COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19.

COVID-19 has taken a huge toll on our lives over the last 3 years. Global initiatives put forward by all stakeholders are still in place to combat this pandemic and help us learn lessons for future ones. While the vaccine rollout was not able to curb the spread of the disease for all strains, the research community is still trying to develop effective therapeutics for COVID-19. Although Paxlovid and remdesivir have been approved by the FDA against COVID-19, they are not free of side effects. Therefore, the search for a therapeutic solution with high efficacy continues in the research community. To support this effort, in this latest version (v3) of COVID-19Base, we have summarized the biomedical entities linked to COVID-19 that have been highlighted in the scientific literature after the vaccine rollout. Eight different topic-specific dictionaries, i.e., gene, miRNA, lncRNA, PDB entries, disease, alternative medicines registered under clinical trials, drugs, and the side effects of drugs, were used to build this knowledgebase. We have introduced a BLSTM-based deep-learning model to predict the drug-disease associations that outperforms the existing model for the same purpose proposed in the earlier version of COVID-19Base. For the very first time, we have incorporated disease-gene, disease-miRNA, disease-lncRNA, and drug-PDB associations covering the largest number of biomedical entities related to COVID-19. We have provided examples of and insights into different biomedical entities covered in COVID-19Base to support the research community by incorporating all of these entities under a single platform to provide evidence-based support from the literature. COVID-19Base v3 can be accessed from: https://covidbase-v3.vercel.app/. The GitHub repository for the source code and data dictionaries is available to the community from: https://github.com/91Abdullah/covidbasev3.0.

Phylogenetic Analyses of SARS-CoV-2 Strains Reveal Its Link to the Spread of COVID-19 Across the Globe.

This study leveraged the phylogenetic analysis of more than 10K strains of novel coronavirus (SARS-CoV-2) from 67 countries. Due to the requirement of high-end computational power for phylogenetic analysis, we leverage a fast yet highly accurate alignment-free method to develop the phylogenetic tree out of all the strains of novel coronavirus. K-Means clustering and PCA-based dimension reduction technique were used to identify a representative strain from each location. The resulting phylogenetic tree was able to highlight evolutionary relationships of SARS-CoV-2 genome and, subsequently, linked to the interpretation of facts and figures across the globe for the spread of COVID-19. Our analysis revealed that the geographical boundaries could not be explained by the phylogenetic analysis of novel coronavirus as it placed different countries from Asia, Europe and the USA in very close proximity in the tree. Instead, the commute of people from one country to another is the key to the spread of COVID-19. We believe our study will support the policymakers to contain the spread of COVID-19 globally.

Linking Tweets Towards Geo-Localized Policies: COVID-19 Perspective.

COVID-19 pandemic is taking a toll on the social, economic, and psychological well-being of people. During this pandemic period, people have utilized social media platforms (e.g., Twitter) to communicate with each other and share their concerns and updates. In this study, we analyzed nearly 25M COVID-19 related tweets generated from 20 different countries and 28 states of USA over a month. We leveraged sentiment analysis and topic modeling over this collection and clustered different geolocations based on their sentiment. Our analysis identified 3 geo-clusters (country- and US state-based) based on public sentiment and discovered 15 topics that could be summarized under three main themes: government actions, medical issues, and people's mood during the home quarantine. The proposed computational pipeline has adequately captured the Twitter population's emotion and sentiment, which could be linked to government/policy makers' decisions and actions (or lack thereof). We believe that our analysis pipeline could be instrumental for the policymakers in sensing the public emotion/support with respect to the interventions/actions taken, for example, by the government instrumentality.

Vaccine Rollout and Shift in Public Sentiment: Twitter-Based Surveillance Study.

This study aims to find out the variation of Twitter users' sentiment before and after the COVID-19 vaccine rollout. We analyzed all COVID-19 related tweets posted on Twitter within two timeframes: September 2020 (T1) and March 2021 (T2). A total of 3 million tweets from over 132 thousand users were analyzed. We then categorized the users into two groups whose overall sentiment shifted positively or negatively from T1 to T2. Our analysis showed that 27% of users' sentiment shifted from T1 to T2 positively and the users were more confident about vaccine safety and efficacy. Users reported positive sentiments about travelling and the easing of lockdown measures. Also, 20.4% of the users' sentiment shifted negatively from T1 to T2. This group of Twitter users were more concerned about the adverse side effects of the vaccine, the pace of vaccine development as well as the emerging novel coronavirus variants. Interestingly, over half of the users' overall sentiment remained the same in both periods of T1 and T2, indicating indifference about vaccine rollout. We believe that our analysis will support the exploration of public reaction to COVID-19 vaccine rollout and assess policy makers' decision to combat the pandemic.

Clinical Trials on Alternative Medicines for COVID-19.

