COVID-19: Epidemiology, Biochemistry, and Diagnostics

Kamal Niaz, Muhammad Farrukh Nisar, Kamal Niaz, Muhammad Farrukh Nisar

• Publisher: Bentham Science Publishers
• Year: 2021
• Print ISBN:
  9789814998956
• eBook ISBN:
  9789814998932
• Topic: Medicine
• Subtopic: Infectious Diseases

COVID-19: Epidemiology, Biochemistry, and Diagnostics explains COVID-19 from multidisciplinary angles such as the evolution of SARS-COV, genetic techniques to study the virus, and diagnostic methodologies widely used in the global COVID-19 pandemic. The chapters in this book provide the reader with up-to-date literature about research on SARS-CoV-2 through three parts: I) Evolution and Entry of SARS-CoV-2 into the host II) Genetic Alteration and Structural Determination of SARS-CoV-2 Proteins III) Quantitative Analysis of SARS-CoV-2 for research and medical diagnosis
Key Features: - 15 chapters on SAR-CoV-2 in a multidisciplinary context - Provides a comprehensive overview of SARS-CoV-2 evolution and genetics - Provides biochemical information about SARS-CoV-2 proteins and receptor targets (both structural and non-structural proteins) - Includes an overview of several methods of detecting SARS-CoV-2 virus particles (ELISA, PCR, Neutralizing Antibodies - Covers some critical diagnostic modalities for COVID-19 diagnosis - Provides bibliographic references for further reading
Readers will understand the significance of phylogenetic analysis of coronaviruses, along with the pathogenesis of COVID-19 and related diseases such as SARS and MERS. Applications of biochemical technologies such as RT-PCR and CRISPR are also demonstrated in the text. This book is a comprehensive introduction to COVID-19 research for medical researchers, microbiologists and virologists. Students in academic programs in life sciences and medicine will also benefit from the information provided in the book.

Part I: Evolution and Entry of SARS-CoV-2

Coronavirus Disease-2019 (COVID- 19) Epidemiology

Ihtisham Ulhaq¹, Abdul Basit², Ijaz Ali¹, Firasat Hussain³, Zahid Ali¹, Faisal Siddique³, Haroon Ahmed¹, Amjad Islam Aqib⁴, Kashif Rahim^{3, *}

¹ Department of Biosciences, COMSATS University Islamabad (CUI) 45550, Pakistan

² Department of Microbiology, Faculty of Life Sciences, University of Okara, Pakistan

³ Department of Microbiology, Cholistan University of Veterinary and Animal Sciences (CUVAS), Punjab, Bahawalpur-63100, Pakistan

⁴ Department of Medicine, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan-63100

Abstract

At the end of December 2019, patients were diagnosed with a pneumonia-like infection in the Wuhan wholesale market of seafood, Hubei Province, China. Laboratory diagnosis revealed a novel coronavirus named severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), that causes coronavirus disease-19 (COVID-19). Initially, the novel virus was reported in bats. Due to the highly contagious nature of pathogens and the susceptibility of every human the virus spread rapidly across China then Globally. Respiratory droplets of infected patients played a significant role in the transmission of COVID-19 from human to human. Wuhan being a transport hub, and the crowd of people during New Chinese Year played a considerable role in the virus spread across the country. In link with earlier coronaviruses, the SARS-CoV-2 was noticed with a more contagious nature, and it quickly spread throughout the world. It was declared a pandemic by the World Health Organization (WHO) on March 12, 2020. In March 2021, the spread of infection decreased in China but increased globally, mainly in Europe. In April 2020, the disease burden increased in the USA. Till April 17 2020, China reported 84,149 cases with 4642 deaths, while worldwide cases reached 2,074,5279 with 139378 deaths. Europe reported confirmed cases 1,050,871 with 93,480 deaths, 743,607 patients in USA regions, Western Pacific regions with 127,595 patients, Eastern Mediterranean Regions reached 115,824 cases, and South-East Asia Regions reported 23,560 cases while African regions had 12,360 cases. The below figure illustrates the analysis of the epidemiological studies of COVID-19 (Fig. 1).

