Source Of Epidemics Research Articles

Economy, migrant labour and sex work: interplay of HIV epidemic drivers in Zimbabwe over three decades.

HIV took off rapidly in Zimbabwe during the 1980s. Yet, between 1998 and 2003, as the economy faltered, HIV prevalence declined abruptly and without clear explanation. We reviewed epidemiological, behavioural, and economic data over three decades to understand changes in economic conditions, migrant labour and sex work that may account for observed fluctuations in Zimbabwe's HIV epidemic. Potential biases related to changing epidemic paradigms and data sources were examined. Early studies describe rural poverty, male migrant labour and sex work as conditions facilitating HIV/sexually transmitted infection (STI) transmission. By the mid-1990s, as Zimbabwe's epidemic became more generalized, research focus shifted to general population household surveys. Yet, less than half as many men than women were found at home during surveys in the 1990s, increasing to 80% during the years of economic decline. Other studies suggest that male demand for sex work fell abruptly as migrant workers were laid off, picking up again when the economy rebounded after 2009. Numbers of clients reported by sex workers, and their STI rates, followed similar patterns reaching a nadir in the early 2000s. Studies from 2009 describe a return to more active sex work, linked to increasing client demand, as well as a revitalized programme reaching sex workers. The importance of the downturn in migrant labour and resultant changes in sex work may be underestimated as drivers of Zimbabwe's rapid HIV incidence and prevalence declines. Household surveys underrepresent populations at the highest risk of HIV/STI acquisition and transmission, and these biases vary with changing economic conditions.

Large-Scale Complete-Genome Sequencing and Phylodynamic Analysis of Eastern Equine Encephalitis Virus Reveals Source-Sink Transmission Dynamics in the United States

Eastern equine encephalitis virus (EEEV) has a high case-fatality rate in horses and humans, and Florida has been hypothesized to be the source of EEEV epidemics for the northeastern United States. To test this hypothesis, we sequenced complete genomes of 433 EEEV strains collected within the United States from 1934 to 2014. Phylogenetic analysis suggested EEEV evolves relatively slowly and that transmission is enzootic in Florida, characterized by higher genetic diversity and long-term local persistence. In contrast, EEEV strains in New York and Massachusetts were characterized by lower genetic diversity, multiple introductions, and shorter local persistence. Our phylogeographic analysis supported a source-sink model in which Florida is the major source of EEEV compared to the other localities sampled. In sum, this study revealed the complex epidemiological dynamics of EEEV in different geographic regions in the United States and provided general insights into the evolution and transmission of other avian mosquito-borne viruses in this region.IMPORTANCE Eastern equine encephalitis virus (EEEV) infections are severe in horses and humans on the east coast of the United States with a >90% mortality rate in horses, an ∼33% mortality rate in humans, and significant brain damage in most human survivors. However, little is known about the evolutionary characteristics of EEEV due to the lack of genome sequences. By generating large collection of publicly available complete genome sequences, this study comprehensively determined the evolution of the virus, described the epidemiological dynamics of EEEV in different states in the United States, and identified Florida as one of the major sources. These results may have important implications for the control and prevention of other mosquito-borne viruses in the Americas.

Post-Exposure Protection in Mice against Sudan Virus by a Two Antibody Cocktail.

Sudan virus (SUDV) and Ebola viruses (EBOV) are both members of the Ebolavirus genus and have been sources of epidemics and outbreaks for several decades. We present here the generation and characterization of cross-reactive antibodies to both SUDV and EBOV, which were produced in a cell-free system and protective against SUDV in mice. A non-human primate, cynomolgus macaque, was immunized with viral-replicon particles expressing the glycoprotein of SUDV-Boniface (8A). Two separate antibody fragment phage display libraries were constructed after four immunogen injections. Both libraries were screened first against the SUDV and a second library was cross-selected against EBOV-Kikwit. Sequencing of 288 selected clones from the two distinct libraries identified 58 clones with distinct VH and VL sequences. Many of these clones were cross-reactive to EBOV and SUDV and able to neutralize SUDV. Three of these recombinant antibodies (X10B1, X10F3, and X10H2) were produced in the scFv-Fc format utilizing a cell-free production system. Mice that were challenged with SUDV-Boniface receiving 100µg of the X10B1/X10H2 scFv-Fc combination 6 and 48-h post-exposure demonstrated partial protection individually and complete protection as a combination. The data herein suggests these antibodies may be promising candidates for further therapeutic development.

