151
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Piccialli F, di Cola VS, Giampaolo F, Cuomo S. The Role of Artificial Intelligence in Fighting the COVID-19 Pandemic. INFORMATION SYSTEMS FRONTIERS : A JOURNAL OF RESEARCH AND INNOVATION 2021; 23:1467-1497. [PMID: 33935585 PMCID: PMC8072097 DOI: 10.1007/s10796-021-10131-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/28/2021] [Indexed: 05/25/2023]
Abstract
The first few months of 2020 have profoundly changed the way we live our lives and carry out our daily activities. Although the widespread use of futuristic robotaxis and self-driving commercial vehicles has not yet become a reality, the COVID-19 pandemic has dramatically accelerated the adoption of Artificial Intelligence (AI) in different fields. We have witnessed the equivalent of two years of digital transformation compressed into just a few months. Whether it is in tracing epidemiological peaks or in transacting contactless payments, the impact of these developments has been almost immediate, and a window has opened up on what is to come. Here we analyze and discuss how AI can support us in facing the ongoing pandemic. Despite the numerous and undeniable contributions of AI, clinical trials and human skills are still required. Even if different strategies have been developed in different states worldwide, the fight against the pandemic seems to have found everywhere a valuable ally in AI, a global and open-source tool capable of providing assistance in this health emergency. A careful AI application would enable us to operate within this complex scenario involving healthcare, society and research.
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Affiliation(s)
- Francesco Piccialli
- Department of Mathematics and Applications “R. Caccioppoli”, University of Naples Federico II, Naples, 80126 Italy
| | - Vincenzo Schiano di Cola
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, 80125 Italy
| | - Fabio Giampaolo
- Department of Mathematics and Applications “R. Caccioppoli”, University of Naples Federico II, Naples, 80126 Italy
| | - Salvatore Cuomo
- Department of Mathematics and Applications “R. Caccioppoli”, University of Naples Federico II, Naples, 80126 Italy
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152
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Singh N, Villoutreix BO. Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. Comput Struct Biotechnol J 2021; 19:2537-2548. [PMID: 33936562 PMCID: PMC8074526 DOI: 10.1016/j.csbj.2021.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines have been developed. But, while the race to find vaccines for COVID-19 has dominated the headlines, other types of therapeutic agents are being developed. In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides. We then give examples of studies that combined in silico and in vitro screening, either for drug repositioning purposes or to search for novel bioactive compounds. Finally, we question the overall lack of discussion and plan observed in academic research in many countries during this crisis and suggest that there is room for improvement.
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Affiliation(s)
- Natesh Singh
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Bruno O. Villoutreix
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
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153
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He Q, Mao Q, Zhang J, Bian L, Gao F, Wang J, Xu M, Liang Z. COVID-19 Vaccines: Current Understanding on Immunogenicity, Safety, and Further Considerations. Front Immunol 2021; 12:669339. [PMID: 33912196 PMCID: PMC8071852 DOI: 10.3389/fimmu.2021.669339] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
The world has entered the second wave of the COVID-19 pandemic, and its intensity is significantly higher than that of the first wave of early 2020. Many countries or regions have been forced to start the second round of lockdowns. To respond rapidly to this global pandemic, dozens of COVID-19 vaccine candidates have been developed and many are undergoing clinical testing. Evaluating and defining effective vaccine candidates for human use is crucial for prioritizing vaccination programs against COVID-19. In this review, we have summarized and analyzed the efficacy, immunogenicity and safety data from clinical reports on different COVID-19 vaccines. We discuss the various guidelines laid out for the development of vaccines and the importance of biological standards for comparing the performance of vaccines. Lastly, we highlight the key remaining challenges, possible strategies for addressing them and the expected improvements in the next generation of COVID-19 vaccines.
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Affiliation(s)
- Qian He
- National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- National Institutes for Food and Drug Control, Beijing, China
| | - Jialu Zhang
- National Institutes for Food and Drug Control, Beijing, China
| | - Lianlian Bian
- National Institutes for Food and Drug Control, Beijing, China
| | - Fan Gao
- National Institutes for Food and Drug Control, Beijing, China
| | - Junzhi Wang
- National Institutes for Food and Drug Control, Beijing, China
| | - Miao Xu
- National Institutes for Food and Drug Control, Beijing, China
| | - Zhenglun Liang
- National Institutes for Food and Drug Control, Beijing, China
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154
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Ghosh N, Sharma N, Saha I. Immunogenicity and antigenicity based T-cell and B-cell epitopes identification from conserved regions of 10664 SARS-CoV-2 genomes. INFECTION GENETICS AND EVOLUTION 2021; 92:104823. [PMID: 33819681 PMCID: PMC8017916 DOI: 10.1016/j.meegid.2021.104823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/23/2022]
Abstract
The surge of SARS-CoV-2 has created a wave of pandemic around the globe due to its high transmission rate. To contain this virus, researchers are working around the clock for a solution in the form of vaccine. Due to the impact of this pandemic, the economy and healthcare have immensely suffered around the globe. Thus, an efficient vaccine design is the need of the hour. Moreover, to have a generalised vaccine for heterogeneous human population, the virus genomes from different countries should be considered. Thus, in this work, we have performed genome-wide analysis of 10,664 SARS-CoV-2 genomes of 73 countries around the globe in order to identify the potential conserved regions for the development of peptide based synthetic vaccine viz. epitopes with high immunogenic and antigenic scores. In this regard, multiple sequence alignment technique viz. Clustal Omega is used to align the 10,664 SARS-CoV-2 virus genomes. Thereafter, entropy is computed for each genomic coordinate of the aligned genomes. The entropy values are then used to find the conserved regions. These conserved regions are refined based on the criteria that their lengths should be greater than or equal to 60 nt and their corresponding protein sequences are without any stop codons. Furthermore, Nucleotide BLAST is used to verify the specificity of the conserved regions. As a result, we have obtained 17 conserved regions that belong to NSP3, NSP4, NSP6, NSP8, RdRp, Helicase, endoRNAse, 2’-O-RMT, Spike glycoprotein, ORF3a protein, Membrane glycoprotein and Nucleocapsid protein. Finally, these conserved regions are used to identify the T-cell and B-cell epitopes with their corresponding immunogenic and antigenic scores. Based on these scores, the most immunogenic and antigenic epitopes are then selected for each of these 17 conserved regions. Hence, we have obtained 30 MHC-I and 24 MHC-II restricted T-cell epitopes with 14 and 13 unique HLA alleles and 21 B-cell epitopes for the 17 conserved regions. Moreover, for validating the relevance of these epitopes, the binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles. Also, the physico-chemical properties of the epitopes are reported along with Ramchandran plots and Z-Scores and the population coverage is shown as well. Overall, the analysis shows that the identified epitopes can be considered as potential candidates for vaccine design.
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Affiliation(s)
- Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
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155
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Sohail MS, Ahmed SF, Quadeer AA, McKay MR. In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives. Adv Drug Deliv Rev 2021; 171:29-47. [PMID: 33465451 PMCID: PMC7832442 DOI: 10.1016/j.addr.2021.01.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/31/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
Growing evidence suggests that T cells may play a critical role in combating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Hence, COVID-19 vaccines that can elicit a robust T cell response may be particularly important. The design, development and experimental evaluation of such vaccines is aided by an understanding of the landscape of T cell epitopes of SARS-CoV-2, which is largely unknown. Due to the challenges of identifying epitopes experimentally, many studies have proposed the use of in silico methods. Here, we present a review of the in silico methods that have been used for the prediction of SARS-CoV-2 T cell epitopes. These methods employ a diverse set of technical approaches, often rooted in machine learning. A performance comparison is provided based on the ability to identify a specific set of immunogenic epitopes that have been determined experimentally to be targeted by T cells in convalescent COVID-19 patients, shedding light on the relative performance merits of the different approaches adopted by the in silico studies. The review also puts forward perspectives for future research directions.
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Affiliation(s)
- Muhammad Saqib Sohail
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Syed Faraz Ahmed
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Matthew R McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
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156
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Uttarilli A, Amalakanti S, Kommoju PR, Sharma S, Goyal P, Manjunath GK, Upadhayay V, Parveen A, Tandon R, Prasad KS, Dakal TC, Ben Shlomo I, Yousef M, Neerathilingam M, Kumar A. Super-rapid race for saving lives by developing COVID-19 vaccines. J Integr Bioinform 2021; 18:27-43. [PMID: 33761582 PMCID: PMC8035961 DOI: 10.1515/jib-2021-0002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/03/2021] [Indexed: 12/24/2022] Open
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people and claimed thousands of lives. Starting in China, it is arguably the most precipitous global health calamity of modern times. The entire world has rocked back to fight against the disease and the COVID-19 vaccine is the prime weapon. Even though the conventional vaccine development pipeline usually takes more than a decade, the escalating daily death rates due to COVID-19 infections have resulted in the development of fast-track strategies to bring in the vaccine under a year’s time. Governments, companies, and universities have networked to pool resources and have come up with a number of vaccine candidates. Also, international consortia have emerged to address the distribution of successful candidates. Herein, we summarize these unprecedented developments in vaccine science and discuss the types of COVID-19 vaccines, their developmental strategies, and their roles as well as their limitations.
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Affiliation(s)
- Anusha Uttarilli
- Institute of Bioinformatics, International Technology Park, Bangalore560066, India.,Manipal Academy of Higher Education (MAHE), Manipal576104, Karnataka, India
| | - Sridhar Amalakanti
- Institute of Bioinformatics, International Technology Park, Bangalore560066, India
| | | | - Srihari Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore560066, India
| | - Pankaj Goyal
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh305817, Rajasthan, India
| | | | - Vineet Upadhayay
- Institute of Bioinformatics, International Technology Park, Bangalore560066, India
| | - Alisha Parveen
- Institute for Experimental Surgery, University of Rostock, RostockD18057, Germany
| | - Ravi Tandon
- School of Biotechnology, Jawaharlal Nehru University, New Delhi110067, India
| | - Kumar Suranjit Prasad
- Centre of Environmental Science, Institute of Interdisciplinary Studies, University of Allahabad (A Central University), Allahabad, Uttar Pradesh, India
| | - Tikam Chand Dakal
- Genome & Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur313001, Rajasthan, India
| | - Izhar Ben Shlomo
- Program of Emergency Medicine, Zefat Academic College, Safed13206, Israel
| | - Malik Yousef
- Department of Information Systems, Zefat Academic College, Zefat13206, Israel.,Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat13206, Israel
| | - Muniasamy Neerathilingam
- Institute of Bioinformatics, International Technology Park, Bangalore560066, India.,Manipal Academy of Higher Education (MAHE), Manipal576104, Karnataka, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore560066, India.,Manipal Academy of Higher Education (MAHE), Manipal576104, Karnataka, India
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157
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Chukwudozie OS, Duru VC, Ndiribe CC, Aborode AT, Oyebanji VO, Emikpe BO. The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment. Bioinform Biol Insights 2021; 15:11779322211002168. [PMID: 33795932 PMCID: PMC7968009 DOI: 10.1177/11779322211002168] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/14/2021] [Indexed: 12/16/2022] Open
Abstract
The application of bioinformatics to vaccine research and drug discovery has never been so essential in the fight against infectious diseases. The greatest combat of the 21st century against a debilitating disease agent SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus discovered in Wuhan, China, December 2019, has piqued an unprecedented usage of bioinformatics tools in deciphering the molecular characterizations of infectious pathogens. With the viral genome data of SARS-COV-2 been made available barely weeks after the reported outbreak, bioinformatics platforms have become an all-time critical tool to gain time in the fight against the disease pandemic. Before the outbreak, different platforms have been developed to explore antigenic epitopes, predict peptide-protein docking and antibody structures, and simulate antigen-antibody reactions and lots more. However, the advent of the pandemic witnessed an upsurge in the application of these pipelines with the development of newer ones such as the Coronavirus Explorer in the development of efficacious vaccines, drug repurposing, and/or discovery. In this review, we have explored the various pipelines available for use, their relevance, and limitations in the timely development of useful therapeutic candidates from genomic data knowledge to clinical therapy.
