Zika virus (ZIKV), the causative agent of Zika fever in humans, is an RNA virus that belongs to the genus Flavivirus. Currently, there is no approved vaccine for clinical use to combat the ZIKV infection and contain the epidemic. Epitope-based peptide vaccines have a large untapped potential for boosting vaccination safety, cross-reactivity, and immunogenicity. Though many attempts have been made to develop vaccines for ZIKV, none of these have proved to be successful. Epitope-based peptide vaccines can act as powerful alternatives to conventional vaccines due to their low production cost, less reactogenic, and allergenic responses. For designing an effective and viable epitope-based peptide vaccine against this deadly virus, it is essential to select the antigenic T-cell epitopes since epitope-based vaccines are considered safe. The in silico machine-learning-based approach for ZIKV T-cell epitope prediction would save a lot of physical experimental time and efforts for speedy vaccine development compared to in vivo approaches. We hereby have trained a machine-learning-based computational model to predict novel ZIKV T-cell epitopes by employing physicochemical properties of amino acids. The proposed ensemble model based on a voting mechanism works by blending the predictions for each class (epitope or nonepitope) from each base classifier. Predictions obtained for each class by the individual classifier are summed up, and the class with the majority vote is predicted upon. An odd number of classifiers have been used to avoid the occurrence of ties in the voting. Experimentally determined ZIKV peptide sequences data set was collected from Immune Epitope Database and Analysis Resource (IEDB) repository. The data set consists of 3,519 sequences, of which 1,762 are epitopes and 1,757 are nonepitopes. The length of sequences ranges from 6 to 30 meter. For each sequence, we extracted 13 physicochemical features. The proposed ensemble model achieved sensitivity, specificity, Gini coefficient, AUC, precision, F-score, and accuracy of 0.976, 0.959, 0.993, 0.994, 0.989, 0.985, and 97.13%, respectively. To check the consistency of the model, we carried out five-fold cross-validation and an average accuracy of 96.072% is reported. Finally, a comparative analysis of the proposed model with existing methods has been carried out using a separate validation data set, suggesting the proposed ensemble model as a better model. The proposed ensemble model will help predict novel ZIKV vaccine candidates to save lives globally and prevent future epidemic-scale outbreaks.

The only part of an antigen (a protein molecule found on the surface of a pathogen) that is composed of epitopes specific to T and B cells is recognized by the human immune system (HIS). Identification of epitopes is considered critical for designing an epitope-based peptide vaccine (EBPV). Although there are a number of vaccine types, EBPVs have received less attention thus far. It is important to mention that EBPVs have a great deal of untapped potential for boosting vaccination safety—they are less expensive and take a short time to produce. Thus, in order to quickly contain global pandemics such as the ongoing outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), as well as epidemics and endemics, EBPVs are considered promising vaccine types. The high mutation rate of SARS-CoV-2 has posed a great challenge to public health worldwide because either the composition of existing vaccines has to be changed or a new vaccine has to be developed to protect against its different variants. In such scenarios, time being the critical factor, EBPVs can be a promising alternative. To design an effective and viable EBPV against different strains of a pathogen, it is important to identify the putative T- and B-cell epitopes. Using the wet-lab experimental approach to identify these epitopes is time-consuming and costly because the experimental screening of a vast number of potential epitope candidates is required. Fortunately, various available machine learning (ML)-based prediction methods have reduced the burden related to the epitope mapping process by decreasing the potential epitope candidate list for experimental trials. Moreover, these methods are also cost-effective, scalable, and fast. This paper presents a systematic review of various state-of-the-art and relevant ML-based methods and tools for predicting T- and B-cell epitopes. Special emphasis is placed on highlighting and analyzing various models for predicting epitopes of SARS-CoV-2, the causative agent of COVID-19. Based on the various methods and tools discussed, future research directions for epitope prediction are presented.

