Influenza Dataset Research Articles

FluPMT: Prediction of Predominant Strains of Influenza A Viruses via Multi-Task Learning.

Seasonal influenza vaccines play a crucial role in saving numerous lives annually. However, the constant evolution of the influenza A virus necessitates frequent vaccine updates to ensure its ongoing effectiveness. The decision to develop a new vaccine strain is generally based on the assessment of the current predominant strains. Nevertheless, the process of vaccine production and distribution is very time-consuming, leaving a window for the emergence of new variants that could decrease vaccine effectiveness, so predictions of influenza A virus evolution can inform vaccine evaluation and selection. Hence, we present FluPMT, a novel sequence prediction model that applies an encoder-decoder architecture to predict the hemagglutinin (HA) protein sequence of the upcoming season's predominant strain by capturing the patterns of evolution of influenza A viruses. Specifically, we employ time series to model the evolution of influenza A viruses, and utilize attention mechanisms to explore dependencies among residues of sequences. Additionally, antigenic distance prediction based on graph network representation learning is incorporated into the sequence prediction as an auxiliary task through a multi-task learning framework. Experimental results on two influenza datasets highlight the exceptional predictive performance of FluPMT, offering valuable insights into virus evolutionary dynamics, as well as vaccine evaluation and production.

Modeling epidemic dynamics using Graph Attention based Spatial Temporal networks.

The COVID-19 pandemic and influenza outbreaks have underscored the critical need for predictive models that can effectively integrate spatial and temporal dynamics to enable accurate epidemic forecasting. Traditional time-series analysis approaches have fallen short in capturing the intricate interplay between these factors. Recent advancements have witnessed the incorporation of graph neural networks and machine learning techniques to bridge this gap, enhancing predictive accuracy and providing novel insights into disease spread mechanisms. Notable endeavors include leveraging human mobility data, employing transfer learning, and integrating advanced models such as Transformers and Graph Convolutional Networks (GCNs) to improve forecasting performance across diverse geographies for both influenza and COVID-19. However, these models often face challenges related to data quality, model transferability, and potential overfitting, highlighting the necessity for more adaptable and robust approaches. This paper introduces the Graph Attention-based Spatial Temporal (GAST) model, which employs graph attention networks (GATs) to overcome these limitations by providing a nuanced understanding of epidemic dynamics through a sophisticated spatio-temporal analysis framework. Our contributions include the development and validation of the GAST model, demonstrating its superior forecasting capabilities for influenza and COVID-19 spread, with a particular focus on short-term, daily predictions. The model's application to both influenza and COVID-19 datasets showcases its versatility and potential to inform public health interventions across a range of infectious diseases.

CPMI: comprehensive neighborhood-based perturbed mutual information for identifying critical states of complex biological processes

BackgroundThere exists a critical transition or tipping point during the complex biological process. Such critical transition is usually accompanied by the catastrophic consequences. Therefore, hunting for the tipping point or critical state is of significant importance to prevent or delay the occurrence of catastrophic consequences. However, predicting critical state based on the high-dimensional small sample data is a difficult problem, especially for single-cell expression data.ResultsIn this study, we propose the comprehensive neighbourhood-based perturbed mutual information (CPMI) method to detect the critical states of complex biological processes. The CPMI method takes into account the relationship between genes and neighbours, so as to reduce the noise and enhance the robustness. This method is applied to a simulated dataset and six real datasets, including an influenza dataset, two single-cell expression datasets and three bulk datasets. The method can not only successfully detect the tipping points, but also identify their dynamic network biomarkers (DNBs). In addition, the discovery of transcription factors (TFs) which can regulate DNB genes and nondifferential ‘dark genes’ validates the effectiveness of our method. The numerical simulation verifies that the CPMI method is robust under different noise strengths and is superior to the existing methods on identifying the critical states.ConclusionsIn conclusion, we propose a robust computational method, i.e., CPMI, which is applicable in both the bulk and single cell datasets. The CPMI method holds great potential in providing the early warning signals for complex biological processes and enabling early disease diagnosis.

Deep-learning reconstruction of complex dynamical networks from incomplete data.