Biological control of olive anthracnose

Olive anthracnose, a fungal disease caused by species of the genus Colletotrichum, is responsible for severe yield losses and poor oil quality. Typical symptoms appear in autumn or early winter, when the drupes begin to ripen. Under favorable conditions, symptoms on branches and leaves can also occur, leading to chlorosis, severe defoliation, and death of woody organs. Symptomless infection of flowers and blights have also been reported. Latent fruit infections could play an important role as the inoculum source for the autumn-winter epidemics. Application of systemic fungicides has proved effective in field trials, and pre-flowering sprays contribute to reduce latent infection and the inoculum density for autumn infection. However, public concerns about potential risks on the environment and human health promoted the search for alternative and sustainable means. Therefore, the activity of a new sulfur-based product and biocontrol agents (Bacillus subtilis, and endophytic isolates of Aureobasidium pullulans) in reducing the incidence of olive anthracnose was evaluated under field conditions. The sulfur-based product and B. subtilis applied at the pre-flowering stage were as effective as the chemical fungicides in reducing the incidence of latent infections on drupes. Moreover, some endophytic strains of A. pullulans provided high protection levels against Colletotrichum spp. when applied at the pre-flowering and veraison stages. Overall, data indicated that olive anthracnose can be controlled by using biological means and new products could be considered for introduction in the list of the organic product specification.

Licencja przymusowa eksportowa jako publicznoprawny instrument zwalczania i zapobiegania chorobom zakaźnym

W dobie postępu cywilizacyjnego i związanej z nim globalizacji problem chorób zakaźnych, ich profilaktyki i zwalczania skutków pozostaje jednym z istotnych w zakresie zadań publicznych lokowanych w obszarze ochrony zdrowia. Z drugiej zaś strony specyfika i przebieg tych chorób stanowią wciąż istotne wyzwanie dla medycyny, zwłaszcza w zakresie związanym z badaniami i rozwojem, w znalezieniu takich rozwiązań chemicznych czy biologicznych, w tym leków i szczepionek, które będą skuteczne. Sektor publiczny skazany jest w tym względzie, w większości przypadków, na aktywność naukową i finansową podejmowaną przez przemysł farmaceutyczny. Ten ostatni, zwłaszcza gdy korzysta z monopolu wynikającego z uzyskanej ochrony patentowej, nie zawsze jednak jest zainteresowany kierowaniem swojej oferty do rynków słabo rozwiniętych. Obszary te zaś często to źródła rozprzestrzeniających się epidemii. Stąd wysiłki organizacji międzynarodowych, a w ślad za nimi także Unii Europejskiej, by stworzyć instrumenty prawne, takie jak przymusowa licencja eksportowa, pozwalające przeciwdziałać tym niekorzystnym zjawiskom. Wydaje się jednak, że wprowadzenie legislacyjnej formuły nie jest wystarczające dla osiągniecia oczekiwanych rezultatów bez odpowiedniego wsparcia politycznego, ekonomicznego i społecznego.

Solving the patient zero inverse problem by using generalized simulated annealing

Identifying patient zero – the initially infected source of a given outbreak – is an important step in epidemiological investigations of both existing and emerging infectious diseases. Here, the use of the Generalized Simulated Annealing algorithm (GSA) to solve the inverse problem of finding the source of an outbreak is studied. The classical disease natural histories susceptible–infected (SI), susceptible–infected–susceptible (SIS), susceptible–infected–recovered (SIR) and susceptible–infected–recovered–susceptible (SIRS) in a regular lattice are addressed. Both the position of patient zero and its time of infection are considered unknown. The algorithm performance with respect to the generalization parameter q̃v and the fraction ρ of infected nodes for whom infection was ascertained is assessed. Numerical experiments show the algorithm is able to retrieve the epidemic source with good accuracy, even when ρ is small, but present no evidence to support that GSA performs better than its classical version. Our results suggest that simulated annealing could be a helpful tool for identifying patient zero in an outbreak where not all cases can be ascertained.