In this study, we addressed the alternative medications that have been targeted in the clinical trials (CTs) to be evidenced as an adjuvant treatment against COVID-19. Based on the outcomes from CTs, we found that dietary supplements such as Lactoferrin, and Probiotics (as SivoMixx) can play a role enhancing the immunity thus can be used as prophylactics against COVID-19 infection. Vitamin D was proven as an effective adjuvant treatment against COVID-19, while Vitamin C role is uncertain and needs more investigation. Herbals such as Guduchi Ghan Vati can be used as prophylactic, while Resveratrol can be used to reduce the hospitalization risk of COVID-19 patients. On the contrary, there were no clinical improvements demonstrated when using Cannabidiol. This study is a part of a two-phase research study. In the first phase, we gathered evidence-based information on alternative therapeutics for COVID-19 that are under CT. In the second phase, we plan to build a mobile health application that will provide evidence based alternative therapy information to health consumers.

Federated Learning and Internet of Medical Things - Opportunities and Challenges.

The recent advancements in artificial intelligence (AI) and the Internet of Medical Things (IoMT) have opened new horizons for healthcare technology. AI models, however, rely on large data that must be shared with the centralized entity developing the model. Data sharing leads to privacy preservation and legal issues. Federated Learning (FL) enables the training of AI models on distributed data. Hence, a large amount of IoMT data can be put into use without the need for sharing the data. This paper presents the opportunities offered by FL for privacy preservation in IoMT data. With FL, the complicated dynamics and agreements for data-sharing can be avoided. Furthermore, it describes the use cases of FL in facilitating collaborative efforts to develop AI for COVID-19 diagnosis. Since handling data from multiple sites poses its challenges, the paper also highlights the critical challenges associated with FL developments for IoMT data. Addressing these challenges will lead to gaining maximum benefit from data-driven AI technologies in IoMT.

Public Sentiment Towards Vaccination After COVID-19 Outbreak in the Arab World.

Public perception about vaccines is imperative for successful vaccination programs. This study aims to measure the shift of sentiment towards vaccines after the COVID-19 outbreak in the Arab-speaking population. The study used vaccine-related Arabic Tweets and analyzed the sentiment of users in two different time frames, before 2020 (T1) and after 2020 (T2). The analysis showed that in T1, 48.05% of tweets were positive, and 16.47% of tweets were negative. In T2, 43.03% of tweets were positive, and 20.56% of tweets were negative. Among the Twitter users, the sentiment of 15.92% users shifted towards positive, and the sentiment of 17.90% users shifted towards negative. Public sentiment that have shifted towards positive may be due to the hope of vaccine efficacy, whereas public sentiment that have shifted towards negative may be due to the concerns related to vaccine side effects and misinformation. This study can support policymakers in the Arab world to combat the COVID-19 pandemic by utilizing tools to understand public opinion and sentiment.

Gulf Cooperation Council Clinical Trials in the Pursuit of Medications for COVID-19.

Tremendous changes have been witnessed in the post-COVID-19 world. Global efforts were initiated to reach a successful treatment for this emerging disease. These efforts have focused on developing vaccinations and/or finding therapeutic agents that can be used to combat the virus or reduce its accompanying symptoms. Gulf Cooperation Council (GCC) countries have initiated efforts on many clinical trials to address the efficacy and the safety of several therapeutic agents used for COVID-19 treatment. In this article, we provide an overview of the GCC's clinical trials and associated drugs' discovery process in the pursuit of an effective medication for COVID-19.

miRCOVID-19: Potential Targets of Human miRNAs in SARS-CoV-2 for RNA-Based Drug Discovery.

Sense-antisense interactions of long and short RNAs in human cells are integral to post-transcriptional gene regulation, in particular that of mRNAs by microRNAs. Many viruses, including severe acute respiratory syndrome coronavirus 2 SARS-CoV-2 (the causative agent of coronavirus disease 2019, COVID-19), have RNA genomes, and interactions between host and viral RNAs, while known to be functional in other viral diseases, have not yet been investigated in COVID-19. To remedy this gap in knowledge, we present miRCOVID-19, a computational meta-analysis framework identifying the predicted binding sites of human microRNAs along the SARS-CoV-2 RNA genome. To highlight the potential relevance of SARS-CoV-2-genome-complementary miRNAs to COVID-19 pathogenesis, we assessed their expression in COVID-19-relevant tissues using public transcriptome data. miRCOVID-19 identified 14 high-confidence mature miRNAs that are highly likely to interact with the SARS-CoV-2 genome and are expressed in diverse respiratory epithelial and immune cell types that are relevant to COVID-19 pathogenesis. As a proof of principle, we have shown that human miR-122, a previously known co-factor of another RNA virus, the hepatitis C virus (HCV) whose genome it binds as a prerequisite for pathogenesis, was predicted to also bind the SARS-CoV-2 RNA genome with high affinity, suggesting the perspective of repurposing anti-HCV RNA-based drugs, such as Miravirsen, to treat COVID-19. Our study is the first to identify all high-confidence binding sites of human miRNAs in the SARS-CoV-2 genome using multiple tools. Our work directly facilitates experimental validation of the reported targets, which would accelerate RNA-based drug discovery for COVID-19 and has the potential to provide new avenues for treating symptomatic COVID-19, and block SARS-CoV-2 replication, in humans.

