A staged strategy for pathogen surveillance and discovery

Recent advances in molecular diagnostics have revolutionized microbiology by facilitating rapid, sensitive pathogen surveillance and differential diagnosis of infectious diseases. Implementation of these technologies can enable intervention when the prognosis is optimal for limiting replication, dissemination, transmission, morbidity and mortality. It may also reveal unappreciated links between infection and chronic diseases. Although new pathogens continue to emerge, we have likely collected much of the "low hanging fruit" (microbes readily associated with diseases). An important task now is to understand those disorders that reflect the interaction of microbes with other environmental factors (toxins, other stressors) and susceptibility genes in a developmental context. Here I will review the strengths and limitations of various assay platforms, describe the challenges associated with proving causation, and delineate a staged strategy for pathogen discovery focused in emerging infectious disease "hot spots," "hot hosts," and prospective birth cohorts

A new arenavirus in a cluster of fatal transplant-associated diseases

Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Culture, polymerase-chain-reaction (PCR) and serologic assays, and oligonucleotide microarray analysis for a wide range of infectious agents were not informative. We evaluated RNA obtained from the liver and kidney transplant recipients. Unbiased high-throughput sequencing was used to identify microbial sequences not found by means of other methods. The specificity of sequences for a new candidate pathogen was confirmed by means of culture and by means of PCR, immunohistochemical, and serologic analyses. High-throughput sequencing yielded 103,632 sequences, of which 14 represented an Old World arenavirus. Additional sequence analysis showed that this new arenavirus was related to lymphocytic choriomeningitis viruses. Specific PCR assays based on a unique sequence confirmed the presence of the virus in the kidneys, liver, blood, and cerebrospinal fluid of the recipients. Immunohistochemical analysis revealed arenavirus antigen in the liver and kidney transplants in the recipients. IgM and IgG antiviral antibodies were detected in the serum of the donor. Seroconversion was evident in serum specimens obtained from one recipient at two time points

A new arenavirus in a cluster of fatal transplant-associated diseases

Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Culture, polymerase-chain-reaction (PCR) and serologic assays, and oligonucleotide microarray analysis for a wide range of infectious agents were not informative. We evaluated RNA obtained from the liver and kidney transplant recipients. Unbiased high-throughput sequencing was used to identify microbial sequences not found by means of other methods. The specificity of sequences for a new candidate pathogen was confirmed by means of culture and by means of PCR, immunohistochemical, and serologic analyses. High-throughput sequencing yielded 103,632 sequences, of which 14 represented an Old World arenavirus. Additional sequence analysis showed that this new arenavirus was related to lymphocytic choriomeningitis viruses. Specific PCR assays based on a unique sequence confirmed the presence of the virus in the kidneys, liver, blood, and cerebrospinal fluid of the recipients. Immunohistochemical analysis revealed arenavirus antigen in the liver and kidney transplants in the recipients. IgM and IgG antiviral antibodies were detected in the serum of the donor. Seroconversion was evident in serum specimens obtained from one recipient at two time points

Newly discovered Ebola virus associated with hemorrhagic fever outbreak in Uganda

In this report we describe a newly discovered ebolavirus species which caused a large hemorrhagic fever outbreak in western Uganda. The virus is genetically distinct, differing by more than 30% at the genome level from all other known ebolavirus species. The unique nature of this virus created challenges for traditional filovirus molecular based diagnostic assays and genome sequencing approaches. Instead, we quickly determined over 70% of the virus genome using a recently developed random-primed pyrosequencing approach that allowed the rapid development of a molecular detection assay that was deployed in the disease outbreak response. This draft sequence allowed easy completion of the whole genome sequence using a traditional primer walking approach and prompt confirmation that this virus represented a new ebolavirus species. Current efforts to design effective diagnostics, antivirals and vaccines will need to take into account the distinct nature of this important new member of the filovirus family