Reconstructing complex networks and predicting the dynamics are particularly challenging in real-world applications because the available information and data are incomplete. We develop a unified collaborative deep-learning framework consisting of three modules: network inference, state estimation, and dynamical learning. The complete network structure is first inferred and the states of the unobserved nodes are estimated, based on which the dynamical learning module is activated to determine the dynamical evolution rules. An alternating parameter updating strategy is deployed to improve the inference and prediction accuracy. Our framework outperforms baseline methods for synthetic and empirical networks hosting a variety of dynamical processes. A reciprocity emerges between network inference and dynamical prediction: better inference of network structure improves the accuracy of dynamical prediction, and vice versa. We demonstrate the superior performance of our framework on an influenza dataset consisting of 37 US States and a PM2.5 dataset covering 184 cities in China.

Machine Learning for COVID-19 and Influenza Classification during Coexisting Outbreaks

This study compares the performance of machine learning models for selecting COVID-19 and influenza tests during coexisting outbreaks in Brazil, avoiding the waste of resources in healthcare units. We used COVID-19 and influenza datasets from Brazil to train the Decision Tree (DT), Multilayer Perceptron (MLP), Gradient Boosting Machine (GBM), Random Forest (RF), eXtreme Gradient Boosting (XGBoost), K-Nearest Neighbors, Support Vector Machine (SVM), and Logistic Regression algorithms. Moreover, we tested the models using the 10-fold cross-validation method to increase confidence in the results. During the experiments, the GBM, DT, RF, XGBoost, and SVM models showed the best performances, with similar results. The high performance of tree-based models is relevant for the classification of COVID-19 and influenza because they are usually easier to interpret, positively impacting the decision-making of health professionals.

Laplace based Bayesian inference for ordinary differential equation models using regularized artificial neural networks

Parameter estimation and associated uncertainty quantification is an important problem in dynamical systems characterised by ordinary differential equation (ODE) models that are often nonlinear. Typically, such models have analytically intractable trajectories which result in likelihoods and posterior distributions that are similarly intractable. Bayesian inference for ODE systems via simulation methods require numerical approximations to produce inference with high accuracy at a cost of heavy computational power and slow convergence. At the same time, Artificial Neural Networks (ANN) offer tractability that can be utilized to construct an approximate but tractable likelihood and posterior distribution. In this paper we propose a hybrid approach, where Laplace-based Bayesian inference is combined with an ANN architecture for obtaining approximations to the ODE trajectories as a function of the unknown initial values and system parameters. Suitable choices of customized loss functions are proposed to fine tune the approximated ODE trajectories and the subsequent Laplace approximation procedure. The effectiveness of our proposed methods is demonstrated using an epidemiological system with non-analytical solutions—the Susceptible-Infectious-Removed (SIR) model for infectious diseases—based on simulated and real-life influenza datasets. The novelty and attractiveness of our proposed approach include (i) a new development of Bayesian inference using ANN architectures for ODE based dynamical systems, and (ii) a computationally fast posterior inference by avoiding convergence issues of benchmark Markov Chain Monte Carlo methods. These two features establish the developed approach as an accurate alternative to traditional Bayesian computational methods, with improved computational cost.

Comparison of pretrained transformer-based models for influenza and COVID-19 detection using social media text data in Saskatchewan, Canada.

