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Multi-Pronged Omics Technologies to Understand COVID-19 Multi-Pronged Omics Technologies to Understand COVID-19 Edited by Sanjeeva Srivastava Professor, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, India First edition published 2022 by CRC Press 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487–2742 and by CRC Press 2 Park Square, Milton Park, Abingdon, Oxon, OX14 4RN © 2022 selection and editorial matter, Sanjeeva Srivastava; individual chapters, the contributors. CRC Press is an imprint of Taylor & Francis Group, LLC Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. 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Library of Congress Cataloging-in-Publication Data Names: Srivastava, Sanjeeva, editor. Title: Multi-pronged omics technologies to understand COVID-19 / edited by Sanjeeva Srivastava. Description: First edition | Boca Raton : CRC Press, 2022. | Includes bibliographical references and index. Identifers: LCCN 2021059642 (print) | LCCN 2021059643 (ebook) | ISBN 9781032116266 (hbk) | ISBN 9781032116297 (pbk) | ISBN 9781003220787 (ebk) Subjects: MESH: COVID-19—genetics | SARS-CoV-2—genetics | Computational Biology Classifcation: LCC RA644.C67 (print) | LCC RA644.C67 (ebook) | NLM WC 506 | DDC 614.5/92414—dc23/eng/20220314 LC record available at https://lccn.loc.gov/2021059642 LC ebook record available at https://lccn.loc.gov/2021059643 ISBN: 978-1-032-11626-6 (hbk) ISBN: 978-1-032-11629-7 (pbk) ISBN: 978-1-003-22078-7 (ebk) DOI: 10.1201/9781003220787 Typeset in Times by Apex CoVantage, LLC Contents Preface ...................................................................................................................vii Editor biography .....................................................................................................ix List of contributors..................................................................................................xi 1 Clinical and epidemiological context of COVID-19.................................... 1 Viswanthram Palanivel, Akanksha Salkar, Radha Yadav, Renuka Bankar, Om Shrivastav, and Arup Acharjee 2 NGS technologies for detection of SARS-CoV-2 strains and mutations ............................................................................................... 21 Manisha Choudhury, Ayushi Verma, Ankit Halder, and Arup Acharjee 3 Mass spectrometry techniques for detection of COVID-19 viral and host proteins using naso-oropharyngeal swab and plasma .................................................................................................... 39 Harsh Khatri and Kruthi Suvarna 4 Targeted proteomic approaches in the context of COVID-19 pandemic ....................................................................................................... 57 Mehar Un Nissa, Alisha Srivastava, and Medha Gayathri J. Pai 5 Metabolomics: Role in pathobiology and therapeutics of COVID-19 ................................................................................................. 75 Shalini Aggarwal, Nirjhar Banerjee, Shashwati Parihari, Jyotirmoy Roy, Kharanshu Bojak, and Rhythm Shah 6 Protein microarrays for COVID-19 research: Biomarker discovery, humoral response and vaccine targets ....................................101 Arup Acharjee, Abhilash Barpanda, Jing Ren, and Xiaobo Yu 7 COVID-19 pathogenesis and host immune response.............................. 121 Surbhi Bihani, Shalini Aggarwal, and Arup Acharjee 8 Putative role of multi-omics technologies in the investigation of persistent effects of COVID-19 on vital human organs ......................147 Susmita Ghosh, Akanksha Salkar, and Firuza Parikh v vi Contents 9 Insights into interactomics-driven drug repurposing to combat COVID-19...................................................................................... 169 Amrita Mukherjee, Ayushi Verma, Ananya Burli, Krishi Mantri, and Surbhi Bihani 10 Spectroscopy methods for SARS-CoV-2 detection.................................. 189 Abhiram Gokhale, Ashwini Khaladkar, and Arghya Banerjee 11 Role of AI and ML in empowering and solving problems linked to COVID-19 pandemic ................................................................. 