Criteria of “persistent vomiting” in the WHO 2009 warning signs for dengue case classification

Introduction: Dengue is a viral disease that spreads rapidly in the tropic and subtropic regions of the world and causes 22,000 deaths annually. In 2009, the World Health Organization (WHO) released a new classification of dengue infections, which divided them into three categories: dengue without warning sign (D), dengue with warning sign (DWS), and severe dengue (SD). However, researchers have been using different criteria to define persistent vomiting; therefore, we aimed to evaluate the ability of the number of vomiting times in early prediction of SD development among D/DWS patients. Method: A hospital-based cohort study was conducted in Ben Tre-south of Vietnam. We enrolled confirmed dengue patients with D and DWS at admission. The final classification was determined on the discharged day for every patient based on the classification of WHO 2009 without using vomiting symptom, using the receiver operating characteristic (ROC) curve to evaluate the ability of the number of vomiting times in early prediction of SD development among D/DWS patients. Result: The prevalence of vomiting symptom was higher in SD group than D/DWS group (92 versus 46 %, p = 0.006), and the median of the number of vomiting times was higher in SD group than D/DWS group (2.5 versus 0, p = 0.001). To distinguish SD from D/DWS, the ROC curve of the number of vomiting episodes showed that the area under the curve was 0.77; with the cut point of two, the sensitivity and specificity were 92 and 52 %, respectively. Conclusion: The number of vomiting times could be a good clinical sign which can early predict SD from the group of D/DWS. We suggest the definition of persistent vomiting should be vomiting two times or more per day

The influence of human genetic variation on early transcriptional responses and protective immunity following immunization with Rotarix vaccine in infants in Ho Chi Minh City in Vietnam : a study protocol for an open single-arm interventional trial [awaiting peer review]

Background: Rotavirus (RoV) remains the leading cause of acute gastroenteritis in infants and children aged under five years in both high- and low-middle-income countries (LMICs). In LMICs, RoV infections are associated with substantial mortality. Two RoV vaccines (Rotarix and Rotateq) are widely available for use in infants, both of which have been shown to be highly efficacious in Europe and North America. However, for unknown reasons, these RoV vaccines have markedly lower efficacy in LMICs. We hypothesize that poor RoV vaccine efficacy across in certain regions may be associated with genetic heritability or gene expression in the human host. Methods/design: We designed an open-label single-arm interventional trial with the Rotarix RoV vaccine to identify genetic and transcriptomic markers associated with generating a protective immune response against RoV. Overall, 1,000 infants will be recruited prior to Expanded Program on Immunization (EPI) vaccinations at two months of age and vaccinated with oral Rotarix vaccine at two and three months, after which the infants will be followed-up for diarrheal disease until 18 months of age. Blood sampling for genetics, transcriptomics, and immunological analysis will be conducted before each Rotarix vaccination, 2-3 days post-vaccination, and at each follow-up visit (i.e. 6, 12 and 18 months of age). Stool samples will be collected during each diarrheal episode to identify RoV infection. The primary outcome will be Rotarix vaccine failure events (i.e. symptomatic RoV infection despite vaccination), secondary outcomes will be antibody responses and genotypic characterization of the infection virus in Rotarix failure events. Discussion: This study will be the largest and best powered study of its kind to be conducted to date in infants, and will be critical for our understanding of RoV immunity, human genetics in the Vietnam population, and mechanisms determining RoV vaccine-mediated protection. Registration: ClinicalTrials.gov, ID: NCT03587389. Registered on 16 July 2018

Extraction Process, Identification of Fatty Acids, Tocopherols, Sterols and Phenolic Constituents, and Antioxidant Evaluation of Seed Oils from Five Fabaceae Species

