The COVID-19 Pandemic: Epidemiology, Molecular Biology and Therapy

Description

The Coronavirus Disease 2019 (COVID-19) pandemic has affected almost every part of the globe with millions of cases and over a million deaths. The pandemic has had a significant global economic impact and addressing it systematically requires significant efforts from researchers, healthcare workers and governments. The COVID-19 Pandemic: Epidemiology, Molecular Biology and Therapy covers relevant aspects of this viral pandemic including information about the SARS-CoV-2 pathogen (morphology, genome, proteins, structural protein genes, replication), global epidemiology, transmission, risk factors, clinical manifestation, management, host immune response, pathogenesis, diagnosis, therapeutic agents (antivirals, natural compounds) and vaccines. Readers will find basic and advanced knowledge about the disease organized into simple and easy-to-read chapters about the disease, making this book a handy and comprehensive reference for general readers, academicians and biology students, alike. FOREWORD ........................................................................................................................................... i PREFACE ................................................................................................................................................ iii LIST OF CONTRIBUTORS .................................................................................................................. v INTRODUCTION .......................................................................................................................... 1 MORPHOLOGY, GENOME, PROTEINS AND VIRAL REPLICATION ............................. 3 STRUCTURAL PROTEINS ......................................................................................................... 3 GLOBAL EPIDEMIOLOGY AND TRANSMISSION .............................................................. 4 RISK FACTORS ............................................................................................................................ 5 CLINICAL SYMPTOMS AND MANAGEMENT ..................................................................... 6 HOST IMMUNE RESPONSE AND PATHOGENESIS ............................................................ 7 DIAGNOSTICS .............................................................................................................................. 7 THERAPEUTICS (ANTIVIRALS AND NATURAL COMPOUNDS) .................................... 8 VACCINE DEVELOPMENT ....................................................................................................... 9 CORONA WARRIORS ................................................................................................................. 10 SOCIO-ECONOMIC-ENVIRONMENTAL IMPACT .............................................................. 10 CONCLUDING REMARKS ......................................................................................................... 11 CONSENT FOR PUBLICATION ................................................................................................ 12 CONFLICT OF INTEREST ......................................................................................................... 12 ACKNOWLEDGEMENTS ........................................................................................................... 12 REFERENCES ............................................................................................................................... 12 INTRODUCTION .......................................................................................................................... 17 VIRAL MORPHOLOGY .............................................................................................................. 18 GENOMIC ORGANIZATION ..................................................................................................... 19 STRUCTURAL PROTEINS ......................................................................................................... 20 Spike Protein (S-protein) ........................................................................................................ 20 Envelope Protein (E-protein) .................................................................................................. 22 Membrane Protein (M-protein) ............................................................................................... 22 Nucleocapsid (N-protein) ........................................................................................................ 23 NON-STRUCTURAL PROTEINS ............................................................................................... 23 VIRAL GENOME REPLICATION ............................................................................................. 26 CONCLUDING REMARKS ......................................................................................................... 28 CONSENT FOR PUBLICATION ................................................................................................ 29 CONFLICT OF INTEREST ......................................................................................................... 29 ACKNOWLEDGEMENTS ........................................................................................................... 29 REFERENCES ............................................................................................................................... 29 INTRODUCTION .......................................................................................................................... 39 MATERIALS AND METHODS ................................................................................................... 40 CHAPTER 1 AN INTRODUCTION TO CORONAVIRUS DISEASE 2019 (COVID-19) ........... 1 Shama Parveen and Sher Ali CHAPTER 2 MORPHOLOGY, GENOMIC ORGANIZATION, PROTEINS AND REPLICATION OF SARS-COV-2 .............................................................................. 17 Nazim Khan, Arshi Islam, Abu Hamza, Zoya Shafat, Asimul Islam, Anwar Ahmed and Shama Parveen CHAPTER 3 STRUCTURAL PROTEIN GENES OF SARS-COV-2: COMPREHENSIVE MOLECULAR CHARACTERIZATION ............................................................................................. 38 Zoya Shafat, Syed Abuzar Raza Rizvi, Mohammad Misbah Urrehmaan, Ayesha Tazeen, Priyanka Sinha, Anwar Ahmed and Shama Parveen Sequences ................................................................................................................................ 40 Compositional Properties ........................................................................................................ 40 Relative Synonymous Codon Usage (RSCU) ......................................................................... 40 Physiochemical Characterization ............................................................................................ 41 Phylogenetic Analyses ............................................................................................................ 41 Dataset I ........................................................................................................................ 41 Dataset II ....................................................................................................................... 