The use of social media data provides an opportunity to complement traditional influenza and COVID-19 surveillance methods for the detection and control of outbreaks and informing public health interventions. The first aim of this study is to investigate the degree to which Twitter users disclose health experiences related to influenza and COVID-19 that could be indicative of recent plausible influenza cases or symptomatic COVID-19 infections. Second, we seek to use the Twitter datasets to train and evaluate the classification performance of Bidirectional Encoder Representations from Transformers (BERT) and variant language models in the context of influenza and COVID-19 infection detection. We constructed two Twitter datasets using a keyword-based filtering approach on English-language tweets collected from December 2016 to December 2022 in Saskatchewan, Canada. The influenza-related dataset comprised tweets filtered with influenza-related keywords from December 13, 2016, to March 17, 2018, while the COVID-19 dataset comprised tweets filtered with COVID-19 symptom-related keywords from January 1, 2020, to June 22, 2021. The Twitter datasets were cleaned, and each tweet was annotated by at least two annotators as to whether it suggested recent plausible influenza cases or symptomatic COVID-19 cases. We then assessed the classification performance of pre-trained transformer-based language models, including BERT-base, BERT-large, RoBERTa-base, RoBERT-large, BERTweet-base, BERTweet-covid-base, BERTweet-large, and COVID-Twitter-BERT (CT-BERT) models, on each dataset. To address the notable class imbalance, we experimented with both oversampling and undersampling methods. The influenza dataset had 1129 out of 6444 (17.5%) tweets annotated as suggesting recent plausible influenza cases. The COVID-19 dataset had 924 out of 11939 (7.7%) tweets annotated as inferring recent plausible COVID-19 cases. When compared against other language models on the COVID-19 dataset, CT-BERT performed the best, supporting the highest scores for recall (94.8%), F1(94.4%), and accuracy (94.6%). For the influenza dataset, BERTweet models exhibited better performance. Our results also showed that applying data balancing techniques such as oversampling or undersampling method did not lead to improved model performance. Utilizing domain-specific language models for monitoring users' health experiences related to influenza and COVID-19 on social media shows improved classification performance and has the potential to supplement real-time disease surveillance.

Revisiting classical SIR modelling in light of the COVID-19 pandemic.

Classical infectious disease models during epidemics have widespread usage, from predicting the probability of new infections to developing vaccination plans for informing policy decisions and public health responses. However, it is important to correctly classify reported data and understand how this impacts estimation of model parameters. The COVID-19 pandemic has provided an abundant amount of data that allow for thorough testing of disease modelling assumptions, as well as how we think about classical infectious disease modelling paradigms. We aim to assess the appropriateness of model parameter estimates and prediction results in classical infectious disease compartmental modelling frameworks given available data types (infected, active, quarantined, and recovered cases) for situations where just one data type is available to fit the model. Our main focus is on how model prediction results are dependent on data being assigned to the right model compartment. We first use simulated data to explore parameter reliability and prediction capability with three formulations of the classical Susceptible-Infected-Removed (SIR) modelling framework. We then explore two applications with reported data to assess which data and models are sufficient for reliable model parameter estimation and prediction accuracy: a classical influenza outbreak in a boarding school in England and COVID-19 data from the fall of 2020 in Missoula County, Montana, USA. We demonstrated the magnitude of parameter estimation errors and subsequent prediction errors resulting from data misclassification to model compartments with simulated data. We showed that prediction accuracy in each formulation of the classical disease modelling framework was largely determined by correct data classification versus misclassification. Using a classical example of influenza epidemics in an England boarding school, we argue that the Susceptible-Infected-Quarantined-Recovered (SIQR) model is more appropriate than the commonly employed SIR model given the data collected (number of active cases). Similarly, we show in the COVID-19 disease model example that reported active cases could be used inappropriately in the SIR modelling framework if treated as infected. We demonstrate the role of misclassification of disease data and thus the importance of correctly classifying reported data to the proper compartment using both simulated and real data. For both a classical influenza data set and a COVID-19 case data set, we demonstrate the implications of using the "right" data in the "wrong" model. The importance of correctly classifying reported data will have downstream impacts on predictions of number of infections, as well as minimal vaccination requirements.

The use of bioinformatics methods to identify the effects of SARS-CoV-2 and influenza viruses on the regulation of gene expression in patients.

SARS-CoV-2 infection is a respiratory infectious disease similar to influenza virus infection. Numerous studies have reported similarities and differences in the clinical manifestations, laboratory tests, and mortality between these two infections. However, the genetic effects of coronavirus and influenza viruses on the host that lead to these characteristics have rarely been reported. COVID-19 (GSE157103) and influenza (GSE111368, GSE101702) datasets were downloaded from the Gene Expression Ominbus (GEO) database. Differential gene, gene set enrichment, protein-protein interaction (PPI) network, gene regulatory network, and immune cell infiltration analyses were performed to identify the critical impact of COVID-19 and influenza viruses on the regulation of host gene expression. The number of differentially expressed genes in the COVID-19 patients was significantly higher than in the influenza patients. 22 common differentially expressed genes (DEGs) were identified between the COVID-19 and influenza datasets. The effects of the viruses on the regulation of host gene expression were determined using gene set enrichment and PPI network analyses. Five HUB genes were finally identified: IFI27, OASL, RSAD2, IFI6, and IFI44L. We identified five HUB genes between COVID-19 and influenza virus infection, which might be helpful in the diagnosis and treatment of COVID-19 and influenza. This knowledge may also guide future mechanistic studies that aim to identify pathogen-specific interventions.