Epidemiological placism in public health emergencies: Ebola in two Dallas neighborhoods

Super-diverse cities face distinctive challenges during infectious disease outbreaks. For refugee and immigrant groups from epidemic source locations, identities of place blend with epidemiological logics in convoluted ways during these crises. This research investigated the relationships of place and stigma during the Dallas Ebola crisis. Ethnographic results illustrate how Africanness, more than neighborhood stigma, informed Dallas residents’ experience of stigma. The problems of place-based stigma, the imprecision of epidemiological placism, and the cohesion of stigma to semiotically powerful levels of place – rather than to realistic risk categories – are discussed. Taking its authority from epidemiology, placism is an important source of potential stigma with critical implications for the success of public health messaging.

Characterization of Carbapenem-Resistant Acinetobacter baumannii Strains Isolated from Hospitalized Patients in Palestine.

The American Centers for Disease Control and Prevention (CDC) recognizes Acinetobacter baumannii as a source of global outbreaks and epidemics especially due to its increasing resistance to commercially available antibiotics. In this study, 69 single patient multidrug resistant isolates collected from all over Palestine, except Gaza, were studied. All the isolates were resistant to all the β–lactam antibiotics including the carbapenems. Of the 69 isolates, 82.6% were positive for blaOXA-23, 14.5% were positive for blaOXA-24, and 3% were positive for blaOXA-58. None were positive for blaOXA-143 and blaOXA-235. In addition, 5.8% and 0% were positive for blaNDM and blaKPC, respectively. Of the 69 isolates, none were positive for the aminoglycoside aphA6 gene while 93% were positive for the aphA1 gene. The acetyltransferases aacC1 and aacA4 genes tested positive in 22% and 13% of the isolates, respectively. The ompA biofilm-producing virulence gene was detected in all isolates. Finally, Multilocus Sequence Typing (MLST) of 13 isolates revealed that more than one strain of A. baumannii was circulating in Palestinian hospitals as results revealed that 7 isolates were of ST208, 2 isolates ST218, 1 isolate ST231, 1 isolate ST348, and 2 new Sequence Types. The detection of these drug resistant pathogens is a reminder of the importance of active surveillance for resistant bacteria in order to prevent their spread in hospital settings.

Snow's case revisited: new tool in geographic profiling of epidemiology

Geographic Profiling technique is used to find the origin of a series of crimes. The method was recently extended to other fields. One of the best renowned data in epidemiology is that by John Snow during an outburst of cholera in London. We wrote Python scripts to perform the analyses to apply the Geographic Profiling for individuating the starting origin of an infection by using the old Snow's data set. We modified the method by applying a weight to each point of the map where cases of cholera were reported. The weight was proportional to the number of cases in a given location.This modification of the Geographic Profiling method allowed to individuate in the map an area of maximum probability of the infection source, which was a few meters wide and including the historically known source of cholera, that is the “classical” water pump at Broad Street.The method appears to be a useful complement in order to individuate the source of epidemics when available data about the cases of the infections can be summarized on a map.

Using epidemic betweenness to measure the influence of users in complex networks

Betweenness is a measure of the centrality of a node in a network, and is normally calculated as the fraction of shortest paths, random walk paths or flow units between node pairs that pass through the node of interest. Betweenness is, in some sense, a measure of the influence a node possesses over the spread of information in the network. However, the traditional betweenness is based on the information dissemination from one node to another. This is conceptually not suitable for the epidemics in which information is disseminated from one node to multiple neighboring nodes and destinations. To address this problem, we propose a novel betweenness measure based on epidemics. The epidemic betweenness counts the average number of the following nodes influenced by the node of interest after it becomes the epidemic source or an intermediary. This measure reflects the potential influence of a node to any epidemic in complex networks. To justify this measure, we introduce real complex networks and estimate the average influential scale of each node in epidemics through a large number of simulations. We compare the simulation results to those of the epidemic betweenness and another seven classic measures, such as Eigenvector and Katz. We further provide correlation studies to expose the differences of the epidemic betweenness in capturing influential nodes. We find that the epidemic betweenness is exclusively the measure that accurately present the potential influence of each node in epidemics. Finally, as an example of application, the epidemic betweenness measure explains the finding in recent research that unpopular users (nodes with small degree) could also lead to large cascades of epidemics.