41 Dataset III ..................................................................................................................... 41 Gene Ontology (GO) ............................................................................................................... 42 Mutational Analysis ................................................................................................................ 42 Selection Pressure Analysis .................................................................................................... 42 Analysis of Entropy of Amino Acid Sequences ..................................................................... 42 RESULTS ........................................................................................................................................ 42 Nucleotide Composition Analysis .......................................................................................... 42 S Gene ........................................................................................................................... 43 E Gene ........................................................................................................................... 43 M Gene .......................................................................................................................... 44 N Gene ........................................................................................................................... 44 U- and A-ending Codons are Preferred in Coding Sequences ................................................ 44 S Gene ........................................................................................................................... 46 E Gene ........................................................................................................................... 47 M Gene .......................................................................................................................... 47 N Gene ........................................................................................................................... 47 Analysis of Protein Sequences ................................................................................................ 47 Spike Protein ................................................................................................................. 47 Envelope Protein ........................................................................................................... 47 Membrane Protein ........................................................................................................ 48 Nucleocapsid Protein .................................................................................................... 48 Phylogenetic Analysis ............................................................................................................. 48 Full Genome of Coronaviruses ..................................................................................... 48 Structural Protein Genes of Coronaviruses .................................................................. 48 Structural Protein Genes of Novel Coronaviruses (SARS-CoV-2) ............................... 49 Computer Predicted Features .................................................................................................. 49 Subcellular Localization Prediction with Functional Annotation ................................ 49 Prediction of Effect of Mutations on Protein Function ................................................. 52 Helical Wheel Plot Analysis .......................................................................................... 53 Analysis of Positive Selection ................................................................................................ 53 S Dataset ....................................................................................................................... 53 E Dataset ....................................................................................................................... 54 M Dataset ...................................................................................................................... 55 N Dataset ....................................................................................................................... 55 Analysis of Entropy of Amino Acid Sequences ..................................................................... 55 DISCUSSION .................................................................................................................................. 55 CONCLUDING REMARKS ......................................................................................................... 58 CONSENT FOR PUBLICATION ................................................................................................ 58 CONFLICT OF INTEREST ......................................................................................................... 58 ACKNOWLEDGEMENTS ........................................................................................................... 58 REFERENCES ............................................................................................................................... 58 INTRODUCTION .......................................................................................................................... 63 METHODOLOGY ......................................................................................................................... 64 Data Collection and Sequence Alignment .............................................................................. 64 Phylogenetic Analysis ............................................................................................................. 64 Selection Pressure Analyses ................................................................................................... 65 Analysis of Shannon Entropy ................................................................................................. 65 Glycosylation Analysis ........................................................................................................... 65 RESULTS ........................................................................................................................................ 66 Phylogenetic Analysis and Genetic Distance Estimation ....................................................... 66 Selection Pressure Analysis .................................................................................................... 68 Shannon Entropy Analysis ...................................................................................................... 69 N-linked and O-linked Glycosylation ..................................................................................... 72 DISCUSSION .................................................................................................................................. 73 CONCLUDING REMARKS ......................................................................................................... 75 CONSENT FOR PUBLICATION ................................................................................................ 