Disease prediction by network information gain on a single sample basis

There are critical transition phenomena during the progression of many diseases. Such critical transitions are usually accompanied by catastrophic disease deterioration, and their prediction is of significant importance for disease prevention and treatment. However, predicting disease deterioration solely based on a single sample is a difficult problem. In this study, we presented the network information gain (NIG) method, for predicting the critical transitions or disease state based on network flow entropy (NFE) from omics data of each individual. NIG can not only efficiently predict disease deteriorations but also detect their dynamic network biomarkers (DNBs) on an individual basis and further identify potential therapeutic targets. The numerical simulation demonstrates the effectiveness of NIG. Moreover, our method was validated by successfully predicting disease deteriorations and identifying their potential therapeutic targets from four real omics datasets, i.e., an influenza dataset and three cancer datasets.

An Evaluation Framework for Comparing Epidemic Intelligence Systems

In the context of Epidemic Intelligence, many Event-Based Surveillance (EBS) systems have been proposed in the literature to promote the early identification and characterization of potential health threats from online sources of any nature. Each EBS system has its own surveillance definitions and priorities, therefore this makes the task of selecting the most appropriate EBS system for a given situation a challenge for end-users. In this work, we propose a new evaluation framework to address this issue. It first transforms the raw input epidemiological event data into a set of normalized events with multi-granularity, then conducts a descriptive retrospective analysis based on four evaluation objectives: spatial, temporal, thematic and source analysis. We illustrate its relevance by applying it to an Avian Influenza dataset collected by a selection of EBS systems, and show how our framework allows identifying their strengths and drawbacks in terms of epidemic surveillance.

Generalized likelihood ratio based risk‐adjusted control chart for zero‐inflated Poisson process

AbstractNowadays, statistical process control has been widely used to monitor processes in various fields. To monitor processes with a large number of zero observations by control charts, the zero‐inflated Poisson (ZIP) model has been adopted. Due to the heterogeneity of each sample in the process, several factors have been taken into account to predict values of two parameters in the ZIP model by risk adjustment. Instead of considering two parameters to be constant directly, risk‐adjusted ZIP control charts can provide more reasonable monitoring results than traditional ones. However, existing methods ignored the interaction between parameters in the ZIP model, which leads to some risk‐adjusted control charts unable to accurately estimate parameters to provide effective monitoring results. To address this problem, this paper presents a generalize likelihood ratio (GLR) based control chart to better monitor the risk‐adjusted ZIP process with EWMA scheme, which can detect the random shift in both parameters efficiently. In the simulation study, the proposed control chart is compared with another two existing control charts and shows superior performance on detecting various types of shifts in parameters. Finally, the proposed control chart is applied to the Hong Kong influenza datasets and the flight delay datasets to illustrate its effectiveness and utility.

IAV-CNN: A 2D Convolutional Neural Network Model to Predict Antigenic Variants of Influenza A Virus.

The rapid evolution of influenza viruses constantly leads to the emergence of novel influenza strains that are capable of escaping from population immunity. The timely determination of antigenic variants is critical to vaccine design. Empirical experimental methods like hemagglutination inhibition (HI) assays are time-consuming and labor-intensive, requiring live viruses. Recently, many computational models have been developed to predict the antigenic variants without considerations of explicitly modeling the interdependencies between the channels of feature maps. Moreover, the influenza sequences consisting of similar distribution of residues will have high degrees of similarity and will affect the prediction outcome. Consequently, it is challenging but vital to determine the importance of different residue sites and enhance the predictive performance of influenza antigenicity. We have proposed a 2D convolutional neural network (CNN) model to infer influenza antigenic variants (IAV-CNN). Specifically, we apply a new distributed representation of amino acids, named ProtVec that can be applied to a variety of downstream proteomic machine learning tasks. After splittings and embeddings of influenza strains, a 2D squeeze-and-excitation CNN architecture is constructed that enables networks to focus on informative residue features by fusing both spatial and channel-wise information with local receptive fields at each layer. Experimental results on three influenza datasets show IAV-CNN achieves state-of-the-art performance combining the new distributed representation with our proposed architecture. It outperforms both traditional machine algorithms with the same feature representations and the majority of existing models in the independent test data. Therefore we believe that our model can be served as a reliable and robust tool for the prediction of antigenic variants.