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Affiliation(s)
| | - Vincent C Duru
- Molecular Genetics Unit, Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Charlotte C Ndiribe
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | | | - Victor O Oyebanji
- Department of Veterinary Pathology, University of Ibadan, Ibadan, Nigeria
| | - Benjamin O Emikpe
- Department of Veterinary Pathology, University of Ibadan, Ibadan, Nigeria
- School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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158
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Zheng B, Cai Y, Zeng F, Lin M, Zheng J, Chen W, Qin G, Guo Y. An Interpretable Model-Based Prediction of Severity and Crucial Factors in Patients with COVID-19. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8840835. [PMID: 33708997 PMCID: PMC7930914 DOI: 10.1155/2021/8840835] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/01/2020] [Accepted: 02/04/2021] [Indexed: 01/08/2023]
Abstract
This study established an interpretable machine learning model to predict the severity of coronavirus disease 2019 (COVID-19) and output the most crucial deterioration factors. Clinical information, laboratory tests, and chest computed tomography (CT) scans at admission were collected. Two experienced radiologists reviewed the scans for the patterns, distribution, and CT scores of lung abnormalities. Six machine learning models were established to predict the severity of COVID-19. After parameter tuning and performance comparison, the optimal model was explained using Shapley Additive explanations to output the crucial factors. This study enrolled and classified 198 patients into mild (n = 162; 46.93 ± 14.49 years old) and severe (n = 36; 60.97 ± 15.91 years old) groups. The severe group had a higher temperature (37.42 ± 0.99°C vs. 36.75 ± 0.66°C), CT score at admission, neutrophil count, and neutrophil-to-lymphocyte ratio than the mild group. The XGBoost model ranked first among all models, with an AUC, sensitivity, and specificity of 0.924, 90.91%, and 97.96%, respectively. The early stage of chest CT, total CT score of the percentage of lung involvement, and age were the top three contributors to the prediction of the deterioration of XGBoost. A higher total score on chest CT had a more significant impact on the prediction. In conclusion, the XGBoost model to predict the severity of COVID-19 achieved excellent performance and output the essential factors in the deterioration process, which may help with early clinical intervention, improve prognosis, and reduce mortality.
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Affiliation(s)
- Bowen Zheng
- Department of Radiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yong Cai
- Department of CT, Maoming People's Hospital, Maoming, Guangdong 525000, China
| | - Fengxia Zeng
- Department of Radiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Min Lin
- Department of Radiology, Honghu People's Hospital, Honghu, Hubei 433220, China
| | - Jun Zheng
- Department of Radiology, Honghu People's Hospital, Honghu, Hubei 433220, China
| | - Weiguo Chen
- Department of Radiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Genggeng Qin
- Department of Radiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yi Guo
- Department of Medical Services Section, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
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159
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Bedi JS, Vijay D, Dhaka P, Singh Gill JP, Barbuddhe SB. Emergency preparedness for public health threats, surveillance, modelling & forecasting. Indian J Med Res 2021; 153:287-298. [PMID: 33906991 PMCID: PMC8204835 DOI: 10.4103/ijmr.ijmr_653_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 11/04/2022] Open
Abstract
In the interconnected world, safeguarding global health security is vital for maintaining public health and economic upliftment of any nation. Emergency preparedness is considered as the key to control the emerging public health challenges at both national as well as international levels. Further, the predictive information systems based on routine surveillance, disease modelling and forecasting play a pivotal role in both policy building and community participation to detect, prevent and respond to potential health threats. Therefore, reliable and timely forecasts of these untoward events could mobilize swift and effective public health responses and mitigation efforts. The present review focuses on the various aspects of emergency preparedness with special emphasis on public health surveillance, epidemiological modelling and capacity building approaches. Global coordination and capacity building, funding and commitment at the national and international levels, under the One Health framework, are crucial in combating global public health threats in a holistic manner.
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Affiliation(s)
- Jasbir Singh Bedi
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Deepthi Vijay
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Pankaj Dhaka
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Jatinder Paul Singh Gill
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Sukhadeo B. Barbuddhe
- Department of Meat Safety, ICAR-National Research Centre on Meat, Chengicherla, Hyderabad, Telangana, India
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160
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Majumdar S, Verma R, Saha A, Bhattacharyya P, Maji P, Surjit M, Kundu M, Basu J, Saha S. Perspectives About Modulating Host Immune System in Targeting SARS-CoV-2 in India. Front Genet 2021; 12:637362. [PMID: 33664772 PMCID: PMC7921795 DOI: 10.3389/fgene.2021.637362] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/19/2021] [Indexed: 12/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of coronavirus induced disease-2019 (COVID-19), is a type of common cold virus responsible for a global pandemic which requires immediate measures for its containment. India has the world's largest population aged between 10 and 40 years. At the same time, India has a large number of individuals with diabetes, hypertension and kidney diseases, who are at a high risk of developing COVID-19. A vaccine against the SARS-CoV-2, may offer immediate protection from the causative agent of COVID-19, however, the protective memory may be short-lived. Even if vaccination is broadly successful in the world, India has a large and diverse population with over one-third being below the poverty line. Therefore, the success of a vaccine, even when one becomes available, is uncertain, making it necessary to focus on alternate approaches of tackling the disease. In this review, we discuss the differences in COVID-19 death/infection ratio between urban and rural India; and the probable role of the immune system, co-morbidities and associated nutritional status in dictating the death rate of COVID-19 patients in rural and urban India. Also, we focus on strategies for developing masks, vaccines, diagnostics and the role of drugs targeting host-virus protein-protein interactions in enhancing host immunity. We also discuss India's strengths including the resources of medicinal plants, good food habits and the role of information technology in combating COVID-19. We focus on the Government of India's measures and strategies for creating awareness in the containment of COVID-19 infection across the country.
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Affiliation(s)
| | - Rohit Verma
- Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Avishek Saha
- Ubiquitous Analytical Techniques, CSIR-Central Scientific Instruments Organisation, Chandigarh, India
| | | | - Pradipta Maji
- Biomedical Imaging and Bioinformatics Lab, Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
| | - Milan Surjit
- Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | | | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata, India
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161
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Identification of HLA-A*02:01-restricted candidate epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2 that may be natural targets of CD8 + T cell recognition in vivo. J Virol 2021; 95:JVI.01837-20. [PMID: 33268522 PMCID: PMC8092843 DOI: 10.1128/jvi.01837-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
COVID-19 vaccines are being rapidly developed and human trials are underway. Almost all of these vaccines have been designed to induce antibodies targeting spike protein of SARS-CoV-2 in expectation of neutralizing activities. However, non-neutralizing antibodies are at risk of causing antibody-dependent enhancement. Further, the longevity of SARS-CoV-2-specific antibodies is very short. Therefore, in addition to antibody-induced vaccines, novel vaccines on the basis of SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs) should be considered in the vaccine development. Here, we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Eighty-two peptides were firstly predicted as epitope candidates on bioinformatics. Fifty-four in 82 peptides showed high or medium binding affinities to HLA-A*02:01. HLA-A*02:01 transgenic mice were then immunized with each of the 54 peptides encapsulated into liposomes. The intracellular cytokine staining assay revealed that 18 out of 54 peptides were CTL epitopes because of the induction of IFN-γ-producing CD8+ T cells. In the 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant CTL epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant over the other peptides. Surprisingly, all mice immunized with the liposomal 10 peptide mixture did not show the same reaction pattern to the 10 peptides. There were three response patterns, suggesting the existence of an immunodominance hierarchy following peptide vaccination, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines.IMPORTANCE For the development of vaccines based on SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs), we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Out of 82 peptides predicted on bioinformatics, 54 peptides showed good binding affinities to HLA-A*02:01. Using HLA-A*02:01 transgenic mice, 18 in 54 peptides were found to be CTL epitopes in the intracellular cytokine staining assay. Out of 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant. Surprisingly, all immunized mice did not show the same reaction pattern to the 10 peptides. There were three reaction patterns, suggesting the existence of an immunodominance hierarchy following peptide vaccination, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines.
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162
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von Kügelgen J, Gresele L, Schölkopf B. Simpson's Paradox in COVID-19 Case Fatality Rates: A Mediation Analysis of Age-Related Causal Effects. IEEE TRANSACTIONS ON ARTIFICIAL INTELLIGENCE 2021; 2:18-27. [PMID: 35233556 PMCID: PMC8791436 DOI: 10.1109/tai.2021.3073088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/28/2021] [Accepted: 04/04/2021] [Indexed: 11/08/2022]
Abstract
We point out an instantiation of Simpson's paradox in COVID-19 case fatality rates (cfrs): comparing a large-scale study from China (February 17) with early reports from Italy (March 9), we find that cfrs are lower in Italy for every age group, but higher overall. This phenomenon is explained by a stark difference in case demographic between the two countries. Using this as a motivating example, we introduce basic concepts from mediation analysis and show how these can be used to quantify different direct and indirect effects when assuming a coarse-grained causal graph involving country, age, and case fatality. We curate an age-stratified cfr dataset with [Formula: see text]750 k cases and conduct a case study, investigating total, direct, and indirect (age-mediated) causal effects between different countries and at different points in time. This allows us to separate age-related effects from others unrelated to age and facilitates a more transparent comparison of cfrs across countries at different stages of the COVID-19 pandemic. Using longitudinal data from Italy, we discover a sign reversal of the direct causal effect in mid-March, which temporally aligns with the reported collapse of the healthcare system in parts of the country. Moreover, we find that direct and indirect effects across 132 pairs of countries are only weakly correlated, suggesting that a country's policy and case demographic may be largely unrelated. We point out limitations and extensions for future work, and finally, discuss the role of causal reasoning in the broader context of using AI to combat the COVID-19 pandemic. Impact Statement-During a global pandemic, understanding the causal effects of risk factors such as age on COVID-19 fatality is an important scientific question. Since randomised controlled trials are typically infeasible or unethical in this context, causal investigations based on observational data-such as the one carried out in this article-will, therefore, be crucial in guiding our understanding of the available data. Causal inference, in particular mediation analysis, can be used to resolve apparent statistical paradoxes; help educate the public and decision-makers alike; avoid unsound comparisons; and answer a range of causal questions pertaining to the pandemic, subject to transparently stated assumptions. Our exposition helps clarify how mediation analysis can be used to investigate direct and indirect effects along different causal paths and thus serves as a stepping stone for future studies of other important risk factors for COVID-19 besides age.