Non-toxigenic environmental Vibrio cholerae O1 strain from Haiti provides evidence of pre-pandemic cholera in Hispaniola.

Vibrio cholerae is ubiquitous in aquatic environments, with environmental toxigenic V. cholerae O1 strains serving as a source for recurrent cholera epidemics and pandemic disease. However, a number of questions remain about long-term survival and evolution of V. cholerae strains within these aquatic environmental reservoirs. Through monitoring of the Haitian aquatic environment following the 2010 cholera epidemic, we isolated two novel non-toxigenic (ctxA/B-negative) Vibrio cholerae O1. These two isolates underwent whole-genome sequencing and were investigated through comparative genomics and Bayesian coalescent analysis. These isolates cluster in the evolutionary tree with strains responsible for clinical cholera, possessing genomic components of 6th and 7th pandemic lineages, and diverge from “modern” cholera strains around 1548 C.E. [95% HPD: 1532–1555]. Vibrio Pathogenicity Island (VPI)-1 was present; however, SXT/R391-family ICE and VPI-2 were absent. Rugose phenotype conversion and vibriophage resistance evidenced adaption for persistence in aquatic environments. The identification of V. cholerae O1 strains in the Haitian environment, which predate the first reported cholera pandemic in 1817, broadens our understanding of the history of pandemics. It also raises the possibility that these and similar environmental strains could acquire virulence genes from the 2010 Haitian epidemic clone, including the cholera toxin producing CTXϕ.

Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens.

Many bacterial pathogens are well characterized but, in some cases, little is known about the populations from which they emerged. This limits understanding of the molecular mechanisms underlying disease. The crop pathogen Pseudomonas syringae sensu lato has been widely isolated from the environment, including wild plants and components of the water cycle, and causes disease in several economically important crops. Here, we compared genome sequences of 45 P. syringae crop pathogen outbreak strains with 69 closely related environmental isolates. Phylogenetic reconstruction revealed that crop pathogens emerged many times independently from environmental populations. Unexpectedly, differences in gene content between environmental populations and outbreak strains were minimal with most virulence genes present in both. However, a genome-wide association study identified a small number of genes, including the type III effector genes hopQ1 and hopD1, to be associated with crop pathogens, but not with environmental populations, suggesting that this small group of genes may play an important role in crop disease emergence. Intriguingly, genome-wide analysis of homologous recombination revealed that the locus Psyr 0346, predicted to encode a protein that confers antibiotic resistance, has been frequently exchanged among lineages and thus may contribute to pathogen fitness. Finally, we found that isolates from diseased crops and from components of the water cycle, collected during the same crop disease epidemic, form a single population. This provides the strongest evidence yet that precipitation and irrigation water are an overlooked inoculum source for disease epidemics caused by P. syringae.

Intersystem Implications of the Developmental Origins of Health and Disease: Advancing Health Promotion in the 21st Century.

The developmental origins of health and disease (DOHaD) theory and life course theory (LCT) are emerging fields of research that have significant implications for the public health and health promotion professions. Using a DOHaD/LCT perspective, social determinants of health (SDH) take on new critical meaning by which health promotion professionals can implement DOHaD/LCT guided interventions, including recommended policies. Through these interventions, public health could further address the sources of worldwide chronic disease epidemics and reduce such disease rates substantially if related policy, programs, and interdisciplinary and multi-sector collaboration are emphasized. Additional characteristics of the most effective interventions involve context-specific adaptation and societal structures that impact upstream, early life environments on a broad scale, influencing multiple locations and/or diseases.

