation questionnaires on their reasons to participate or to decline participation and experiences with the Moodbuster platform. Results: Main reasons for the organisations to participate in the implementation study were a general interest in e-mental health and seeing it is a helpful add-on to regular treatment. The actual use of Moodbuster by professionals and patients proved to be challenging with only 10 professionals and 24 patients participating. Implementation was hindered by technical difficulties and inpatient care specific factors such as lack of structural facilities to use e-mental health and patient-specific factors. Professionals saw value in using e-mental health applications for bridging the transition from inpatient to outpatient care. Twenty-two professionals and 31 patients completed the questionnaire on reasons not to participate. For the patients, lack of motivation because of too severe depressive symptoms was the most important reason not to participate. For professionals, it was lack of time and high workload. Conclusions: The current implementation study reveals several important barriers to overcome in order to successfully implement e-mental health in inpatient psychiatric care.

Motion Sensor-Based Detection of Outlier Days Supporting Continuous Health Assessment for Single Older Adults.

The aging population has resulted in interest in remote monitoring of elderly individuals' health and well being. This paper describes a simple unsupervised monitoring system that can automatically detect if an elderly individual's pattern of presence deviates substantially from the recent past. The proposed system uses a small set of low-cost motion sensors and analyzes the produced data to establish an individual's typical presence pattern. Then, the algorithm uses a distance function to determine whether the individual's observed presence for each day significantly deviates from their typical pattern. Empirically, the algorithm is validated on both synthetic data and data collected by installing our system in the residences of three older individuals. In the real-world setting, the system detected, respectively, five, four, and one deviating days in the three locations. The deviating days detected by the system could result from a health issue that requires attention. The information from the system can aid caregivers in assessing the subject's health status and allows for a targeted intervention. Although the system can be refined, we show that otherwise hidden but relevant events (e.g., fall incident and irregular sleep patterns) are detected and reported to the caregiver.

Artificial intelligence supported patient self-care in chronic heart failure: a paradigm shift from reactive to predictive, preventive and personalised care.

Heart failure (HF) is one of the most complex chronic disorders with high prevalence, mainly due to the ageing population and better treatment of underlying diseases. Prevalence will continue to rise and is estimated to reach 3% of the population in Western countries by 2025. It is the most important cause of hospitalisation in subjects aged 65 years or more, resulting in high costs and major social impact. The current "one-size-fits-all" approach in the treatment of HF does not result in best outcome for all patients. These facts are an imminent threat to good quality management of patients with HF. An unorthodox approach from a new vision on care is required. We propose a novel predictive, preventive and personalised medicine approach where patients are truly leading their management, supported by an easily accessible online application that takes advantage of artificial intelligence. This strategy paper describes the needs in HF care, the needed paradigm shift and the elements that are required to achieve this shift. Through the inspiring collaboration of clinical and high-tech partners from North-West Europe combining state of the art HF care, artificial intelligence, serious gaming and patient coaching, a virtual doctor is being created. The results are expected to advance and personalise self-care, where standard care tasks are performed by the patients themselves, in principle without involvement of healthcare professionals, the latter being able to focus on complex conditions. This new vision on care will significantly reduce costs per patient while improving outcomes to enable long-term sustainability of top-level HF care.

Laboratory Findings, Compassionate Use of Favipiravir, and Outcome in Patients With Ebola Virus Disease, Guinea, 2015-A Retrospective Observational Study.

BACKGROUND: In 2015, the laboratory at the Ebola treatment center in Coyah, Guinea, confirmed Ebola virus disease (EVD) in 286 patients. The cycle threshold (Ct) of an Ebola virus-specific reverse transcription-polymerase chain reaction assay and 13 blood chemistry parameters were measured on admission and during hospitalization. Favipiravir treatment was offered to patients with EVD on a compassionate-use basis. METHODS: To reduce biases in the raw field data, we carefully selected 163 of 286 patients with EVD for a retrospective study to assess associations between potential risk factors, alterations in blood chemistry findings, favipiravir treatment, and outcome. RESULTS: The case-fatality rate in favipiravir-treated patients was lower than in untreated patients (42.5% [31 of 73] vs 57.8% [52 of 90]; P = .053 by univariate analysis). In multivariate regression analysis, a higher Ct and a younger age were associated with survival (P < .001), while favipiravir treatment showed no statistically significant effect (P = .11). However, Kaplan-Meier analysis indicated a longer survival time in the favipiravir-treated group (P = .015). The study also showed characteristic changes in blood chemistry findings in patients who died, compared with survivors. CONCLUSIONS: Consistent with the JIKI trial, this retrospective study revealed a trend toward improved survival in favipiravir- treated patients; however, the effect of treatment was not statistically significant, except for its influence on survival time.