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Affiliation(s)
- Julius von Kügelgen
- Max Planck Institute for Intelligent Systems72076TübingenGermany
- University of CambridgeCambridgeCB2 1PZU.K.
| | - Luigi Gresele
- Max Planck Institute for Intelligent Systems72076TübingenGermany
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163
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Bhattacharya S, Reddy Maddikunta PK, Pham QV, Gadekallu TR, Krishnan S SR, Chowdhary CL, Alazab M, Jalil Piran M. Deep learning and medical image processing for coronavirus (COVID-19) pandemic: A survey. SUSTAINABLE CITIES AND SOCIETY 2021; 65:102589. [PMID: 33169099 PMCID: PMC7642729 DOI: 10.1016/j.scs.2020.102589] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Since December 2019, the coronavirus disease (COVID-19) outbreak has caused many death cases and affected all sectors of human life. With gradual progression of time, COVID-19 was declared by the world health organization (WHO) as an outbreak, which has imposed a heavy burden on almost all countries, especially ones with weaker health systems and ones with slow responses. In the field of healthcare, deep learning has been implemented in many applications, e.g., diabetic retinopathy detection, lung nodule classification, fetal localization, and thyroid diagnosis. Numerous sources of medical images (e.g., X-ray, CT, and MRI) make deep learning a great technique to combat the COVID-19 outbreak. Motivated by this fact, a large number of research works have been proposed and developed for the initial months of 2020. In this paper, we first focus on summarizing the state-of-the-art research works related to deep learning applications for COVID-19 medical image processing. Then, we provide an overview of deep learning and its applications to healthcare found in the last decade. Next, three use cases in China, Korea, and Canada are also presented to show deep learning applications for COVID-19 medical image processing. Finally, we discuss several challenges and issues related to deep learning implementations for COVID-19 medical image processing, which are expected to drive further studies in controlling the outbreak and controlling the crisis, which results in smart healthy cities.
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Affiliation(s)
- Sweta Bhattacharya
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | - Quoc-Viet Pham
- Research Institute of Computer, Information and Communication, Pusan National University, Busan 46241, Republic of Korea
| | - Thippa Reddy Gadekallu
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Siva Rama Krishnan S
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Chiranji Lal Chowdhary
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Mamoun Alazab
- College of Engineering, IT & Environment, Charles Darwin University, Australia
| | - Md Jalil Piran
- Department of Computer Science and Engineering, Sejong University, 05006, Seoul, Republic of Korea
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164
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Rahmani A, Baee M, Saleki K, Moradi S, Nouri HR. Applying high throughput and comprehensive immunoinformatics approaches to design a trivalent subunit vaccine for induction of immune response against emerging human coronaviruses SARS-CoV, MERS-CoV and SARS-CoV-2. J Biomol Struct Dyn 2021; 40:6097-6113. [PMID: 33509045 PMCID: PMC7852294 DOI: 10.1080/07391102.2021.1876774] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Coronaviruses (CoVs) cause diseases such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19). Therefore, this study was conducted to combat major CoVs via a trivalent subunit vaccine, which was engineered by implementing sequences of spike (S) protein, nucleocapsid (N), envelope (E), membrane (M) protein, non-structural protein (nsp) 3, and nsp8 antigens. The CTL, HTL, MHC I, and IFN-γ epitopes were predicted via CTLPRED, IEDB, and IFN epitope servers, respectively. Also, to stimulate strong helper T lymphocytes (HTLs) responses, Pan HLA DR-binding epitope (PADRE) was used. Also, for boosting the immune response, β-defensin 2 was added to the construct as an adjuvant. Furthermore, TAT was applied to the vaccine to facilitate the intracellular delivery. Finally, TAT, adjuvant, PADRE, and selected epitopes were appropriately assembled. Based on the predicted epitopes, a trivalent multi-epitope vaccine with a molecular weight of 74.8 kDa was constructed. Further analyses predicted the molecule to be a strong antigen, and a non-allergenic and soluble protein. Secondary and tertiary structures were predicted. Additionally, analyses validated the stability of the proposed vaccine. Molecular docking and molecular dynamics simulation (MDS) showed binding affinity and stability of the vaccine-TLR3 complex was favorable. The predicted epitopes demonstrated a strong potential to stimulate T and B-cell mediated immune responses. Furthermore, codon optimization and in silico cloning guaranteed increased expression. In summary, investigations demonstrated that this next-generation approach might provide a new horizon for the development of a highly immunogenic vaccine against SARS‐CoV, MERS‐CoV, and SARS-CoV-2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Abolfazl Rahmani
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Masoud Baee
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Kiarash Saleki
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Saead Moradi
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Hamid Reza Nouri
- USERN Office, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.,Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
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165
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Wong NA, Saier MH. The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis. Int J Mol Sci 2021; 22:1308. [PMID: 33525632 PMCID: PMC7865831 DOI: 10.3390/ijms22031308] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a novel epidemic strain of Betacoronavirus that is responsible for the current viral pandemic, coronavirus disease 2019 (COVID-19), a global health crisis. Other epidemic Betacoronaviruses include the 2003 SARS-CoV-1 and the 2009 Middle East Respiratory Syndrome Coronavirus (MERS-CoV), the genomes of which, particularly that of SARS-CoV-1, are similar to that of the 2019 SARS-CoV-2. In this extensive review, we document the most recent information on Coronavirus proteins, with emphasis on the membrane proteins in the Coronaviridae family. We include information on their structures, functions, and participation in pathogenesis. While the shared proteins among the different coronaviruses may vary in structure and function, they all seem to be multifunctional, a common theme interconnecting these viruses. Many transmembrane proteins encoded within the SARS-CoV-2 genome play important roles in the infection cycle while others have functions yet to be understood. We compare the various structural and nonstructural proteins within the Coronaviridae family to elucidate potential overlaps and parallels in function, focusing primarily on the transmembrane proteins and their influences on host membrane arrangements, secretory pathways, cellular growth inhibition, cell death and immune responses during the viral replication cycle. We also offer bioinformatic analyses of potential viroporin activities of the membrane proteins and their sequence similarities to the Envelope (E) protein. In the last major part of the review, we discuss complement, stimulation of inflammation, and immune evasion/suppression that leads to CoV-derived severe disease and mortality. The overall pathogenesis and disease progression of CoVs is put into perspective by indicating several stages in the resulting infection process in which both host and antiviral therapies could be targeted to block the viral cycle. Lastly, we discuss the development of adaptive immunity against various structural proteins, indicating specific vulnerable regions in the proteins. We discuss current CoV vaccine development approaches with purified proteins, attenuated viruses and DNA vaccines.
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Affiliation(s)
- Nicholas A. Wong
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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166
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Alafif T, Tehame AM, Bajaba S, Barnawi A, Zia S. Machine and Deep Learning towards COVID-19 Diagnosis and Treatment: Survey, Challenges, and Future Directions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18031117. [PMID: 33513984 PMCID: PMC7908539 DOI: 10.3390/ijerph18031117] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 12/13/2022]
Abstract
With many successful stories, machine learning (ML) and deep learning (DL) have been widely used in our everyday lives in a number of ways. They have also been instrumental in tackling the outbreak of Coronavirus (COVID-19), which has been happening around the world. The SARS-CoV-2 virus-induced COVID-19 epidemic has spread rapidly across the world, leading to international outbreaks. The COVID-19 fight to curb the spread of the disease involves most states, companies, and scientific research institutions. In this research, we look at the Artificial Intelligence (AI)-based ML and DL methods for COVID-19 diagnosis and treatment. Furthermore, in the battle against COVID-19, we summarize the AI-based ML and DL methods and the available datasets, tools, and performance. This survey offers a detailed overview of the existing state-of-the-art methodologies for ML and DL researchers and the wider health community with descriptions of how ML and DL and data can improve the status of COVID-19, and more studies in order to avoid the outbreak of COVID-19. Details of challenges and future directions are also provided.
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Affiliation(s)
- Tarik Alafif
- Computer Science Department, Jamoum University College, Umm Al-Qura University, Jamoum 25375, Saudi Arabia
- Correspondence:
| | - Abdul Muneeim Tehame
- Department of Software Engineering, Sir Syed University of Engineering and Technology, Karachi 75300, Pakistan;
| | - Saleh Bajaba
- Business Administration Department, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Ahmed Barnawi
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Saad Zia
- IT Department, Jeddah Cable Company, Jeddah 31248, Saudi Arabia;
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167
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Mottaqi MS, Mohammadipanah F, Sajedi H. Contribution of machine learning approaches in response to SARS-CoV-2 infection. INFORMATICS IN MEDICINE UNLOCKED 2021; 23:100526. [PMID: 33869730 PMCID: PMC8044633 DOI: 10.1016/j.imu.2021.100526] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
Problem The lately emerged SARS-CoV-2 infection, which has put the whole world in an aberrant demanding situation, has generated an urgent need for developing effective responses through artificial intelligence (AI). Aim This paper aims to overview the recent applications of machine learning techniques contributing to prevention, diagnosis, monitoring, and treatment of coronavirus disease (SARS-CoV-2). Methods A progressive investigation of the recent publications up to November 2020, related to AI approaches towards managing the challenges of COVID-19 infection was made. Results For patient diagnosis and screening, Convolutional Neural Network (CNN) and Support Vector Machine (SVM) are broadly applied for classification purposes. Moreover, Deep Neural Network (DNN) and homology modeling are the most used SARS-CoV-2 drug repurposing models. Conclusion While the fields of diagnosis of the SARS-CoV-2 infection by medical image processing and its dissemination pattern through machine learning have been sufficiently studied, some areas such as treatment outcome in patients and drug development need to be further investigated using AI approaches.