203 Deeptarup Biswas, Gaurish Loya, and Graham Roy Ball Index .....................................................................................................................219 Preface The World Health Organization (WHO) declared COVID-19 (also referred to as SARS-CoV-2 disease) as a global pandemic on March 11, 2020. Since then, COVID-19 infections have been spreading at an alarming rate globally. The high transmission rates, limited diagnosis, and no effective therapy pose a considerable challenge in controlling and diminishing the pandemic. Scientists, researchers, and healthcare professionals worldwide are racing to use the best possible technologies and therapeutic strategies, which are being expedited in an unprecedented way. Along with this outbreak, 2020–2021 has also witnessed omics, bioinformatics, and machine learning revolution making advances in high-resolution mass spectrometry, next-generation sequencing (NGS), microarray technologies, and other spectroscopy-related methods. The scientifc community continues to gather data and share information across the globe through preprint servers as well as peer- reviewed scientifc publications. Several federal agencies freely share COVID-19 open access data and other resources with the research community. This book summarizes the recent advances in understanding SARS-CoV-2 disease using the latest omics-based technologies and inventions. Chapters 1 and 2 focus on the epidemiology and strength of NGS technology for tracking mutations across the globe. These chapters summarize the epidemiological characteristics, clinical features, and detection of emerging mutations of SARS- CoV-2 that have played a crucial role in public health decisions. Chapters 3, 4, and 5 summarize the use of high-throughput mass spectrometry technology for the detection and prognosis of COVID-19 progression. These technologies have been applied for the in-depth proteomics and metabolomics study of the COVID-19-infected host. Such studies will aid in providing valuable insights into the altered proteome and metabolome of the host leading to severe clinical manifestation. Moreover, the panel of potential biomarkers can be used in the clinics for the prognosis of disease outcomes before it could lead to fatal symptoms. Currently, the proteome microarray technique is widely explored as a robust diagnostic platform to detect infectious diseases, including COVID-19. Chapter 6 outlines the recent development in microarray techniques for the detection and monitoring of diseases. Chapters 7 and 8 summarize the understanding of the host immune response toward the infection and the impact of SARS-CoV-2 on different organs of the body post-recovery. These chapters thus discuss the role of multi-omics technologies for the prognosis and management of the long-term impact of COVID-19 infection. The application of omics technology for understanding the mechanism of COVID-19 infection has revealed several potential targets for therapeutic inter- ventions. Chapter 9 summarizes the in silico drug repurposing for combating COVID-19. Chapter 10 provides an overview of several other spectrometry-based methods used to detect the SARS-CoV-2 virus from the clinical samples. With the vii viii Preface recent development of machine learning technology and the rate at which COVID- 19 omics data accumulates, researchers have also tried to use the freely available resources to build the COVID-19 prediction model. Thus, Chapter 11 summarizes the use of big data and machine learning–based approaches to predict the clinical markers of COVID-19. This book aims to summarize valuable insights from the recent resources on applications of omics-based technology for the management of COVID-19. These resources lay the foundation for understanding the mechanism of SARS-CoV-2 infection in humans and allow us to examine the constantly evolving feld of omics. This book will provide the readers with a broad scientifc outlook on the future scope of omics and their application in managing SARS-CoV-2 infections. Editor biography Sanjeeva Srivastava is a professor and the group leader of the Proteomics Laboratory at the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, India. High-throughput proteomics, protein microarrays, and mass spectrometry are among his specialties. He has implemented ground- breaking AI-driven data analytics on big biological datasets. He has been at the forefront of clinical and biomedical research based on big data. His group’s current research focuses on the development of clinical biomarkers for infectious diseases and malignancies. His group has also pioneered therapeutic target identifcation efforts and decoded protein interaction networks in human illnesses like gliomas and contagious diseases like COVID-19 and malaria. His group has developed diagnostic biomarkers and described the pathophysiology of severe malaria (falci- parum and vivax) and COVID-19, especially the underlying mechanisms that lead to the development of severe sequelae. Dr. Srivastava is an active contributor to global proteomics research and development. He serves on the Executive Committee of Human Proteome Organization (HUPO) and Proteomics Society, India (PSI). He has more than 135 publications from his work as an independent researcher at IIT Bombay. To date, he has fled 19 patents that include biomarkers for various types of cancers, infectious diseases like malaria, leptospirosis, COVID-19, and proteomics method development in uncharted territories such as fsh and plant proteomics. ix