Use of wearable technology to quantify fall risk in psychogeriatric environments: a feasability study.

Fall incidents with elderly suffering from psychological pathologies, in combination with a comorbidity of clinical problems are highly prevalent. In our research setting, the psychiatric hospital OPZ in Geel, Belgium, 1790 fall incidents were recorded with 283 patients since 2013. The nature of the patients' profiles makes a valid, objective fall risk assessment very difficult; for them, instructions to perform the tests are difficult to understand and execute. Therefore, the currently used instruments are not suited for this complex situation. In this study we propose an alternative system for the assessment of fall risk for patients of a psychogeriatric ward. We also study the essential precautions needed for acceptance of wearables in this complex setting.We collected individual daily mean gait speeds of 17 patients at a psychogeriatric ward over a period of five months. We show that it is possible, using wearable technology, to measure individual gait speed. We also show that it is possible to have the wearable technology accepted by the target group. The results obtained so far are promising to use automatical gait measurement to correlate to the currently used risk assessment tests and to eventually replace these tests.

A one-step multiplex real-time RT-PCR for the universal detection of all currently known CCHFV genotypes.

Crimean-Congo hemorrhagic fever (CCHF) is a fatal disease in humans, which is endemic in many countries of Africa, Southern Asia and Southeastern Europe. It is caused by the Crimean-Congo hemorrhagic fever virus (CCHFV), which is an arthropod-borne virus (arbovirus) transmitted by ixodid ticks, mainly of the genus Hyalomma. Animals like hares, hedgehogs, cattle, camels and small ruminants can become infected without developing clinical signs. Seroconversion occurs after a short viremia of up to two weeks, and thus seroprevalence studies in ruminants can be used to reveal risk areas for the human population. Virus detection by real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) is essential to prove an actual circulation of CCHFV in a country and is also used as diagnostic method for acute human CCHFV infections. In this study, a new universal one-step multiplex real-time RT-qPCR for the sensitive and specific detection of CCHFV is presented. For this purpose, 14 new primers and 2 probes were simultaneously used to detect RNAs representing all six CCHFV genotypes. Additionally, a GC-mirrored sequence within the synthetic RNAs enables the discrimination between true positive samples and unintentional laboratory contaminations. CCHFV negative samples from different animal species and ten different members of the order Bunyavirales were eventually tested to reveal the specificity of the new RT-qPCR.

A novel double-antigen sandwich ELISA for the species-independent detection of Crimean-Congo hemorrhagic fever virus-specific antibodies.

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease in humans caused by the CCHF virus (CCHFV). The detection of anti-CCHFV antibodies in animals is used to reveal infection risk areas. Therefore a simple, quick and reliable multispecies assay for the detection of CCHFV-specific antibodies is needed. This work presents the development and validation of a novel CCHF double-antigen ELISA for the detection of anti-CCHFV nucleoprotein antibodies. The test requires 30 µl of serum, and results are obtained within 90 min. As the ELISA is based on recombinant N-protein of the IbAr10200 virus, it can be run under standard biosafety conditions. For assay validation, sera from 95 cattle and 176 small ruminants from CCHF-endemic regions (origin: Albania, Cameroon, Kosovo, Former Yugoslav Republic of Macedonia, Mauritania, Pakistan, Turkey) served as a positive reference serum panel. The CCHF antibody status of the positive reference samples had been previously confirmed by two serological assays (species-adapted VectorBest ELISA and Euroimmun IFA). CCHFV strains belonging to three different clades are known to circulate in the countries where the positive samples originated. Sera from 402 cattle and 804 small ruminants from Germany and France served as the negative serum panel, as both countries are considered outside of the CCHFV endemic zone. Sera from monkeys, camels, rats, ferrets, raccoon dogs, raccoons, foxes, hares, pigs and humans were also tested, to determine the suitability of this novel ELISA for these species. All negative reference sera were confirmed by the CCHF double-antigen ELISA, indicating a specificity of 100%. 268 of 271 positive reference sera tested positive for CCHFV-specific antibodies, 8sensitivity of 99%9. Further analysis are needed to ensure a recognition of the IbAr10200 nucleoprotein by antibodies directed against all known CCHFV clades. This is planned to be realized with sera from other regions covering the three missing clades.