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Affiliation(s)
- Mohammad Sadeq Mottaqi
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Fatemeh Mohammadipanah
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Hedieh Sajedi
- Department of Computer Science, School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, 14155-6455, Tehran, Iran
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168
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Syeda HB, Syed M, Sexton KW, Syed S, Begum S, Syed F, Prior F, Yu F. Role of Machine Learning Techniques to Tackle the COVID-19 Crisis: Systematic Review. JMIR Med Inform 2021; 9:e23811. [PMID: 33326405 PMCID: PMC7806275 DOI: 10.2196/23811] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/27/2020] [Accepted: 11/15/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND SARS-CoV-2, the novel coronavirus responsible for COVID-19, has caused havoc worldwide, with patients presenting a spectrum of complications that have pushed health care experts to explore new technological solutions and treatment plans. Artificial Intelligence (AI)-based technologies have played a substantial role in solving complex problems, and several organizations have been swift to adopt and customize these technologies in response to the challenges posed by the COVID-19 pandemic. OBJECTIVE The objective of this study was to conduct a systematic review of the literature on the role of AI as a comprehensive and decisive technology to fight the COVID-19 crisis in the fields of epidemiology, diagnosis, and disease progression. METHODS A systematic search of PubMed, Web of Science, and CINAHL databases was performed according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines to identify all potentially relevant studies published and made available online between December 1, 2019, and June 27, 2020. The search syntax was built using keywords specific to COVID-19 and AI. RESULTS The search strategy resulted in 419 articles published and made available online during the aforementioned period. Of these, 130 publications were selected for further analyses. These publications were classified into 3 themes based on AI applications employed to combat the COVID-19 crisis: Computational Epidemiology, Early Detection and Diagnosis, and Disease Progression. Of the 130 studies, 71 (54.6%) focused on predicting the COVID-19 outbreak, the impact of containment policies, and potential drug discoveries, which were classified under the Computational Epidemiology theme. Next, 40 of 130 (30.8%) studies that applied AI techniques to detect COVID-19 by using patients' radiological images or laboratory test results were classified under the Early Detection and Diagnosis theme. Finally, 19 of the 130 studies (14.6%) that focused on predicting disease progression, outcomes (ie, recovery and mortality), length of hospital stay, and number of days spent in the intensive care unit for patients with COVID-19 were classified under the Disease Progression theme. CONCLUSIONS In this systematic review, we assembled studies in the current COVID-19 literature that utilized AI-based methods to provide insights into different COVID-19 themes. Our findings highlight important variables, data types, and available COVID-19 resources that can assist in facilitating clinical and translational research.
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Affiliation(s)
- Hafsa Bareen Syeda
- Department of Neurology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Mahanazuddin Syed
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Kevin Wayne Sexton
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Surgery, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Health Policy and Management, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Shorabuddin Syed
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Salma Begum
- Department of Information Technology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Farhanuddin Syed
- College of Medicine, Shadan Institute of Medical Sciences, Hyderabad, India
| | - Fred Prior
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Radiology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Feliciano Yu
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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169
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Heffron AS, McIlwain SJ, Amjadi MF, Baker DA, Khullar S, Sethi AK, Palmenberg AC, Shelef MA, O'Connor DH, Ong IM. The landscape of antibody binding in SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.10.10.334292. [PMID: 33052349 PMCID: PMC7553183 DOI: 10.1101/2020.10.10.334292] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The search for potential antibody-based diagnostics, vaccines, and therapeutics for pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has focused almost exclusively on the spike (S) and nucleocapsid (N) proteins. Coronavirus membrane (M), ORF3a, and ORF8 proteins are humoral immunogens in other coronaviruses (CoVs) but remain largely uninvestigated for SARS-CoV-2. Here we use ultradense peptide microarray mapping to show that SARS-CoV-2 infection induces robust antibody responses to epitopes throughout the SARS-CoV-2 proteome, particularly in M, in which one epitope achieved excellent diagnostic accuracy. We map 79 B cell epitopes throughout the SARS-CoV-2 proteome and demonstrate that antibodies that develop in response to SARS-CoV-2 infection bind homologous peptide sequences in the six other known human CoVs. We also confirm reactivity against four of our top-ranking epitopes by enzyme-linked immunosorbent assay (ELISA). Illness severity correlated with increased reactivity to nine SARS-CoV-2 epitopes in S, M, N, and ORF3a in our population. Our results demonstrate previously unknown, highly reactive B cell epitopes throughout the full proteome of SARS-CoV-2 and other CoV proteins.
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170
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Artificial Intelligence in Clinical Immunology. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_83-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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171
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Tayarani N MH. Applications of artificial intelligence in battling against covid-19: A literature review. CHAOS, SOLITONS, AND FRACTALS 2021; 142:110338. [PMID: 33041533 PMCID: PMC7532790 DOI: 10.1016/j.chaos.2020.110338] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/01/2020] [Indexed: 05/14/2023]
Abstract
Colloquially known as coronavirus, the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), that causes CoronaVirus Disease 2019 (COVID-19), has become a matter of grave concern for every country around the world. The rapid growth of the pandemic has wreaked havoc and prompted the need for immediate reactions to curb the effects. To manage the problems, many research in a variety of area of science have started studying the issue. Artificial Intelligence is among the area of science that has found great applications in tackling the problem in many aspects. Here, we perform an overview on the applications of AI in a variety of fields including diagnosis of the disease via different types of tests and symptoms, monitoring patients, identifying severity of a patient, processing covid-19 related imaging tests, epidemiology, pharmaceutical studies, etc. The aim of this paper is to perform a comprehensive survey on the applications of AI in battling against the difficulties the outbreak has caused. Thus we cover every way that AI approaches have been employed and to cover all the research until the writing of this paper. We try organize the works in a way that overall picture is comprehensible. Such a picture, although full of details, is very helpful in understand where AI sits in current pandemonium. We also tried to conclude the paper with ideas on how the problems can be tackled in a better way and provide some suggestions for future works.
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Affiliation(s)
- Mohammad-H Tayarani N
- Biocomputation Group, School of Computer Science, University of Hertfordshire, Hatfield, AL10 9AB, United Kingdom
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172
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Ciarambino T, Para O, Giordano M. Immune system and COVID-19 by sex differences and age. WOMEN'S HEALTH (LONDON, ENGLAND) 2021; 17:17455065211022262. [PMID: 34096383 PMCID: PMC8188967 DOI: 10.1177/17455065211022262] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/19/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022]
Abstract
In COVID-19 disease, are reported gender differences in relation to severity and death. The aim of this review is to highlight gender differences in the immune response to COVID-19. The included studies were identified using PubMed, until 30 October 2020. The search included the following keywords: SARS-CoV-2, COVID-19, gender, age, sex, and immune system. Literature described that females compared to males have greater inflammatory, antiviral, and humoral immune responses. In female, estrogen is a potential ally to alleviate SARS-COV-2 disease. In male, testosterone reduces vaccination response and depresses the cytokine response. In the older patients, and in particular, in female older patients, it has been reported a progressive functional decline in the immune systems. Differences by gender were reported in infection diseases, including SARS-CoV-2. These data should be confirmed by the other epidemiological studies.
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Affiliation(s)
- Tiziana Ciarambino
- Department of Internal Medicine, Marcianise Hospital, ASL Caserta, Italy
| | - Ombretta Para
- Department of Internal Medicine, Careggi Hospital, University of Florence, Florence, Italy
| | - Mauro Giordano
- Department of Internal Medicine, University of Campania, L. Vanvitelli, Naples, Italy
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173
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Nguyen DC, Ding M, Pathirana PN, Seneviratne A. Blockchain and AI-Based Solutions to Combat Coronavirus (COVID-19)-Like Epidemics: A Survey. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2021; 9:95730-95753. [PMID: 34812398 DOI: 10.20944/preprints202004.0325.v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/27/2021] [Indexed: 05/21/2023]
Abstract
The beginning of 2020 has seen the emergence of coronavirus outbreak caused by a novel virus called SARS-CoV-2. The sudden explosion and uncontrolled worldwide spread of COVID-19 show the limitations of existing healthcare systems in timely handling public health emergencies. In such contexts, innovative technologies such as blockchain and Artificial Intelligence (AI) have emerged as promising solutions for fighting coronavirus epidemic. In particular, blockchain can combat pandemics by enabling early detection of outbreaks, ensuring the ordering of medical data, and ensuring reliable medical supply chain during the outbreak tracing. Moreover, AI provides intelligent solutions for identifying symptoms caused by coronavirus for treatments and supporting drug manufacturing. Therefore, we present an extensive survey on the use of blockchain and AI for combating COVID-19 epidemics. First, we introduce a new conceptual architecture which integrates blockchain and AI for fighting COVID-19. Then, we survey the latest research efforts on the use of blockchain and AI for fighting COVID-19 in various applications. The newly emerging projects and use cases enabled by these technologies to deal with coronavirus pandemic are also presented. A case study is also provided using federated AI for COVID-19 detection. Finally, we point out challenges and future directions that motivate more research efforts to deal with future coronavirus-like epidemics.
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Affiliation(s)
- Dinh C Nguyen
- School of EngineeringDeakin University Waurn Ponds VIC 3216 Australia
| | - Ming Ding
- Data61CSIRO Eveleigh NSW 2015 Australia
| | | | - Aruna Seneviratne
- School of Electrical Engineering and TelecommunicationsUniversity of New South Wales (UNSW) Sydney NSW 2052 Australia
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174
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Ahuja V, Nair LV. Artificial Intelligence and technology in COVID Era: A narrative review. J Anaesthesiol Clin Pharmacol 2021; 37:28-34. [PMID: 34103818 PMCID: PMC8174437 DOI: 10.4103/joacp.joacp_558_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/19/2020] [Accepted: 12/31/2020] [Indexed: 12/19/2022] Open
Abstract
Application of artificial intelligence (AI) in the medical field during the coronavirus disease 2019 (COVID-19) era is being explored further due to its beneficial aspects such as self-reported data analysis, X-ray interpretation, computed tomography (CT) image recognition, and patient management. This narrative review article included published articles from MEDLINE/PubMed, Google Scholar and National Informatics Center egov mobile apps. The database was searched for "Artificial intelligence" and "COVID-19" and "respiratory care unit" written in the English language during a period of one year 2019-2020. The relevance of AI for patients is in hands of people with digital health tools, Aarogya setu app and Smartphone technology. AI shows about 95% accuracy in detecting COVID-19-specific chest findings. Robots with AI are being used for patient assessment and drug delivery to patients to avoid the spread of infection. The pandemic outbreak has replaced the classroom method of teaching with the online execution of teaching practices and simulators. AI algorithms have been used to develop major organ tissue characterization and intelligent pain management techniques for patients. The Blue-dot AI-based algorithm helps in providing early warning signs. The AI model automatically identifies a patient in respiratory distress based on face detection, face recognition, facial action unit detection, expression recognition, posture, extremity movement analysis, visitation frequency detection sound pressure, and light level detection. There is now no looking back as AI and machine learning are to stay in the field of training, teaching, patient care, and research in the future.