A Comprehensive Overview of the COVID-19 Literature: Machine Learning-Based Bibliometric Analysis.

BACKGROUND: Shortly after the emergence of COVID-19, researchers rapidly mobilized to study numerous aspects of the disease such as its evolution, clinical manifestations, effects, treatments, and vaccinations. This led to a rapid increase in the number of COVID-19-related publications. Identifying trends and areas of interest using traditional review methods (eg, scoping and systematic reviews) for such a large domain area is challenging. OBJECTIVE: We aimed to conduct an extensive bibliometric analysis to provide a comprehensive overview of the COVID-19 literature. METHODS: We used the COVID-19 Open Research Dataset (CORD-19) that consists of a large number of research articles related to all coronaviruses. We used a machine learning-based method to analyze the most relevant COVID-19-related articles and extracted the most prominent topics. Specifically, we used a clustering algorithm to group published articles based on the similarity of their abstracts to identify research hotspots and current research directions. We have made our software accessible to the community via GitHub. RESULTS: Of the 196,630 publications retrieved from the database, we included 28,904 in our analysis. The mean number of weekly publications was 990 (SD 789.3). The country that published the highest number of COVID-19-related articles was China (2950/17,270, 17.08%). The highest number of articles were published in bioRxiv. Lei Liu affiliated with the Southern University of Science and Technology in China published the highest number of articles (n=46). Based on titles and abstracts alone, we were able to identify 1515 surveys, 733 systematic reviews, 512 cohort studies, 480 meta-analyses, and 362 randomized control trials. We identified 19 different topics covered among the publications reviewed. The most dominant topic was public health response, followed by clinical care practices during the COVID-19 pandemic, clinical characteristics and risk factors, and epidemic models for its spread. CONCLUSIONS: We provide an overview of the COVID-19 literature and have identified current hotspots and research directions. Our findings can be useful for the research community to help prioritize research needs and recognize leading COVID-19 researchers, institutes, countries, and publishers. Our study shows that an AI-based bibliometric analysis has the potential to rapidly explore a large corpus of academic publications during a public health crisis. We believe that this work can be used to analyze other eHealth-related literature to help clinicians, administrators, and policy makers to obtain a holistic view of the literature and be able to categorize different topics of the existing research for further analyses. It can be further scaled (for instance, in time) to clinical summary documentation. Publishers should avoid noise in the data by developing a way to trace the evolution of individual publications and unique authors.

Toward Preparing a Knowledge Base to Explore Potential Drugs and Biomedical Entities Related to COVID-19: Automated Computational Approach.

BACKGROUND: Novel coronavirus disease 2019 (COVID-19) is taking a huge toll on public health. Along with the non-therapeutic preventive measurements, scientific efforts are currently focused, mainly, on the development of vaccines and pharmacological treatment with existing drugs. Summarizing evidences from scientific literatures on the discovery of treatment plan of COVID-19 under a platform would help the scientific community to explore the opportunities in a systematic fashion. OBJECTIVE: The aim of this study is to explore the potential drugs and biomedical entities related to coronavirus related diseases, including COVID-19, that are mentioned on scientific literature through an automated computational approach. METHODS: We mined the information from publicly available scientific literature and related public resources. Six topic-specific dictionaries, including human genes, human miRNAs, diseases, Protein Databank, drugs, and drug side effects, were integrated to mine all scientific evidence related to COVID-19. We employed an automated literature mining and labeling system through a novel approach to measure the effectiveness of drugs against diseases based on natural language processing, sentiment analysis, and deep learning. We also applied the concept of cosine similarity to confidently infer the associations between diseases and genes. RESULTS: Based on the literature mining, we identified 1805 diseases, 2454 drugs, 1910 genes that are related to coronavirus related diseases including COVID-19. Integrating the extracted information, we developed the first knowledgebase platform dedicated to COVID-19, which highlights potential list of drugs and related biomedical entities. For COVID-19, we highlighted multiple case studies on existing drugs along with a confidence score for their applicability in the treatment plan. Based on our computational method, we found Remdesivir, Statins, Dexamethasone, and Ivermectin could be considered as potential effective drugs to improve clinical status and lower mortality in patients hospitalized with COVID-19. We also found that Hydroxychloroquine could not be considered as an effective drug for COVID-19. The resulting knowledgebase is made available as an open source tool, named COVID-19Base. CONCLUSIONS: Proper investigation of the mined biomedical entities along with the identified interactions among those would help the research community to discover possible ways for the therapeutic treatment of COVID-19.