Serosurvey for Crimean-Congo hemorrhagic fever virus infections in ruminants in Katanga province, Democratic Republic of the Congo.

Crimean-Congo hemorrhagic fever virus (CCHFV) has been detected in many African countries. Unfortunately, little is known about the current CCHFV situation in most of those countries including the Democratic Republic of the Congo (DRC). In over 50 years, three human CCHF cases have been detected in DRC but no seroepidemiological investigation was performed so far. To determine the prevalence of CCHFV-specific antibodies we tested 838 serum samples of cattle, goat and sheep from the southern province Katanga, DRC. The detected seroprevalence in ruminants was 1.6% ranging from 0.4% to 3.4% between the two sampling sites, Kamina and Lubumbashi. The low prevalence indicates only sporadic introduction of CCHFV into this part of the country. DRC is a very large country and the study was performed only at two locations in one province; therefore, the investigations can be only a starting point for further epidemiological activities.

Serosurvey of Crimean-Congo Hemorrhagic Fever Virus in Cattle, Mali, West Africa.

AbstractCrimean-Congo hemorrhagic fever is a tick-borne disease caused by the arbovirus Crimean-Congo hemorrhagic fever virus (CCHFV, family Bunyaviridae, genus Nairovirus). CCHFV can cause a severe hemorrhagic fever with high-case fatality rates in humans. CCHFV has a wide geographic range and has been described in around 30 countries in the Middle East, Asia, Europe, and Africa including Mali and neighboring countries. To date, little is known about the prevalence rates of CCHFV in Mali. Here, using banked bovine serum samples from across the country, we describe the results of a seroepidemiological study for CCHFV aimed at identifying regions of circulation in Mali. In total, 1,074 serum samples were tested by a modified in-house CCHFV-IgG-enzyme-linked immunosorbent assay (ELISA) with confirmatory testing by commercial ELISA and immunofluorescence assay. Overall, 66% of samples tested were positive for CCHFV-specific IgG antibodies. Regional seroprevalence rates ranged from 15% to 95% and seemed to correlate with cattle density. Our results demonstrate that CCHFV prevalence is high in many regions in Mali and suggest that CCHFV surveillance should be established.

Crimean-Congo Hemorrhagic Fever Virus-Specific Antibody Detection in Cattle in Mauritania.

BACKGROUND: Crimean-Congo hemorrhagic fever virus (CCHFV) was detected for the first time in Mauritania in 1983 and several CCHFV outbreaks were reported in the following years. The last human case was diagnosed in 2015. However, no recent data exist about the prevalence of CCHFV in animals, although it is already described that prevalence studies in animals serve as good risk indicators. CCHFV can cause a severe hemorrhagic fever with a high case fatality rate in humans. Therefore, a precise risk assessment on the basis of updated data is very important. This article gives an overview about the current CCHFV prevalence in cattle in Mauritania. METHODS AND FINDINGS: A seroprevalence study was carried out using 495 cattle sera from Mauritania, which were collected in the year 2013. The sera were analyzed by an inhouse CCHFV-IgG-ELISA. As second screening test, an adapted commercial CCHFV-IgG-ELISA was performed. Inconclusive sera were additionally tested by a modified commercial CCHFV-IgG-IFA. All assays showed high diagnostic sensitivity (>95%) and specificity (>98%). The overall prevalence of CCHFV-specific antibodies found in Mauritanian cattle was 67%, ranging from 56% to 90% in different provinces. CONCLUSION: This study shows a very high CCHFV-specific antibody prevalence in cattle in Mauritania. It is the highest seroprevalence detected in Mauritania so far. This strengthens the hypothesis that CCHFV is a serious and ongoing threat for public health in Mauritania.