State of well-water quality in Kakua Chiefdom, Sierra Leone

Water is the difference between living and non-living and water for drinking should be pollutant free. Thus, in supplies for urban and rural consumption, water quality is one of the most critical parameters to verify. Well and/or open-water systems are easily liable to anthropogenic contaminations, the source of most water-borne epidemics especially in developing countries like Sierra Leone. This study analyses 10 representative well-water systems for 18 water quality parameters in Kakua Chiefdom of Bo District, Sierra Leone. The study notes that well-water quality parameters such as total dissolved solids (TDS), turbidity, electrical conductivity, coliform and nitrate (NO3−) are fairly high above safe drinking water standard. The incidence of coliform in the well waters is highest in April and that of iron (Fe2+) and nitrate is highest in May. The Dipha Street well is amongst the most contaminated and has the highest scores for TDS, non-faecal coliform and fluoride (F−). Correlation analysis shows an interesting bond among the water quality parameters, ranging from strongly positive (R = 1.0) to strongly negative (R = −1.0). Fe2+ is strongly positively correlated with most of the well-water quality parameters. Irrespectively, the use of contaminated water in domestic and/or agro-industrial sectors could pose various health risks and epidemic outbreaks of different intensities.

Doença Meningocócica: Características Epidemiológicas do Hospital Municipal Souza Aguiar no Rio de Janeiro, Rio de Janeiro, Brasil entre 2010-2014

A doença meningocócica (DM) representa uma importante preocupação à saúde pública mundial. No âmbito do estado e da cidade do Rio de Janeiro a DM possui primordial relevância, tendo sido historicamente fonte de vários surtos e epidemias. Esse estudo longitudinal retrospectivo tem como objetivo analisar as características epidemiológicas das internações por doença meningocócica no Hospital Municipal Souza Aguiar (HMSA) a partir de três variáveis: sexo, idade, motivo de alta ou evolução entre o período de janeiro de 2010 a abril de 2014. Esses dados apontam numericamente o perfil dos pacientes diagnosticados com DM no HMSA, destarte, pode auxiliar o sistema de vigilância epidemiológica do município do Rio de Janeiro a intervir mais especificamente tanto no que tange a prevenção de incidência quanto de óbitos decorrentes das infecções meningocócicas.

Characterization of environmental Vibrio cholerae serogroups O1 and O139 in the Pearl River Estuary, China.

Toxigenic isolates of Vibrio cholerae serogroups O1 and O139 from aquatic reservoirs are a key source for recurrent epidemics of cholera in human populations. However, we do not have an optimal understanding of the microbiology of the strains within these reservoirs, particularly outside of the time periods when there are active cholera cases in the surrounding community. The main objective of the present study was to identify and characterize V. cholerae O1 and O139 in the Pearl River Estuary at a time when active disease was not being identified, despite prior occurrence of epidemic cholera in the region. Water samples were collected at 24 sites in the research area at monthly intervals between 2007 and 2010, and screened for the presence of V. cholerae O1 and O139. All isolates were screened for the presence of ctxAB, ompW, toxR, and tcpA genes. Multilocus variable number tandem repeat analysis (MLVA) was used to assess possible relationships among strains. The results show that Vibrio cholerae O1 or O139 was isolated, on average, from 6.7% of the sites screened at each time point. All V. cholerae O1 and O139 isolates were ctxAB negative, and 37% were positive for tcpA. Isolation was most common in the oldest, most urbanized district compared with other districts, and was associated with lower pH. Despite year-to-year variability in isolation rates, there was no evidence of seasonality. MLVA of 27 selected isolates showed evidence of high genetic diversity, with no evidence of clustering by year or geographic location. In this region where cholera has been epidemic in the past, there is evidence of environmental persistence of V. cholerae O1 and O139 strains. However, environmental strains were consistently nontoxigenic, with a high level of genetic diversity; their role as current or future agents of human disease remains uncertain.