A Novel Stacking-Based Deterministic Ensemble Model for Infectious Disease Prediction

Infectious Disease Prediction aims to anticipate the aspects of both seasonal epidemics and future pandemics. However, a single model will most likely not capture all the dataset’s patterns and qualities. Ensemble learning combines multiple models to obtain a single prediction that uses the qualities of each model. This study aims to develop a stacked ensemble model to accurately predict the future occurrences of infectious diseases viewed at some point in time as epidemics, namely, dengue, influenza, and tuberculosis. The main objective is to enhance the prediction performance of the proposed model by reducing prediction errors. Autoregressive integrated moving average, exponential smoothing, and neural network autoregression are applied to the disease dataset individually. The gradient boosting model combines the regress values of the above three statistical models to obtain an ensemble model. The results conclude that the forecasting precision of the proposed stacked ensemble model is better than that of the standard gradient boosting model. The ensemble model reduces the prediction errors, root-mean-square error, for the dengue, influenza, and tuberculosis dataset by approximately 30%, 24%, and 25%, respectively.

Self-Attention-Based Deep Learning Network for Regional Influenza Forecasting.

Early prediction of influenza plays an important role in minimizing the damage caused, as it provides the resources and time needed to formulate preventive measures. Compared to traditional mechanistic approach, deep/machine learning-based models have demonstrated excellent forecasting performance by efficiently handling various data such as weather and internet data. However, due to the limited availability and reliability of such data, many forecasting models use only historical occurrence data and formulate the influenza forecasting as a multivariate time-series task. Recently, attention mechanisms have been exploited to deal with this issue by selecting valuable data in the input data and giving them high weights. Particularly, self-attention has shown its potential in various forecasting tasks by utilizing the predictive relationship between objects from the input data describing target objects. Hence, in this study, we propose a forecasting model based on self-attention for regional influenza forecasting, called SAIFlu-Net. The model exploits a long short-term memory network for extracting time-series patterns of each region and the self-attention mechanism to find the similarities between the occurrence patterns. To evaluate its performance, we conducted extensive experiments with existing forecasting models using weekly regional influenza datasets. The results show that the proposed model outperforms other models in terms of root mean square error and Pearson correlation coefficient.