Detection of Crimean-Congo hemorrhagic fever virus-specific IgG antibodies in ruminants residing in Central and Western Macedonia, Greece.

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus which causes lethal hemorrhagic fever in humans. Although, several reports regarding CCHFV antibody prevalence in humans exist in Greece, information about the current distribution is limited. The aim of the present study is to investigate the prevalence of CCHFV-specific IgG antibodies in cattle and sheep in Macedonia-Greece. The samplings were performed during spring 2013, in 5 regional units of Central Macedonia (Chalkidiki, Imathia, Kilkis, Pella and Thessaloniki) and in the 4 regional units of Western Macedonia (Grevena, Florina, Kastoria and Kozani). Specifically, sera from 538 cattle and 81 sheep underwent testing against CCHFV-specific IgG antibodies. Antiviral immune responses were observed in 31 cattle (6%, 95% CI: 4-8%) and in one sheep (1%, 95% CI: 0-8%). The total seroprevalence in the cattle sampled in Central Macedonia was 7% (28 out of 396, 95% CI: 5-10%). Within Central Macedonia, the highest seroprevalence was detected in Chalkidiki (38%, 95% CI: 23-56%), which was significantly higher (p<0.01) compared to the overall seroprevalence detected in cattle. In Western Macedonia, the total seroprevalence in cattle was 2% (3 out of 142, 95% CI: 1-7%). The 3 seropositive cattle were residing in the regional unit of Grevena. The one IgG-positive sheep serum was obtained from an animal residing in Thessaloniki. In this regional unit, the prevalence in sheep (2%, 95% CI: 0-10%) was much lower compared to the prevalence in cattle (12%, 95% CI: 6-22%), but significance was not achieved (p=0.03). The here presented seroepidemiological study demonstrates high transmission risk to human in specific geographical areas, which should be communicated to national and local public health authorities, so as to intensify preventive measures for public health protection.

High seroprevalence for indigenous spotted fever group rickettsiae in forestry workers from the federal state of Brandenburg, Eastern Germany.

In the last decade six Rickettsia species, including Rickettsia slovaca have been characterized in Germany. All of these species could be linked to distinct clinical syndromes in humans. However, due to lack of seroepidemiological data an estimation of the prevalence and the public health impact of rickettsial infections in Germany is difficult. The aim of the present study was to determine the seroprevalence of spotted fever group (SFG) rickettsiae in a population with an elevated exposure risk to ticks. For that purpose, 559 sera of forestry workers in the federal state of Brandenburg, Eastern Germany, were screened for SFG-rickettsiae reactive IgG antibodies. Positive sera were subsequently titrated by microimmunofluorescence assay against R. helvetica, R. raoultii, R. felis, "R. monacensis" and R. slovaca. The total average IgG seroprevalence rate against SFG rickettsiae of 27.5% was found to be represented by 9.7% R. helvetica, 5% R. raoultii, 2.7% R. felis, 0.5% "R. monacensis" and 0.5% R. slovaca. The remaining 9.1% positive test results were of non-differentiable origin. IgG seroprevalences ranged from 11% to 55% in the different forestry districts. Older and male participants had a significantly higher probability for seropositivity and higher anti-rickettsia antibody titer level. In addition, the number of recent as well as the recalled lifetime tick bites was significantly associated with seropositivity and higher titers against SFG rickettsiae. In conclusion, we found an unexpected high total seroprevalence against SFG rickettsiae in forestry workers and serological evidence confirming the occurrence of R. raoultii, R. felis, "R. monacensis" and R. helvetica in the federal State of Brandenburg.

A competitive ELISA for species-independent detection of Crimean-Congo hemorrhagic fever virus specific antibodies.