Zika fever is an infectious disease caused by the Zika virus (ZIKV). The disease is claiming millions of lives worldwide, primarily in developing countries. In addition to vector control strategies, the most effective way to prevent the spread of ZIKV infection is vaccination. There is no clinically approved vaccine to combat ZIKV infection and curb its pandemic. An epitope-based peptide vaccine (EBPV) is seen as a powerful alternative to conventional vaccinations because of its low production cost and short production time. Nonetheless, EBPVs have gotten less attention, despite the fact that they have a significant untapped potential for enhancing vaccine safety, immunogenicity, and cross-reactivity. Such a vaccine technology is based on target pathogen’s selected antigenic peptides called T-cell epitopes (TCE), which are synthesized chemically based on their amino acid sequences. The identification of TCEs using wet-lab experimental approach is challenging, expensive, and time-consuming. Therefore in this study, we present computational model for the prediction of ZIKV TCEs. The model proposed is an ensemble of decision trees that utilizes the physicochemical properties of amino acids. In this way a large amount of time and efforts would be saved for quick vaccine development. The peptide sequences dataset for model training was retrieved from Virus Pathogen Database and Analysis Resource (ViPR) database. The sequences dataset consist of experimentally verified T-cell epitopes (TCEs) and non-TCEs. The model demonstrated promising results when evaluated on test dataset. The evaluation metrics namely, accuracy, AUC, sensitivity, specificity, Gini and Mathew’s correlation coefficient (MCC) recorded values of 0.9789, 0.984, 0.981, 0.987, 0.974 and 0.948 respectively. The consistency and reliability of the model was assessed by carrying out the five (05)-fold cross-validation technique, and the mean accuracy of 0.97864 was reported. Finally, model was compared with standard machine learning (ML) algorithms and the proposed model outperformed all of them. The proposed model will aid in predicting novel and immunodominant TCEs of ZIKV. The predicted TCEs may have a high possibility of acting as prospective vaccine targets subjected to in-vivo and in-vitro scientific assessments, thereby saving lives worldwide, preventing future epidemic-scale outbreaks, and lowering the possibility of mutation escape.

An ongoing outbreak of coronavirus disease 2019 (COVID-19), caused by a single-stranded RNA virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a worldwide pandemic that continues to date. Vaccination has proven to be the most effective technique, by far, for the treatment of COVID-19 and to combat the outbreak. Among all vaccine types, epitope-based peptide vaccines have received less attention and hold a large untapped potential for boosting vaccine safety and immunogenicity. Peptides used in such vaccine technology are chemically synthesized based on the amino acid sequences of antigenic proteins (T-cell epitopes) of the target pathogen. Using wet-lab experiments to identify antigenic proteins is very difficult, expensive, and time-consuming. We hereby propose an ensemble machine learning (ML) model for the prediction of T-cell epitopes (also known as immune relevant determinants or antigenic determinants) against SARS-CoV-2, utilizing physicochemical properties of amino acids. To train the model, we retrieved the experimentally determined SARS-CoV-2 T-cell epitopes from Immune Epitope Database and Analysis Resource (IEDB) repository. The model so developed achieved accuracy, AUC (Area under the ROC curve), Gini, specificity, sensitivity, F-score, and precision of 98.20%, 0.991, 0.994, 0.971, 0.982, 0.990, and 0.981, respectively, using a test set consisting of SARS-CoV-2 peptides (T-cell epitopes and non-epitopes) obtained from IEDB. The average accuracy of 97.98% was recorded in repeated 5-fold cross validation. Its comparison with 05 robust machine learning classifiers and existing T-cell epitope prediction techniques, such as NetMHC and CTLpred, suggest the proposed work as a better model. The predicted epitopes from the current model could possess a high probability to act as potential peptide vaccine candidates subjected to in vitro and in vivo scientific assessments. The model developed would help scientific community working in vaccine development save time to screen the active T-cell epitope candidates of SARS-CoV-2 against the inactive ones.

The term heart-related disease is stated as the range of condition that impacts an individual heart negatively. In the current scenario, cardiovascular diseases are causing more deaths when compared with other ailments, it has been estimated that there are nearly 18 million deaths annually as per the recent report released by World Health Organization (WHO). It has been stated that unhealthy habits and other related aspects adopted by individuals are considered as the primary reasons for an increase in the risk of heart diseases. High cholesterol, eating more junk foods, hypertension, etc., created the issue related to heart diseases. Hence, addressing food quality and suggesting better eating habits enable individuals to enhance their living and support better health. The application of new technologies like machine learning, deep learning, and other models support doctors, nurses, and radiologists to predict heart disease effectively. Studies have stated that the various models are used mainly for the classification and forecasting of the diagnosis of heart-related diseases. The researchers have identified that critical algorithms like CART support the predictability of the disease by 93.3% whereas the conventional models possess vert less specificity. Furthermore, deep neural networks can be applied for analyzing and detecting heart failures effectively and supporting medical practitioners in making better and more critical clinical decisions making. The researchers focus on using a descriptive research study for performing the study; moreover, the researcher collates the data using the questionnaire method, which enables sourcing the critical information from the medical practitioners and supports in making critical data analysis effectively. The researchers also use secondary data modes for sourcing the information related to past studies on the related topic. The researchers use the frequency analysis, correlation analysis, and structural equation model analysis for performing the study, and the results are stated in detail in the respective sections.