VIRONIX: REMOTE SCREENING, MONITORING, AND TRIAGE OF VIRAL RESPIRATORY ILLNESS

TOPIC: Chest Infections TYPE: Original Investigations PURPOSE: Viral Respiratory illnesses such as Covid-19 and Influenza pose significant health challenges worldwide. There are more than 150M confirmed cases of Covid-19 with a reported 3.15M deaths (as of April, 2021). The WHO reports there to be ~ 1 billion influenza cases and 290-650K influenza-associated deaths annually. A signature feature of these illnesses is an early infection period that, if insufficiently recognized and controlled early, can lead to viral spread and avoidable morbidity/mortality. The need for personalized, remote care tools that facilitate early detection and triage of viral illness has never been greater. To address this gap, we developed an institutional software, Vironix, that uses machine-learned (ML) prediction models to enable real-time risk stratification and decision support for global organizations. METHODS: ML models were trained on clinical characteristic data from East and South Asia, Western Europe, and USA. Algorithms take an input of symptom, profile, biometric, and exposure data and return an assessment of disease severity. Covid-19 algorithms were validated on computer generated patient vigenttes and deployed in the Vironix web app among 22 participants in a small business commercial pilot for member self-screening. Members conducted daily health assessments and received personalized decision support while organization managers received work-from-home recommendations and compliant symptom monitoring without seeing member health data. For influenza, Vironix ML algorithms were tested on a dataset (with a 90/10 train test split) collected from one academic and two community emergency rooms from March 2014 to July 2017 (Hong et al.). RESULTS: ML-predictions showed 87.6% accuracy, 85.5% sensitivity, and 87.8% specificity in identifying severe Covid-19 presentations in an out-of-sample validation set of 5,000 patient cases. After 4-months pilot use, Vironix issued 14 stay-at-home and 10 healthcare escalation recommendations while maintaining 30-day and 7-day user retention of 66% and 72%, greatly exceeding common app adoption rates. ML predictions for the Influenza data set showed 67.8% accuracy, 71.7% sensitivity, and 65.4% specificity in identifying admissible or dischargeable presentations of influenza in an out-of-sample validation set of 56,000 patient cases. CONCLUSIONS: Covid-19 ML-severity assessments showed strong accuracy, sensitivity, and specificity in identifying severe clinical presentations. The deployed web-app showed high adoption with members receiving relevant decision support. Flu algorithm performance could be bolstered by inclusion of biometric features. Additional controlled trials could be conducted to establish validated markers of health improvement and early illness detection resulting from Vironix use. The overall methodology for mapping clinical characteristic data into patient scenarios for training ML classifiers of health deterioration is generalizable for a variety of potential software and hardware deployments across disease spaces. CLINICAL IMPLICATIONS: The technology detailed in this study represents a potential low cost, scalable, hardware/software agnostic, global solution for early detection and intervention on infectious respiratory illness. These solutions can be integrated into remote care and institutional wellness workflows to support public health initiatives. DISCLOSURES: No relevant relationships by Anna Berryman, source=Web Response No relevant relationships by Shreyas Iyer, source=Web Response No relevant relationships by Vinay Konda, source=Web Response Advisory Committee Member relationship with ABMRCC Please note: $1-$1000 by Chris Landon, source=Web Response, value=Consulting fee Removed 04/28/2021 by Chris Landon, source=Web Response Consultant relationship with ABM Respiratory Please note: 11/20 - date Added 04/30/2021 by Chris Landon, source=Web Response, value=Consulting fee no disclosure on file for Nicholas Mark; No relevant relationships by James Morrill, source=Web Response No relevant relationships by Sriram Ramanathan, source=Web Response Owner/Founder relationship with Vironix Health, Inc Please note: 05/2020 - Present Added 04/28/2021 by Sumanth Swaminathan, source=Web Response, value=Ownership interest Owner/Founder relationship with Vironix Health Please note: 04/2020-Now Added 05/10/2021 by Botros Toro, source=Web Response, value=Ownership interest Consultant relationship with Vironix Please note: 2019-present Added 04/28/2021 by Nicholas Wysham, source=Web Response, value=Ownership interest

English

Wellness depends on health and that, in turn, depends on the absence of disease. Analogous models based on physical laws have long been utilized by researchers to understand epidemic expansion in urban communities.  Perhaps the most significant of this class is the gravity model in which population size is equated with planetary mass and distance between cities to that separating planets. While the model assumes homogeneity among different bodies, cities or planets, in epidemiology the likelihood of disease spread may depend on other heterogeneous, non-constant factors. The study used a public dataset of H1N1 Influenza in 2009 as the focus. A natural log regression was applied in an attempt to sort the relative importance of gravity model variables as predictors of influenza occurrence and diffusion. It was found that while the model population size serves as a general predictor of disease expansion that distance failed as an indicator of disease dynamics. Furthermore, findings from the study show that disease progression was irregular and not, as one might expect from the gravity model, consistent in space or over time. The study concludes that the gravity model may serve only as a coarse predictor of disease expansion over time. By extension, this raises similar questions about other models in which homogeneity between populations or network of populations is assumed.   Key words: Gravity model, H1N1influenza, regression, spatial epidemiology.

Infectious Disease Relational Data Analysis Using String Grammar Non-Euclidean Relational Fuzzy C-Means.