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Affiliation(s)
- Vanita Ahuja
- Department of Anaesthesia and Intensive Care, Government Medical College and Hospital, Sector 32 Chandigarh, India
| | - Lekshmi V. Nair
- Department of Anaesthesia and Intensive Care, Government Medical College and Hospital, Sector 32 Chandigarh, India
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175
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Chintagunta AD, M SK, Nalluru S, N. S. SK. Nanotechnology: an emerging approach to combat COVID-19. EMERGENT MATERIALS 2021; 4:119-130. [PMID: 33615141 PMCID: PMC7883336 DOI: 10.1007/s42247-021-00178-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 01/27/2021] [Indexed: 05/04/2023]
Abstract
The recent outbreak of coronavirus disease (COVID-19) has challenged the survival of human existence in the last 1 year. Frontline healthcare professionals were struggling in combating the pandemic situation and were continuously supported with literature, skill set, research activities, and technologies developed by various scientists/researchers all over the world. To handle the continuously mutating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requires amalgamation of conventional technology with emerging approaches. Nanotechnology is science, engineering, and technology dealing at the nanoscale level. It has made possible the development of nanomaterials, nano-biosensors, nanodrugs, and vaccines for diagnosis, therapy, and prevention of COVID-19. This review has elaborately highlighted the role of nanotechnology in developing various detection kits such as nanoparticle-assisted diagnostics, antibody assay, lateral flow immunoassay, nanomaterial biosensors, etc., in detection of SARS-CoV-2. Similarly, various advancements supervene through nanoparticle-based therapeutic drugs for inhibiting viral infection by blocking virus attachment/cell entry, multiplication/replication, and direct inactivation of the virus. Furthermore, information on vaccine development and the role of nanocarriers/nanoparticles were highlighted with a brief outlining of nanomaterial usage in sterilization and preventive mechanisms engineered to combat COVID-19 pandemic.
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Affiliation(s)
- Anjani Devi Chintagunta
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Andhra Pradesh 522213 India
| | - Sai Krishna M
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Andhra Pradesh 522213 India
| | - Sanjana Nalluru
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Andhra Pradesh 522213 India
| | - Sampath Kumar N. S.
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Andhra Pradesh 522213 India
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176
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Singh R, Singh PK, Kumar R, Kabir MT, Kamal MA, Rauf A, Albadrani GM, Sayed AA, Mousa SA, Abdel-Daim MM, Uddin MS. Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19. Front Pharmacol 2021. [PMID: 34054532 DOI: 10.3389/fphar2021652335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.
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Affiliation(s)
- Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Pradhyumna Kumar Singh
- Plant Molecular Biology and Biotechnology Division, Council of Scientific and Industrial Research- National Botanical Research Institute (CSIR-NBRI), Lucknow, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | | | - Mohammad Amjad Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Ghadeer M Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amany A Sayed
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Shaker A Mousa
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, United States
| | - Mohamed M Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
- Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
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177
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Ong E, Huang X, Pearce R, Zhang Y, He Y. Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering. Comput Struct Biotechnol J 2020; 19:518-529. [PMID: 33398234 PMCID: PMC7773544 DOI: 10.1016/j.csbj.2020.12.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 01/12/2023] Open
Abstract
The development of effective and safe vaccines is the ultimate way to efficiently stop the ongoing COVID-19 pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Built on the fact that SARS-CoV-2 utilizes the association of its Spike (S) protein with the human angiotensin-converting enzyme 2 (ACE2) receptor to invade host cells, we computationally redesigned the S protein sequence to improve its immunogenicity and antigenicity. Toward this purpose, we extended an evolutionary protein design algorithm, EvoDesign, to create thousands of stable S protein variants that perturb the core protein sequence but keep the surface conformation and B cell epitopes. The T cell epitope content and similarity scores of the perturbed sequences were calculated and evaluated. Out of 22,914 designs with favorable stability energy, 301 candidates contained at least two pre-existing immunity-related epitopes and had promising immunogenic potential. The benchmark tests showed that, although the epitope restraints were not included in the scoring function of EvoDesign, the top S protein design successfully recovered 31 out of the 32 major histocompatibility complex (MHC)-II T cell promiscuous epitopes in the native S protein, where two epitopes were present in all seven human coronaviruses. Moreover, the newly designed S protein introduced nine new MHC-II T cell promiscuous epitopes that do not exist in the wildtype SARS-CoV-2. These results demonstrated a new and effective avenue to enhance a target protein's immunogenicity using rational protein design, which could be applied for new vaccine design against COVID-19 and other pathogens.
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Affiliation(s)
- Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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178
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Malik YS, Sircar S, Bhat S, Ansari MI, Pande T, Kumar P, Mathapati B, Balasubramanian G, Kaushik R, Natesan S, Ezzikouri S, El Zowalaty ME, Dhama K. How artificial intelligence may help the Covid-19 pandemic: Pitfalls and lessons for the future. Rev Med Virol 2020; 31:1-11. [PMID: 33476063 PMCID: PMC7883226 DOI: 10.1002/rmv.2205] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 12/16/2022]
Abstract
The clinical severity, rapid transmission and human losses due to coronavirus disease 2019 (Covid‐19) have led the World Health Organization to declare it a pandemic. Traditional epidemiological tools are being significantly complemented by recent innovations especially using artificial intelligence (AI) and machine learning. AI‐based model systems could improve pattern recognition of disease spread in populations and predictions of outbreaks in different geographical locations. A variable and a minimal amount of data are available for the signs and symptoms of Covid‐19, allowing a composite of maximum likelihood algorithms to be employed to enhance the accuracy of disease diagnosis and to identify potential drugs. AI‐based forecasting and predictions are expected to complement traditional approaches by helping public health officials to select better response and preparedness measures against Covid‐19 cases. AI‐based approaches have helped address the key issues but a significant impact on the global healthcare industry is yet to be achieved. The capability of AI to address the challenges may make it a key player in the operation of healthcare systems in future. Here, we present an overview of the prospective applications of the AI model systems in healthcare settings during the ongoing Covid‐19 pandemic.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India.,College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Mohd Ikram Ansari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Tripti Pande
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University, Noida, Uttar Pradesh, India
| | - Basavaraj Mathapati
- Polio Virus Group, Microbial Containment Complex, I.C.M.R. National Institute of Virology, Pune, Maharashtra, India
| | - Ganesh Balasubramanian
- Laboratory Division, Indian Council of Medical Research -National Institute of Epidemiology, Ministry of Health & Family Welfare, Chennai, Tamil Nadu, India
| | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa, Japan
| | | | - Sayeh Ezzikouri
- Viral Hepatitis Laboratory, Virology Unit, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Mohamed E El Zowalaty
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
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179
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Ghosh N, Sharma N, Saha I, Saha S. Genome-wide analysis of Indian SARS-CoV-2 genomes to identify T-cell and B-cell epitopes from conserved regions based on immunogenicity and antigenicity. Int Immunopharmacol 2020; 91:107276. [PMID: 33385714 PMCID: PMC7831793 DOI: 10.1016/j.intimp.2020.107276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/21/2020] [Accepted: 12/02/2020] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 has a high transmission rate and shows frequent mutations, thus making vaccine development an arduous task. However, researchers around the globe are working hard to find a solution e.g. synthetic vaccine. Here, we have performed genome-wide analysis of 566 Indian SARS-CoV-2 genomes to extract the potential conserved regions for identifying peptide based synthetic vaccines, viz. epitopes with high immunogenicity and antigenicity. In this regard, different multiple sequence alignment techniques are used to align the SARS-CoV-2 genomes separately. Subsequently, consensus conserved regions are identified after finding the conserved regions from each aligned result of alignment techniques. Further, the consensus conserved regions are refined considering that their lengths are greater than or equal to 60nt and their corresponding proteins are devoid of any stop codons. Subsequently, their specificity as query coverage are verified using Nucleotide BLAST. Finally, with these consensus conserved regions, T-cell and B-cell epitopes are identified based on their immunogenic and antigenic scores which are then used to rank the conserved regions. As a result, we have ranked 23 consensus conserved regions that are associated with different proteins. This ranking also resulted in 34 MHC-I and 37 MHC-II restricted T-cell epitopes with 16 and 19 unique HLA alleles and 29 B-cell epitopes. After ranking, the consensus conserved region from NSP3 gene is obtained that is highly immunogenic and antigenic. In order to judge the relevance of the identified epitopes, the physico-chemical properties and binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles.
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Affiliation(s)
- Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Orissa, India
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
| | - Sudipto Saha
- Division of Bioinformatics Bose Institute, Kolkata, West Bengal, India
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180
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Abd-Alrazaq A, Alajlani M, Alhuwail D, Schneider J, Al-Kuwari S, Shah Z, Hamdi M, Househ M. Artificial Intelligence in the Fight Against COVID-19: Scoping Review. J Med Internet Res 2020; 22:e20756. [PMID: 33284779 PMCID: PMC7744141 DOI: 10.2196/20756] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND In December 2019, COVID-19 broke out in Wuhan, China, leading to national and international disruptions in health care, business, education, transportation, and nearly every aspect of our daily lives. Artificial intelligence (AI) has been leveraged amid the COVID-19 pandemic; however, little is known about its use for supporting public health efforts. OBJECTIVE This scoping review aims to explore how AI technology is being used during the COVID-19 pandemic, as reported in the literature. Thus, it is the first review that describes and summarizes features of the identified AI techniques and data sets used for their development and validation. METHODS A scoping review was conducted following the guidelines of PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews). We searched the most commonly used electronic databases (eg, MEDLINE, EMBASE, and PsycInfo) between April 10 and 12, 2020. These terms were selected based on the target intervention (ie, AI) and the target disease (ie, COVID-19). Two reviewers independently conducted study selection and data extraction. A narrative approach was used to synthesize the extracted data. RESULTS We considered 82 studies out of the 435 retrieved studies. The most common use of AI was diagnosing COVID-19 cases based on various indicators. AI was also employed in drug and vaccine discovery or repurposing and for assessing their safety. Further, the included studies used AI for forecasting the epidemic development of COVID-19 and predicting its potential hosts and reservoirs. Researchers used AI for patient outcome-related tasks such as assessing the severity of COVID-19, predicting mortality risk, its associated factors, and the length of hospital stay. AI was used for infodemiology to raise awareness to use water, sanitation, and hygiene. The most prominent AI technique used was convolutional neural network, followed by support vector machine. CONCLUSIONS The included studies showed that AI has the potential to fight against COVID-19. However, many of the proposed methods are not yet clinically accepted. Thus, the most rewarding research will be on methods promising value beyond COVID-19. More efforts are needed for developing standardized reporting protocols or guidelines for studies on AI.