Keywords: Bats, COVID-19, Host Susceptibilities, Morbidity, Mortality, Pandemic, SARS-CoV-2, Virology.

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^* Corresponding author Kashif Rahim: Department of Microbiology, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences (CUVAS), Punjab, Bahawalpur 63100, Pakistan; E-mail: [email protected]

INTRODUCTION

A patient with respiratory signs and symptoms was diagnosed in Wuhan city, Hubei Province, China at the end of December 2019 [1]. The patients were diagnosed having pneumonia infection-like symptoms. Still, after genomic analysis by next-generation sequence (NGS) and real-time reverse transcription-polymerase chain reaction (RT-PCR) of the throat, samples revealed a pathogen like a coronavirus [2]. Hence a novel coronavirus was identified and initially named novel coronavirus-2019 (nCOV-19) by World Health Organization (WHO) on January 7, 2020 [1, 3]. However, because of genetic similarity with previous SARS-CoV (severe acute respiratory syndrome coronavirus), the nCoV-19 was renamed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses (ICTV) [4]. The disease caused by SARS-CoV-2 was officially named coronavirus disease-19 (COVID-19) by WHO on February 11, 2020 [5]. The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) appeared to be more pathogenic in comparison with other coronaviruses, till January 2^nd, 2020, it affected 42 individuals in China [6]. On January 13, 2020, the first COVID-19 disease case was reported in Thailand, which was the first case outside China [7]. First death due to COVID-19 disease outside China was reported in the Philippines [8]. The COVID-19 disease affects the human's respiratory tract, and disease symptoms include fever, cough, flu, sneezing, and fatigue. In contrast, the production of sputum, lymphopenia, dyspnoea, and diarrhea is observed in severe clinical conditions of patients [6, 9^-11]. Additionally, the other severe symptoms include acute kidney failure, dysfunction of various organs, and even mental confusion is also expected [12]. The COVID-19 disease incubation period is almost two weeks [13], with a median of 4-5 days [14, 15]. However, the incubation period fluctuates in proportion to the patient's age, immune status and shorter old patients younger than 70 years [16]. The COVID-19 emergence in China was then rapidly expanded to various provinces and later to the globe, resulting in the declaration of a pandemic on March 12 2020 by the WHO [17]. Because of the highly contagious nature of SARS-CoV-2, non-availability of vaccines and antiviral drugs COVID-19 disease rapidly and as of April 7 2020, the disease affected 1,349,660 people worldwide in more...

Table of contents

• Welcome
• Table of Content
• Title
• BENTHAM SCIENCE PUBLISHERS LTD.
• FOREWORD
• PREFACE
• List of Contributors
• Part I: Evolution and Entry of SARS-CoV-2
• Coronavirus Disease-2019 (COVID- 19) Epidemiology
• Studying Evolutionary Adaptation of SARS-CoV-2
• Evaluating SARS-CoV-2 Entry Pathways
• Part II: Genetic Alteration and Structural Determination of SARS-CoV-2 Proteins
• Genomic Characterization of SARS-CoV-2
• Mutation of SARS-CoV-2
• Biochemical Characterization of SARS-CoV-2 Spike Protein Proteolytic Processing
• Crystal Structure Determination and Receptor Recognition Basis of SARS-CoV-2 Spike Glycoprotein
• Structural Elucidation of SARS-CoV-2 Accessory Proteins
• Part III: Quantitation Analysis of SARS-CoV-2
• Antigen Capture Enzyme-Linked Immunosorbent Assay (ELISA) for the Detection of the Novel SARS-CoV-2 in Humans
• Quantification of the SARS-CoV-2 RNA in Tissues by Quantitative Real Time-PCR
• Evaluation of SARS-CoV-2 Neutralizing Antibodies in Sera Using Live Virus Microneutralization Assay
• Pseudovirus Neutralization Assay for SARS-CoV-2
• Quantitative and Qualitative Determination of COVID-19 (SARS-CoV-2) Specific Antibodies Using ELISA
• Chest CT Scan: An Ideal Diagnostic Tool for COVID-19
• Nucleic Acid-Based Detection of COVID-19