The present study aimed to extract seed oils and characterize the chemical composition, including fatty acid profiles, tocopherols, sterols, and total phenolics of oils and extracts from five Fabaceae seeds: Glycine soja, Vigna angularis, Phaseolus lunatus, Phaseolus vulgarisand, and Phaseolus coccineus. The composition and content of all substance layers in total lipids of the extracted seed oils from five Fabaceae species contain: polar lipid (PL), sterol (ST), diacylglycerol (DG), triacylglycerol (TG), free fatty acid (FFA), and hydrocarbon and wax (HC + W). Antioxidant activity determined by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) method was also estimated. Among these examined samples, Phaseolus vulgarisand and Phaseolus coccineus seed oils showed high content of α-linolenic acid (59.39% and 49.38%, respectively). Linoleic acid was abundantly found in Vigna angularis (49.01%). Ferunic and caffeic acid, γ-tocopherol, and β-sistosterol were the main ingredients present in the species studied. The V. angularis seed extract displayed significant antioxidant activity

A Dataset of Vietnamese Junior High School Students’ Reading Preferences and Habits

Books are the invaluable, colossal storage of mankind’s immense scholarship and are still commonly perceived as a more reliable source of knowledge even in this age of digitized information. Extensive reading is often promoted as being vital to cognitive development, especially for students in primary and secondary education. While it could now be considered common knowledge that reading is highly beneficial, reading habits vary among individuals in the same culture and receiving the same public education. This could be due to demographic variations and differences in socioeconomic status, or other factors such as family background and education. Despite the ample literature on reading habits, there still exists a lack of holistic approach with empirical results concerning the reciprocal interactions of reading and its relevant affecting factors. This data article presents a dataset of 1676 responses to the survey “Studying reading habits and preferences„ of junior high school students in Vietnam. Result analysis facilitates evaluation of reading habits and their affecting factors, thus holding implications on education measures and policy. The dataset is available with the paper

Microarray-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals

Definitive diagnosis of vesicular or vesicular-like lesions in livestock animals presents challenges both for veterinary clinicians and diagnostic laboratories. It is often impossible to diagnose the causative disease agent on a clinical basis alone and difficult to collect ample vesicular epithelium samples. Due to restrictions of time and sample size, once laboratory tests have ruled out foot-and-mouth disease, vesicular stomatitis and swine vesicular disease a definitive diagnosis may remain elusive. With the ability to test a small quantity of sample for a large number of pathogens simultaneously, DNA microarrays represent a potential solution to this problem. This study describes the application of a long oligonucleotide microarray assay to the identification of viruses known to cause vesicular or vesicular-like lesions in livestock animals. Eighteen virus isolates from cell culture were successfully identified to genus level, including representatives of each foot-and-mouth disease virus serotype, two species of vesicular stomatitis virus (VSV), swine vesicular disease virus, vesicular exanthema of swine virus (VESV), bovine herpesvirus 1, orf virus, pseudocowpox virus, bluetongue virus serotype 1 and bovine viral diarrhoea virus 1. VSV and VESV were also identified in vesicular epithelium samples, with varying levels of sensitivity. The results indicate that with further development this microarray assay could be a valuable tool for the diagnosis of vesicular and vesicular-like diseases. Crow

Exploration of Youth’s Digital Competencies: A Dataset in the Educational Context of Vietnam

The recent surge of the Fourth Industrial Revolution has set forth demands for a new generation of the labor force with a comprehensive set of skills to meet the standards of the global market. Despite widespread concerns about educational reforms and renovations to enhance the workforce capacity in terms of information and communication technology (ICT) skills, research into the digital proficiencies of students has been limited in Vietnam. This dataset contains 1061 observations on the digital competency level of 10th-grade students in 20 surveyed schools from five provinces in Vietnam. The investigation, joining frequentist and Bayesian analyses, aims to provide valuable insights into the current state of children’s attitudes, behaviors, competency levels, and use of ICT within the Vietnamese educational context. The values of the dataset lie in its proposed scientific framework for replication in multiple regions and contexts as well as the feasibility of categorical regression techniques together with Bayesian statistics for hierarchical regression analysis