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Affiliation(s)
- Alaa Abd-Alrazaq
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Mohannad Alajlani
- Institute of Digital Healthcare, University of Warwick, Coventry, United Kingdom
| | - Dari Alhuwail
- Information Science Department, College of Life Sciences, Kuwait University, Kuwait, Kuwait
| | - Jens Schneider
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Saif Al-Kuwari
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Zubair Shah
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Mounir Hamdi
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Mowafa Househ
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
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181
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Rasheed J, Jamil A, Hameed AA, Aftab U, Aftab J, Shah SA, Draheim D. A survey on artificial intelligence approaches in supporting frontline workers and decision makers for the COVID-19 pandemic. CHAOS, SOLITONS, AND FRACTALS 2020; 141:110337. [PMID: 33071481 PMCID: PMC7547637 DOI: 10.1016/j.chaos.2020.110337] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/01/2020] [Indexed: 05/04/2023]
Abstract
While the world has experience with many different types of infectious diseases, the current crisis related to the spread of COVID-19 has challenged epidemiologists and public health experts alike, leading to a rapid search for, and development of, new and innovative solutions to combat its spread. The transmission of this virus has infected more than 18.92 million people as of August 6, 2020, with over half a million deaths across the globe; the World Health Organization (WHO) has declared this a global pandemic. A multidisciplinary approach needs to be followed for diagnosis, treatment and tracking, especially between medical and computer sciences, so, a common ground is available to facilitate the research work at a faster pace. With this in mind, this survey paper aimed to explore and understand how and which different technological tools and techniques have been used within the context of COVID-19. The primary contribution of this paper is in its collation of the current state-of-the-art technological approaches applied to the context of COVID-19, and doing this in a holistic way, covering multiple disciplines and different perspectives. The analysis is widened by investigating Artificial Intelligence (AI) approaches for the diagnosis, anticipate infection and mortality rate by tracing contacts and targeted drug designing. Moreover, the impact of different kinds of medical data used in diagnosis, prognosis and pandemic analysis is also provided. This review paper covers both medical and technological perspectives to facilitate the virologists, AI researchers and policymakers while in combating the COVID-19 outbreak.
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Affiliation(s)
- Jawad Rasheed
- Department of Computer Engineering, Istanbul Sabahattin Zaim University, Istanbul 34303, Turkey
| | - Akhtar Jamil
- Department of Computer Engineering, Istanbul Sabahattin Zaim University, Istanbul 34303, Turkey
| | - Alaa Ali Hameed
- Department of Computer Engineering, Istanbul Sabahattin Zaim University, Istanbul 34303, Turkey
| | - Usman Aftab
- Department of Pharmacology, University of Health Sciences, Lahore 54700, Pakistan
| | - Javaria Aftab
- Department of Chemistry, Istanbul Technical University, Istanbul 34467, Turkey
| | - Syed Attique Shah
- Department of IT, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta 87300, Pakistan
| | - Dirk Draheim
- Information Systems Group, Tallinn University of Technology, Akadeemia tee 15a, 12618, Tallinn, Estonia
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182
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Rastogi M, Pandey N, Shukla A, Singh SK. SARS coronavirus 2: from genome to infectome. Respir Res 2020; 21:318. [PMID: 33261606 PMCID: PMC7706175 DOI: 10.1186/s12931-020-01581-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/22/2020] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the group of Betacoronaviruses. The SARS-CoV-2 is closely related to SARS-CoV-1 and probably originated either from bats or pangolins. SARS-CoV-2 is an etiological agent of COVID-19, causing mild to severe respiratory disease which escalates to acute respiratory distress syndrome (ARDS) or multi-organ failure. The virus was first reported from the animal market in Hunan, Hubei province of China in the month of December, 2019, and was rapidly transmitted from animal to human and human-to-human. The human-to-human transmission can occur directly or via droplets generated during coughing and sneezing. Globally, around 53.9 million cases of COVID-19 have been registered with 1.31 million confirmed deaths. The people > 60 years, persons suffering from comorbid conditions and immunocompromised individuals are more susceptible to COVID-19 infection. The virus primarily targets the upper and the lower respiratory tract and quickly disseminates to other organs. SARS-CoV-2 dysregulates immune signaling pathways which generate cytokine storm and leads to the acute respiratory distress syndrome and other multisystemic disorders.
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Affiliation(s)
- Meghana Rastogi
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Neha Pandey
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Astha Shukla
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sunit K Singh
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
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183
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Muhammad LJ, Algehyne EA, Usman SS, Ahmad A, Chakraborty C, Mohammed IA. Supervised Machine Learning Models for Prediction of COVID-19 Infection using Epidemiology Dataset. ACTA ACUST UNITED AC 2020; 2:11. [PMID: 33263111 PMCID: PMC7694891 DOI: 10.1007/s42979-020-00394-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 11/05/2020] [Indexed: 12/15/2022]
Abstract
COVID-19 or 2019-nCoV is no longer pandemic but rather endemic, with more than 651,247 people around world having lost their lives after contracting the disease. Currently, there is no specific treatment or cure for COVID-19, and thus living with the disease and its symptoms is inevitable. This reality has placed a massive burden on limited healthcare systems worldwide especially in the developing nations. Although neither an effective, clinically proven antiviral agents' strategy nor an approved vaccine exist to eradicate the COVID-19 pandemic, there are alternatives that may reduce the huge burden on not only limited healthcare systems but also the economic sector; the most promising include harnessing non-clinical techniques such as machine learning, data mining, deep learning and other artificial intelligence. These alternatives would facilitate diagnosis and prognosis for 2019-nCoV pandemic patients. Supervised machine learning models for COVID-19 infection were developed in this work with learning algorithms which include logistic regression, decision tree, support vector machine, naive Bayes, and artificial neutral network using epidemiology labeled dataset for positive and negative COVID-19 cases of Mexico. The correlation coefficient analysis between various dependent and independent features was carried out to determine a strength relationship between each dependent feature and independent feature of the dataset prior to developing the models. The 80% of the training dataset were used for training the models while the remaining 20% were used for testing the models. The result of the performance evaluation of the models showed that decision tree model has the highest accuracy of 94.99% while the Support Vector Machine Model has the highest sensitivity of 93.34% and Naïve Bayes Model has the highest specificity of 94.30%.
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Affiliation(s)
- L J Muhammad
- Department of Mathematics and Computer Science, Faculty of Science, Federal University of Kashere, P.M.B. 0182, Gombe, Nigeria
| | - Ebrahem A Algehyne
- Department of Mathematics, University of Tabuk, Tabuk, 71491 Saudi Arabia
| | - Sani Sharif Usman
- Department of Biological Sciences, Faculty of Science, Federal University of Kashere, P.M.B. 0182, Gombe, Nigeria
| | - Abdulkadir Ahmad
- Department of Computer Science, Kano University of Science and Technology, Wudil, Kano Nigeria
| | - Chinmay Chakraborty
- Department of Electronics and Communication Engineering, Birla Institute of Technology, Ranchi, Jharkhand India
| | - I A Mohammed
- Computer Science Department, Yobe StateUniversity, Damaturu, Yobe State Nigeria
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184
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Abstract
The COVID-19 pandemic has lead to catastrophic number of deaths and revealed that much work still remains with data and artificial intelligence. To fully comprehend the dynamics of a pandemic with relevance to artificial intelligence, a primer on global health concepts is first presented. Following this, various aspects of diagnosis and therapy and the relationship to artificial intelligence are presented along with a future projection of an ideal deployment of artificial intelligence in a pandemic. Final thoughts are made about lessons learned and what lies ahead.
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Affiliation(s)
- Anthony C Chang
- The Sharon Disney Lund, Medical Intelligence and Innovation Institute (MI3), Children's Hospital of Orange County, USA
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185
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Affiliation(s)
- Neelima Arora
- Centre for Biotechnology, Institute of Science & Technology, JawaharLal Nehru Technological University, Hyderabad 500085, Telangana, India
| | - Amit K Banerjee
- Biology Division, Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India
| | - Mangamoori L Narasu
- Centre for Biotechnology, Institute of Science & Technology, JawaharLal Nehru Technological University, Hyderabad 500085, Telangana, India
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186
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Chen W. Promise and challenges in the development of COVID-19 vaccines. Hum Vaccin Immunother 2020; 16:2604-2608. [PMID: 32703069 PMCID: PMC7733917 DOI: 10.1080/21645515.2020.1787067] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/08/2020] [Indexed: 12/23/2022] Open
Abstract
The pandemic outbreak of COVID-19, caused by coronavirus SARS-CoV-2, created an unprecedented challenge to global public health system and biomedical community. Vaccination is an effective way to prevent viral infection, stop its transmission, and develop herd immunity. Rapid progress and advances have been made to date in the development of COVID-19 vaccines. Currently, more than 115 vaccine candidates have been developed from different technology platforms with several of them in clinical trials. Most of those vaccine candidates are developed based on the experience with other coronaviruses with an aim to induce neutralizing antibodies against the viral spike protein or its different receptor binding domains. Here, we discuss the promise, potential scientific challenges, and future directions for the development of a safe and effective COVID-19 vaccine. We also emphasize the importance of a better understanding of the infection pathogenesis and host defense mechanisms against SARS-CoV-2 infection.
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Affiliation(s)
- Wangxue Chen
- Human Health Therapeutics Research Center (HHT), National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biology, Brock University, St. Catharines, Ontario, Canada
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187
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Rahman MA, Zaman N, Asyhari AT, Al-Turjman F, Alam Bhuiyan MZ, Zolkipli MF. Data-driven dynamic clustering framework for mitigating the adverse economic impact of Covid-19 lockdown practices. SUSTAINABLE CITIES AND SOCIETY 2020; 62:102372. [PMID: 32834935 PMCID: PMC7333601 DOI: 10.1016/j.scs.2020.102372] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 05/18/2023]
Abstract
The COVID-19 disease has once again reiterated the impact of pandemics beyond a biomedical event with potential rapid, dramatic, sweeping disruptions to the management, and conduct of everyday life. Not only the rate and pattern of contagion that threaten our sense of healthy living but also the safety measures put in place for containing the spread of the virus may require social distancing. Three different measures to counteract this pandemic situation have emerged, namely: (i) vaccination, (ii) herd immunity development, and (iii) lockdown. As the first measure is not ready at this stage and the second measure is largely considered unreasonable on the account of the gigantic number of fatalities, a vast majority of countries have practiced the third option despite having a potentially immense adverse economic impact. To mitigate such an impact, this paper proposes a data-driven dynamic clustering framework for moderating the adverse economic impact of COVID-19 flare-up. Through an intelligent fusion of healthcare and simulated mobility data, we model lockdown as a clustering problem and design a dynamic clustering algorithm for localized lockdown by taking into account the pandemic, economic and mobility aspects. We then validate the proposed algorithms by conducting extensive simulations using the Malaysian context as a case study. The findings signify the promises of dynamic clustering for lockdown coverage reduction, reduced economic loss, and military unit deployment reduction, as well as assess potential impact of uncooperative civilians on the contamination rate. The outcome of this work is anticipated to pave a way for significantly reducing the severe economic impact of the COVID-19 spreading. Moreover, the idea can be exploited for potentially the next waves of corona virus-related diseases and other upcoming viral life-threatening calamities.