Statistical analysis in infectious diseases is becoming more important, especially in prevention policy development. To achieve that, the epidemiology, a study of the relationship between the occurrence and who/when/where, is needed. In this paper, we develop the string grammar non-Euclidean relational fuzzy C-means (sgNERF-CM) algorithm to determine a relationship inside the data from the age, career, and month viewpoint for all provinces in Thailand for the dengue fever, influenza, and Hepatitis B virus (HBV) infection. The Dunn’s index is used to select the best models because of its ability to identify the compact and well-separated clusters. We compare the results of the sgNERF-CM algorithm with the string grammar relational hard C-means (sgRHCM) algorithm. In addition, their numerical counterparts, i.e., relational hard C-means (RHCM) and non-Euclidean relational fuzzy C-means (NERF-CM) algorithms are also applied in the comparison. We found that the sgNERF-CM algorithm is far better than the numerical counterparts and better than the sgRHCM algorithm in most cases. From the results, we found that the month-based dataset does not help in relationship-finding since the diseases tend to happen all year round. People from different age ranges in different regions in Thailand have different numbers of dengue fever infections. The occupations that have a higher chance to have dengue fever are student and teacher groups from the central, north-east, north, and south regions. Additionally, students in all regions, except the central region, have a high risk of dengue infection. For the influenza dataset, we found that a group of people with the age of more than 1 year to 64 years old has higher number of influenza infections in every province. Most occupations in all regions have a higher risk of infecting the influenza. For the HBV dataset, people in all regions with an age between 10 to 65 years old have a high risk in infecting the disease. In addition, only farmer and general contractor groups in all regions have high chance of infecting HBV as well.

VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all eight segments.

Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics. The evolution of influenza viruses remains to be the main obstacle in the effectiveness of antiviral treatments due to rapid mutations. Previous work has been investigated to reveal the determinants of virulence of the influenza A virus. To further facilitate flu surveillance, explicit detection of influenza virulence is crucial to protect public health from potential future pandemics. In this article, we propose a weighted ensemble convolutional neural network (CNN) for the virulence prediction of influenza A viruses named VirPreNet that uses all eight segments. Firstly, mouse lethal dose 50 is exerted to label the virulence of infections into two classes, namely avirulent and virulent. A numerical representation of amino acids named ProtVec is applied to the eight-segments in a distributed manner to encode the biological sequences. After splittings and embeddings of influenza strains, the ensemble CNN is constructed as the base model on the influenza dataset of each segment, which serves as the VirPreNet's main part. Followed by a linear layer, the initial predictive outcomes are integrated and assigned with different weights for the final prediction. The experimental results on the collected influenza dataset indicate that VirPreNet achieves state-of-the-art performance combining ProtVec with our proposed architecture. It outperforms baseline methods on the independent testing data. Moreover, our proposed model reveals the importance of PB2 and HA segments on the virulence prediction. We believe that our model may provide new insights into the investigation of influenza virulence. Codes and data to generate the VirPreNet are publicly available at https://github.com/Rayin-saber/VirPreNet. Supplementary data are available at Bioinformatics online.

Normal modes analysis and surface electrostatics of haemagglutinin proteins as fingerprints for high pathogenic type A influenza viruses

BackgroundType A influenza viruses circulate and spread among wild birds and mostly consist of low pathogenic strains. However, fast genome variation timely results in the insurgence of high pathogenic strains, which when infecting poultry birds may cause a million deaths and strong commercial damage. More importantly, the host shift may concern these viruses and sustained human-to-human transmission may result in a dangerous pandemic outbreak. Therefore, fingerprints specific to either low or high pathogenic strains may represent a very important tool for global surveillance.ResultsWe combined Normal Modes Analysis and surface electrostatic analysis of a mixed strain dataset of influenza A virus haemagglutinins from high and low pathogenic strains in order to infer specific fingerprints. Normal Modes Analysis sorted the strains in two different, homogeneous clusters; sorting was independent of clades and specific instead to high vs low pathogenicity. A deeper analysis of fluctuations and flexibility regions unveiled a special role for the 110-helix region. Specific sorting was confirmed by surface electrostatics analysis, which further allowed to focus on regions and mechanisms possibly crucial to the low-to-high transition.ConclusionsEvidence from previous work demonstrated that changes in surface electrostatics are associated with the evolution and spreading of avian influenza A virus clades, and seemingly involved also in the avian to mammalian host shift. This work shows that a combination of electrostatics and Normal Modes Analysis can also identify fingerprints specific to high and low pathogenicity. The possibility to predict which specific mutations may result in a shift to high pathogenicity may help in surveillance and vaccine development.