Crimean-Congo hemorrhagic fever virus (CCHFV) circulates in many countries of Asia, Africa, and Europe. CCHFV can cause a severe hemorrhagic fever in humans with case-fatality rates of up to 80%. CCHF is considered to be one of the major emerging diseases spreading to and within Europe. Ticks of the genus Hyalomma function as vector as well as natural reservoir of CCHFV. Ticks feed on various domestic animals (e.g. cattle, sheep, goats) and on wildlife (e.g. hares, hedgehogs). Those animal species play an important role in the life cycle of the ticks as well as in amplification of CCHFV. Here we present a competitive ELISA (cELISA) for the species-independent detection of CCHFV-specific antibodies. For this purpose nucleocapsid (N) protein specific monoclonal antibodies (mAbs) were generated against an Escherichia coli (E. coli) expressed CCHFV N-protein. Thirty-three mAbs reacted with homologous and heterologous recombinant CCHFV antigens in ELISA and Western blot test and 20 of those 33 mAbs reacted additionally in an immunofluorescence assay with eukaryotic cells expressing the N-protein. Ten mAbs were further characterized in a prototype of the cELISA and nine of them competed with positive control sera of bovine origin. The cELISA was established by using the mAb with the strongest competition. For the validation, 833 sera from 12 animal species and from humans were used. The diagnostic sensitivity and specificity of the cELISA was determined to be 95% and 99%, respectively, and 2% of the sera gave inconclusive results. This cELISA offers the possibility for future large-scale screening approaches in various animal species to evaluate their susceptibility to CCHFV infection and to identify and monitor the occurrence of CCHFV.

Crimean-Congo Hemorrhagic Fever Virus in Bulgaria and Turkey.

Infections of humans with the tick-borne Crimean-Congo hemorrhagic fever virus (CCHFV) can cause a severe hemorrhagic fever with case fatality rates of up to 80%. Most humans are infected by tick bite, crushing infected ticks by hand or by unprotected contact with blood of viremic mammals. Next to the notified human CCHF cases, the real distribution and the situation in animals in Southeastern Europe are nearly unknown. Since domestic ruminants play a crucial role in the life cycle of the vector ticks and the transmission and amplification of the virus, the antibody prevalence in those animals is a good indicator for the presence of CCHFV in a region. Therefore, the prevalence of CCHFV-specific antibodies was investigated in domestic ruminants of different regions of Bulgaria and Turkey. Sera of 1165 ruminants were tested and a prevalence of up to 90% was identified. The overall prevalence for Bulgaria was 26% and for Turkey 57%. The results highlight the risk of human infections in those regions and the importance of the investigation of the prevalence in animals for identification of risk areas. This article provides a unique overview about published CCHFV antibody prevalence in animals in comparison to human incidences in different areas of Bulgaria and Turkey. Although it will help to complete the understanding of the CCHFV situation in these countries, it also demonstrates the lack of unpublished and published data even in these highly endemic areas.

Unique human immune signature of Ebola virus disease in Guinea.

Despite the magnitude of the Ebola virus disease (EVD) outbreak in West Africa, there is still a fundamental lack of knowledge about the pathophysiology of EVD. In particular, very little is known about human immune responses to Ebola virus. Here we evaluate the physiology of the human T cell immune response in EVD patients at the time of admission to the Ebola Treatment Center in Guinea, and longitudinally until discharge or death. Through the use of multiparametric flow cytometry established by the European Mobile Laboratory in the field, we identify an immune signature that is unique in EVD fatalities. Fatal EVD was characterized by a high percentage of CD4(+) and CD8(+) T cells expressing the inhibitory molecules CTLA-4 and PD-1, which correlated with elevated inflammatory markers and high virus load. Conversely, surviving individuals showed significantly lower expression of CTLA-4 and PD-1 as well as lower inflammation, despite comparable overall T cell activation. Concomitant with virus clearance, survivors mounted a robust Ebola-virus-specific T cell response. Our findings suggest that dysregulation of the T cell response is a key component of EVD pathophysiology.

Real-time, portable genome sequencing for Ebola surveillance.

The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10(-3) and 1.42 × 10(-3) mutations per site per year. This is equivalent to 16-27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15-60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.