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Affiliation(s)
- Md Arafatur Rahman
- Faculty of Computing, University Malaysia Pahang, Gambang 26300, Malaysia
- IBM CoE, Malaysia
| | | | - A Taufiq Asyhari
- School of Computing and Digital Technology, Birmingham City University, Millennium Point, Birmingham, B4 7XG, UK
| | - Fadi Al-Turjman
- Research Center for AI and IoT, Near East University, 99138 Nicosia, Turkey
| | - Md Zakirul Alam Bhuiyan
- Department of Computer and Information Sciences, Fordham University, New York, NY 10458, USA
| | - M F Zolkipli
- Faculty of Computing, University Malaysia Pahang, Gambang 26300, Malaysia
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188
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Jaiswal S, Kumar M, Mandeep, Sunita, Singh Y, Shukla P. Systems Biology Approaches for Therapeutics Development Against COVID-19. Front Cell Infect Microbiol 2020; 10:560240. [PMID: 33194800 PMCID: PMC7655984 DOI: 10.3389/fcimb.2020.560240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the systems biology approaches for promoting the development of new therapeutic drugs is attaining importance nowadays. The threat of COVID-19 outbreak needs to be vanished for global welfare, and every section of research is focusing on it. There is an opportunity for finding new, quick, and accurate tools for developing treatment options, including the vaccine against COVID-19. The review at this moment covers various aspects of pathogenesis and host factors for exploring the virus target and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers the extensive details of multiomics tools i.e., transcriptomics, proteomics, genomics, lipidomics, immunomics, and in silico computational modeling aiming towards the study of host-virus interactions in search of therapeutic targets against the COVID-19.
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Affiliation(s)
- Shweta Jaiswal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Mohit Kumar
- Soil Microbial Ecology and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, Delhi, India
- Department of Zoology, Hindu College, University of Delhi, Delhi, India
| | - Mandeep
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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189
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Black S, Bloom DE, Kaslow DC, Pecetta S, Rappuoli R. Transforming vaccine development. Semin Immunol 2020; 50:101413. [PMID: 33127296 PMCID: PMC7591868 DOI: 10.1016/j.smim.2020.101413] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 12/23/2022]
Abstract
The urgency to develop vaccines against Covid-19 is putting pressure on the long and expensive development timelines that are normally required for development of lifesaving vaccines. There is a unique opportunity to take advantage of new technologies, the smart and flexible design of clinical trials, and evolving regulatory science to speed up vaccine development against Covid-19 and transform vaccine development altogether.
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Affiliation(s)
- Steve Black
- Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - David E Bloom
- Harvard T.H. Chan School of Public Health, Harvard University, Boston MA 02115, USA
| | | | | | - Rino Rappuoli
- GSK, 53100 Siena, Italy; Imperial College London, London SW7 2AZ, UK.
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190
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Bird JJ, Barnes CM, Premebida C, Ekárt A, Faria DR. Country-level pandemic risk and preparedness classification based on COVID-19 data: A machine learning approach. PLoS One 2020; 15:e0241332. [PMID: 33112931 PMCID: PMC7592809 DOI: 10.1371/journal.pone.0241332] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 12/23/2022] Open
Abstract
In this work we present a three-stage Machine Learning strategy to country-level risk classification based on countries that are reporting COVID-19 information. A K% binning discretisation (K = 25) is used to create four risk groups of countries based on the risk of transmission (coronavirus cases per million population), risk of mortality (coronavirus deaths per million population), and risk of inability to test (coronavirus tests per million population). The four risk groups produced by K% binning are labelled as 'low', 'medium-low', 'medium-high', and 'high'. Coronavirus-related data are then removed and the attributes for prediction of the three types of risk are given as the geopolitical and demographic data describing each country. Thus, the calculation of class label is based on coronavirus data but the input attributes are country-level information regardless of coronavirus data. The three four-class classification problems are then explored and benchmarked through leave-one-country-out cross validation to find the strongest model, producing a Stack of Gradient Boosting and Decision Tree algorithms for risk of transmission, a Stack of Support Vector Machine and Extra Trees for risk of mortality, and a Gradient Boosting algorithm for the risk of inability to test. It is noted that high risk for inability to test is often coupled with low risks for transmission and mortality, therefore the risk of inability to test should be interpreted first, before consideration is given to the predicted transmission and mortality risks. Finally, the approach is applied to more recent risk levels to data from September 2020 and weaker results are noted due to the growth of international collaboration detracting useful knowledge from country-level attributes which suggests that similar machine learning approaches are more useful prior to situations later unfolding.
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Affiliation(s)
- Jordan J. Bird
- Aston Robotics, Vision, and Intelligent Systems Lab (ARVIS), School of Engineering and Applied Science, Aston University, Birmingham, United Kingdom
| | - Chloe M. Barnes
- Aston Robotics, Vision, and Intelligent Systems Lab (ARVIS), School of Engineering and Applied Science, Aston University, Birmingham, United Kingdom
| | - Cristiano Premebida
- Department of Electrical and Computer Engineering, Institute of Systems and Robotics, University of Coimbra, Coimbra, Portugal
| | - Anikó Ekárt
- Aston Robotics, Vision, and Intelligent Systems Lab (ARVIS), School of Engineering and Applied Science, Aston University, Birmingham, United Kingdom
| | - Diego R. Faria
- Aston Robotics, Vision, and Intelligent Systems Lab (ARVIS), School of Engineering and Applied Science, Aston University, Birmingham, United Kingdom
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191
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Chen J, See KC. Artificial Intelligence for COVID-19: Rapid Review. J Med Internet Res 2020; 22:e21476. [PMID: 32946413 PMCID: PMC7595751 DOI: 10.2196/21476] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/25/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND COVID-19 was first discovered in December 2019 and has since evolved into a pandemic. OBJECTIVE To address this global health crisis, artificial intelligence (AI) has been deployed at various levels of the health care system. However, AI has both potential benefits and limitations. We therefore conducted a review of AI applications for COVID-19. METHODS We performed an extensive search of the PubMed and EMBASE databases for COVID-19-related English-language studies published between December 1, 2019, and March 31, 2020. We supplemented the database search with reference list checks. A thematic analysis and narrative review of AI applications for COVID-19 was conducted. RESULTS In total, 11 papers were included for review. AI was applied to COVID-19 in four areas: diagnosis, public health, clinical decision making, and therapeutics. We identified several limitations including insufficient data, omission of multimodal methods of AI-based assessment, delay in realization of benefits, poor internal/external validation, inability to be used by laypersons, inability to be used in resource-poor settings, presence of ethical pitfalls, and presence of legal barriers. AI could potentially be explored in four other areas: surveillance, combination with big data, operation of other core clinical services, and management of patients with COVID-19. CONCLUSIONS In view of the continuing increase in the number of cases, and given that multiple waves of infections may occur, there is a need for effective methods to help control the COVID-19 pandemic. Despite its shortcomings, AI holds the potential to greatly augment existing human efforts, which may otherwise be overwhelmed by high patient numbers.
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Affiliation(s)
- Jiayang Chen
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kay Choong See
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Respiratory & Critical Care Medicine, Department of Medicine, National University Hospital, Singapore, Singapore
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192
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Dey L, Chakraborty S, Mukhopadhyay A. Machine learning techniques for sequence-based prediction of viral-host interactions between SARS-CoV-2 and human proteins. Biomed J 2020; 43:438-450. [PMID: 33036956 PMCID: PMC7470713 DOI: 10.1016/j.bj.2020.08.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/22/2020] [Accepted: 08/05/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND COVID-19 (Coronavirus Disease-19), a disease caused by the SARS-CoV-2 virus, has been declared as a pandemic by the World Health Organization on March 11, 2020. Over 15 million people have already been affected worldwide by COVID-19, resulting in more than 0.6 million deaths. Protein-protein interactions (PPIs) play a key role in the cellular process of SARS-CoV-2 virus infection in the human body. Recently a study has reported some SARS-CoV-2 proteins that interact with several human proteins while many potential interactions remain to be identified. METHOD In this article, various machine learning models are built to predict the PPIs between the virus and human proteins that are further validated using biological experiments. The classification models are prepared based on different sequence-based features of human proteins like amino acid composition, pseudo amino acid composition, and conjoint triad. RESULT We have built an ensemble voting classifier using SVMRadial, SVMPolynomial, and Random Forest technique that gives a greater accuracy, precision, specificity, recall, and F1 score compared to all other models used in the work. A total of 1326 potential human target proteins of SARS-CoV-2 have been predicted by the proposed ensemble model and validated using gene ontology and KEGG pathway enrichment analysis. Several repurposable drugs targeting the predicted interactions are also reported. CONCLUSION This study may encourage the identification of potential targets for more effective anti-COVID drug discovery.
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Affiliation(s)
- Lopamudra Dey
- Department of Computer Science & Engineering, Heritage Institute of Technology, Kolkata, India; Department of Information Technology, Techno Main, Saltlake, Kolkata, India; Department of. Computer Science & Engineering, University of Kalyani, Kalyani, India
| | - Sanjay Chakraborty
- Department of Computer Science & Engineering, Heritage Institute of Technology, Kolkata, India; Department of Information Technology, Techno Main, Saltlake, Kolkata, India; Department of. Computer Science & Engineering, University of Kalyani, Kalyani, India
| | - Anirban Mukhopadhyay
- Department of Computer Science & Engineering, Heritage Institute of Technology, Kolkata, India; Department of Information Technology, Techno Main, Saltlake, Kolkata, India; Department of. Computer Science & Engineering, University of Kalyani, Kalyani, India.
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193
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Abstract
The impact of host adaptive immune response on COVID-19 has now become a critical issue in absence of specific therapy and immunotherapies. In SARS CoV-2 infection, the immune response is thought to contribute both to the pathogenesis of the disease and to protection during its resolution. While mild cases develop an immune response that contributes to host protection, immunity of severely infected patients is a balance between harmful and protective immune responses. The severity of the disease has raised many questions about the kinetic, amplitude and the quality of adaptive immunity to the virus and its generation during the early phases of infection in severe, mild and asymptomatic patients. The role of antibody and CD4+ and CD8+ T cell responses have been studied and the development of an adaptive immunity seems to correlate with convalescence. The bioinformatics study of the T and B epitopes of coronaviruses has raised the question of the existence of cross-immunity between SARS-CoV-2 and other coronaviruses such as MERS-CoV and SARS-CoV. In this review, we discuss the adaptive immune responses and their potential roles in protection during COVID-19.