Typing of Fungi in an Outbreak Setting: Lessons Learned

Typing is applied to highlight the genetic relationships between environmental and clinical fungal isolates involved in colonization or infection. A variety of techniques can be used to type fungi, depending on the epidemiological question and the available equipment. The use of typing techniques during clinical fungal outbreak investigations demonstrated patient-to-patient propagation in dermatophytoses outbreaks, patient-to-health-care worker and health-care worker-to-patient transmission in yeast infection outbreaks, airborne patient-to-patient transmission of the non-cultivable Pneumocystis jirovecii fungus involved in pneumonia outbreaks, and environmental sources of several mold outbreaks including aspergillosis or fusariosis keratitis. Typing was also useful to trace the source of invasive fungal disease outbreaks or epidemics, such as contaminated medical devices. More generally, typing provided important insights into fungal outbreak characteristics and helped to implement appropriate measures to control fungal infections, which are often severe, progress rapidly, and are difficult to diagnose and treat.

A novel approach for detecting multiple rumor sources in networks with partial observations

Locating source of information diffusion in networks has very important applications such as locating the sources of epidemics, news/rumors in social networks or online computer virus. In this paper, we consider detecting multiple rumor sources from a deterministic point of view by modeling it as the set resolving set (SRS) problem. Let G be a network on n nodes. A node subset K is an SRS of G if all detectable node sets are distinguishable by K. The problem of multiple rumor source detection (MRSD) in the network can be modeled as finding an SRS K with the smallest cardinality. In this paper, we propose a polynomial-time greedy algorithm for finding a minimum SRS in a general network, achieving performance ratio $$O(\ln n)$$O(lnn). This is the first work establishing a relation between the MRSD problem and a deterministic concept of SRS, and a first work to give the minimum SRS problem a polynomial-time performance-guaranteed approximation algorithm. Our framework suggests a robust and efficient approach for estimating multiple rumor sources independent of diffusion models in networks.

Identification of Patient Zero in Static and Temporal Networks: Robustness and Limitations.

Detection of patient zero can give new insights to epidemiologists about the nature of first transmissions into a population. In this Letter, we study the statistical inference problem of detecting the source of epidemics from a snapshot of spreading on an arbitrary network structure. By using exact analytic calculations and MonteCarlo estimators, we demonstrate the detectability limits for the susceptible-infected-recovered model, which primarily depend on the spreading process characteristics. Finally, we demonstrate the applicability of the approach in a case of a simulated sexually transmitted infection spreading over an empirical temporal network of sexual interactions.

Detection and characterisation of novel bocavirus (genus Bocaparvovirus) and gastroenteritis viruses from asymptomatic pigs in Ireland

BackgroundLivestock animals have been the assumed source of several human epidemics in recent years, for example, influenza H1N1, rotavirus G8/G9, and MERS-CoV. Surveillance of novel viruses in animals is essential to evaluate the risk to human and animal health and to determine any economic impact, for example, failure to thrive. There is a paucity of data regarding detection and characterisation of gastroenteritis viruses, particularly novel viruses, in porcines in Ireland. Recently, a number of small novel porcine DNA viruses have emerged globally, for example, torque teno sus virus, porcine bocavirus, and parvoviruses 2 & 4, and little is known about the biology and potential pathogenicity of these viruses. Bocaparvovirus is a genetically distinct group of viruses which has been recently detected in humans and animals.MethodsIn this study, the presence of gastroenteritis viruses (rotavirus A, porcine circovirus, adenovirus, and porcine bocavirus) was investigated in a selection of archived faecal samples from asymptomatic piglets from a commercial farm in Ireland. A total of 104 specimens were pooled and screened using conventional molecular techniques (PCR and RT-PCR), a subset of specimens (n=44) were then examined individually. Viral diversity was then investigated using statistical and phylogenetic techniques.ResultsInitial screening showed a high prevalence of PBoV in this farm, with the formation of three distinct groups in phylogenetic analysis. Other viruses were also investigated in this study with the first report of PCV, PAdV and lineage I G5 RVA in Ireland. Some specimens contained >1 virus, with statistical analysis indicating a strong correlation for mixed infections of PBoV and PAdV on this farm.ConclusionInvestigating the diversity of circulating enteric viruses on Irish porcine farms is important to improve the prophylactic tools available and to facilitate the early detection of changes in circulating viruses.