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Affiliation(s)
- Béhazine Combadière
- Sorbonne Université, Inserm U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), 91 boulevard de l'Hôpital, 75013 Paris, France
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194
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Smitha T, Thomas A. A brief outlook on the current emerging trends of COVID 19 vaccines. J Oral Maxillofac Pathol 2020; 24:206-211. [PMID: 33456225 PMCID: PMC7802844 DOI: 10.4103/jomfp.jomfp_334_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 11/04/2022] Open
Affiliation(s)
- T Smitha
- Department of Oral and Maxillofacial Pathology, VSDCH, Bengaluru, Karnataka, India
| | - Anela Thomas
- Department of Oral and Maxillofacial Pathology, VSDCH, Bengaluru, Karnataka, India
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195
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Campos EVR, Pereira AES, de Oliveira JL, Carvalho LB, Guilger-Casagrande M, de Lima R, Fraceto LF. How can nanotechnology help to combat COVID-19? Opportunities and urgent need. J Nanobiotechnology 2020; 18:125. [PMID: 32891146 PMCID: PMC7474329 DOI: 10.1186/s12951-020-00685-4] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Incidents of viral outbreaks have increased at an alarming rate over the past decades. The most recent human coronavirus known as COVID-19 (SARS-CoV-2) has already spread around the world and shown R0 values from 2.2 to 2.68. However, the ratio between mortality and number of infections seems to be lower in this case in comparison to other human coronaviruses (such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV)). These outbreaks have tested the limits of healthcare systems and have posed serious questions about management using conventional therapies and diagnostic tools. In this regard, the use of nanotechnology offers new opportunities for the development of novel strategies in terms of prevention, diagnosis and treatment of COVID-19 and other viral infections. In this review, we discuss the use of nanotechnology for COVID-19 virus management by the development of nano-based materials, such as disinfectants, personal protective equipment, diagnostic systems and nanocarrier systems, for treatments and vaccine development, as well as the challenges and drawbacks that need addressing.
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Affiliation(s)
- Estefânia V R Campos
- Human and Natural Sciences Center, Federal University of ABC. Av. dos Estados, 5001. Bl. A, T3 Lab. 503-3. Bangú, Santo André, SP, Brazil
| | - Anderson E S Pereira
- São Paulo State University-UNESP, Institute of Science and Technology, Sorocaba, SP, Brazil
| | | | | | | | - Renata de Lima
- Universidade de Sorocaba, Rodovia Raposo Tavares km 92,5, Sorocaba, São Paulo, Brazil.
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196
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Abstract
Novel corona virus caused pneumonia first reported in December, 2019 in Wuhan, China was later named COVID-19. Due to its special pathogenicity, COVID-19 transmitted with high speed beyond borders and has significantly affected normal life. Currently, no specific drugs, treatment or vaccines are available. Vaccine development for COVID-19 is a highly complex process involving viral genomic studies, identification of target for vaccine, vaccine design, manufacturing, storage and distribution, preclinical and clinical safety and efficacy studies. The high levels of efforts and global collaboration at this scale is unprecedented. The World Health Organization (WHO) has documented 160 different COVID-19 vaccine candidates as of July 13, 2020 with 26 currently on clinical evaluation while 137 vaccines on preclinical evaluation. COVID-19 vaccine efforts mark the first use of mRNA-type vaccines ever evaluated. Numerous research organizations have successfully initiated clinical evaluation of COVID-19 vaccines. This review aims to summarize the advances and challenges for COVID-19 vaccines development.
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197
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Rakib A, Sami SA, Mimi NJ, Chowdhury MM, Eva TA, Nainu F, Paul A, Shahriar A, Tareq AM, Emon NU, Chakraborty S, Shil S, Mily SJ, Ben Hadda T, Almalki FA, Emran TB. Immunoinformatics-guided design of an epitope-based vaccine against severe acute respiratory syndrome coronavirus 2 spike glycoprotein. Comput Biol Med 2020; 124:103967. [PMID: 32828069 PMCID: PMC7423576 DOI: 10.1016/j.compbiomed.2020.103967] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/08/2020] [Accepted: 08/08/2020] [Indexed: 02/07/2023]
Abstract
AIMS With a large number of fatalities, coronavirus disease-2019 (COVID-19) has greatly affected human health worldwide. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes COVID-19. The World Health Organization has declared a global pandemic of this contagious disease. Researchers across the world are collaborating in a quest for remedies to combat this deadly virus. It has recently been demonstrated that the spike glycoprotein (SGP) of SARS-CoV-2 is the mediator by which the virus enters host cells. MAIN METHODS Our group comprehensibly analyzed the SGP of SARS-CoV-2 through multiple sequence analysis and a phylogenetic analysis. We predicted the strongest immunogenic epitopes of the SGP for both B cells and T cells. KEY FINDINGS We focused on predicting peptides that would bind major histocompatibility complex class I. Two optimal epitopes were identified, WTAGAAAYY and GAAAYYVGY. They interact with the HLA-B*15:01 allele, which was further validated by molecular docking simulation. This study also found that the selected epitopes are able to be recognized in a large percentage of the world's population. Furthermore, we predicted CD4+ T-cell epitopes and B-cell epitopes. SIGNIFICANCE Our study provides a strong basis for designing vaccine candidates against SARS-CoV-2. However, laboratory work is required to validate our theoretical results, which would lay the foundation for the appropriate vaccine manufacturing and testing processes.
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MESH Headings
- Amino Acid Sequence
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Vaccines
- Computational Biology
- Coronavirus Infections/epidemiology
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Drug Design
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- HLA-B15 Antigen/chemistry
- HLA-B15 Antigen/metabolism
- HLA-DRB1 Chains/chemistry
- HLA-DRB1 Chains/metabolism
- Humans
- Molecular Docking Simulation
- Pandemics/prevention & control
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/immunology
- Viral Vaccines/chemistry
- Viral Vaccines/genetics
- Viral Vaccines/immunology
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Affiliation(s)
- Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Nusrat Jahan Mimi
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Md Mustafiz Chowdhury
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Taslima Akter Eva
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Tamalanrea, Kota Makassar, Sulawesi Selatan, 90245, Indonesia
| | - Arkajyoti Paul
- Drug Discovery, GUSTO A Research Group, Chittagong, 4203, Bangladesh; Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Asif Shahriar
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh
| | - Abu Montakim Tareq
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Nazim Uddin Emon
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Sajal Chakraborty
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Sagar Shil
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Sabrina Jahan Mily
- Department of Gynaecology and Obstetrics, Banshkhali Upazila Health Complex, Jaldi Union, Chittagong, 4390, Bangladesh
| | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, University Mohammed the First, BP 524, 60000, Oujda, Morocco; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, 21955, Saudi Arabia.
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, 21955, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
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Keshavarzi Arshadi A, Webb J, Salem M, Cruz E, Calad-Thomson S, Ghadirian N, Collins J, Diez-Cecilia E, Kelly B, Goodarzi H, Yuan JS. Artificial Intelligence for COVID-19 Drug Discovery and Vaccine Development. Front Artif Intell 2020; 3:65. [PMID: 33733182 PMCID: PMC7861281 DOI: 10.3389/frai.2020.00065] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/17/2020] [Indexed: 12/31/2022] Open
Abstract
SARS-COV-2 has roused the scientific community with a call to action to combat the growing pandemic. At the time of this writing, there are as yet no novel antiviral agents or approved vaccines available for deployment as a frontline defense. Understanding the pathobiology of COVID-19 could aid scientists in their discovery of potent antivirals by elucidating unexplored viral pathways. One method for accomplishing this is the leveraging of computational methods to discover new candidate drugs and vaccines in silico. In the last decade, machine learning-based models, trained on specific biomolecules, have offered inexpensive and rapid implementation methods for the discovery of effective viral therapies. Given a target biomolecule, these models are capable of predicting inhibitor candidates in a structural-based manner. If enough data are presented to a model, it can aid the search for a drug or vaccine candidate by identifying patterns within the data. In this review, we focus on the recent advances of COVID-19 drug and vaccine development using artificial intelligence and the potential of intelligent training for the discovery of COVID-19 therapeutics. To facilitate applications of deep learning for SARS-COV-2, we highlight multiple molecular targets of COVID-19, inhibition of which may increase patient survival. Moreover, we present CoronaDB-AI, a dataset of compounds, peptides, and epitopes discovered either in silico or in vitro that can be potentially used for training models in order to extract COVID-19 treatment. The information and datasets provided in this review can be used to train deep learning-based models and accelerate the discovery of effective viral therapies.
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Affiliation(s)
- Arash Keshavarzi Arshadi
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States
| | - Julia Webb
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States
| | - Milad Salem
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL, United States
| | | | | | - Niloofar Ghadirian
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Jennifer Collins
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States
| | | | | | - Hani Goodarzi
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Jiann Shiun Yuan
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL, United States
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199
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Ong E, Huang X, Pearce R, Zhang Y, He Y. Rational Design of SARS-CoV-2 Spike Glycoproteins To Increase Immunogenicity By T Cell Epitope Engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.14.251496. [PMID: 32817949 PMCID: PMC7430581 DOI: 10.1101/2020.08.14.251496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The current COVID-19 pandemic caused by SARS-CoV-2 has resulted in millions of confirmed cases and thousands of deaths globally. Extensive efforts and progress have been made to develop effective and safe vaccines against COVID-19. A primary target of these vaccines is the SARS-CoV-2 spike (S) protein, and many studies utilized structural vaccinology techniques to either stabilize the protein or fix the receptor-binding domain at certain states. In this study, we extended an evolutionary protein design algorithm, EvoDesign, to create thousands of stable S protein variants without perturbing the surface conformation and B cell epitopes of the S protein. We then evaluated the mutated S protein candidates based on predicted MHC-II T cell promiscuous epitopes as well as the epitopes' similarity to human peptides. The presented strategy aims to improve the S protein's immunogenicity and antigenicity by inducing stronger CD4 T cell response while maintaining the protein's native structure and function. The top EvoDesign S protein candidate (Design-10705) recovered 31 out of 32 MHC-II T cell promiscuous epitopes in the native S protein, in which two epitopes were present in all seven human coronaviruses. This newly designed S protein also introduced nine new MHC-II T cell promiscuous epitopes and showed high structural similarity to its native conformation. The proposed structural vaccinology method provides an avenue to rationally design the antigen's structure with increased immunogenicity, which could be applied to the rational design of new COVID-19 vaccine candidates.
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Affiliation(s)
- Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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Wang J, Peng Y, Xu H, Cui Z, Williams RO. The COVID-19 Vaccine Race: Challenges and Opportunities in Vaccine Formulation. AAPS PharmSciTech 2020; 21:225. [PMID: 32761294 PMCID: PMC7405756 DOI: 10.1208/s12249-020-01744-7] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022] Open
Abstract
In the race for a safe and effective vaccine against coronavirus disease (COVID)-19, pharmaceutical formulation science plays a critical role throughout the development, manufacturing, distribution, and vaccination phases. The proper choice of the type of vaccine, carrier or vector, adjuvant, excipients, dosage form, and route of administration can directly impact not only the immune responses induced and the resultant efficacy against COVID-19, but also the logistics of manufacturing, storing and distributing the vaccine, and mass vaccination. In this review, we described the COVID-19 vaccines that are currently tested in clinical trials and provided in-depth insight into the various types of vaccines, their compositions, advantages, and potential limitations. We also addressed how challenges in vaccine distribution and administration may be alleviated by applying vaccine-stabilization strategies and the use of specific mucosal immune response-inducing, non-invasive routes of administration, which must be considered early in the development process.
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Affiliation(s)
- Jieliang Wang
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Ying Peng
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Haiyue Xu
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Zhengrong Cui
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Robert O Williams
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA.
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