76 CONFLICT OF INTEREST ......................................................................................................... 76 ACKNOWLEDGEMENTS ........................................................................................................... 76 REFERENCES ............................................................................................................................... 76 INTRODUCTION .......................................................................................................................... 79 THE SPREAD ................................................................................................................................. 80 INCREASE IN INFECTIVITY OF SARS-COV-2 ..................................................................... 86 THE SPILLOVER ZOONOTIC EVENTS .................................................................................. 89 TRANSMISSION ........................................................................................................................... 91 Droplet and Aerosol Mediated Transmission ......................................................................... 92 Airborne Transmission ............................................................................................................ 93 Faecal Transmission ................................................................................................................ 94 Vertical Transmission ............................................................................................................. 94 Fomites Transmission ............................................................................................................. 94 Familial Transmission ............................................................................................................. 95 Nosocomial Transmission ....................................................................................................... 95 CONCLUDING REMARKS ......................................................................................................... 96 CONSENT FOR PUBLICATION ................................................................................................ 96 CONFLICT OF INTEREST ......................................................................................................... 96 ACKNOWLEDGEMENT ............................................................................................................. 96 REFRENCES .................................................................................................................................. 97 Arshi Islam, Nazish Parveen, Md. Shakir Hussain Haider, Ravins Dohare, Anwar Ahmed, Sher Ali and Shama Parveen CHAPTER 5 GLOBAL EPIDEMIOLOGY AND TRANSMISSION OF COVID-19 ................... 78 Md. Wasim Khan, Sajda Ara, Farah Deeba, Ayesha Tazeen, Nasir Salam, Irshad H. Naqvi and Shama Parveen CHAPTER 6 RISK FACTORS FOR SEVERE COVID-19 DISEASE ........................................... 103 Mohammad Misbah Urrehmaan, Abu Hamza, Zoya Shafat, Saba Parveen, Saima Wajid and Shama Parveen INTRODUCTION .......................................................................................................................... 103 RISK FACTORS FOR SEVERE COVID-19 INFECTION ....................................................... 106 Age Distribution ...................................................................................................................... 106 Gender ..................................................................................................................................... 108 Blood Groups .......................................................................................................................... 109 CHAPTER 4 CODON BASED CHARACTERIZATION OF S2 SUBUNIT OF SEVERE ACUTE RESPIRATORY SYNDROME-RELATED CORONAVIRUSES ............ 62 CONCLUDING REMARKS ......................................................................................................... 118 CONSENT FOR PUBLICATION ................................................................................................ 118 CONFLICT OF INTEREST ......................................................................................................... 118 ACKNOWLEDGEMENTS ........................................................................................................... 118 REFERENCES ............................................................................................................................... 118 INTRODUCTION .......................................................................................................................... 124 CLINICAL MANIFESTATIONS ................................................................................................. 124 Incubation Period .................................................................................................................... 126 Transmission of Disease ......................................................................................................... 126 Quarantine and Isolation ......................................................................................................... 126 Peculiar Course of COVID-19 ................................................................................................ 127 CLINICAL MANAGEMENT ....................................................................................................... 127 Oxygen Therapy: The First Step ............................................................................................. 127 Symptomatic or Pre-symptomatic Infection ........................................................................... 129 Mild Illness ............................................................................................................................. 129 Moderate Illness ...................................................................................................................... 130 Clinical Management of Moderate Disease ............................................................................ 130 SEVERE CASES MANAGEMENT ............................................................................................. 131 Urgent Supportive Therapy with Dedicated Monitoring ........................................................ 131 Management of Respiratory Failure with Acute Respiratory Distress Syndrome (ARSD) ... 131 Management of Extrapulmonary Manifestations and Systemic Complications ..................... 131 Management of Septic Shock ................................................................................................. 132 Other Therapeutic Measures ................................................................................................... 132 NEW INVESTIGATIONAL THERAPIES ................................................................................. 133 Anti-Viral Drugs ..................................................................................................................... 133 Tocilizumab ............................................................................................................................ 133 Hydroxychloroquine ............................................................................................................... 133 Anticoagulant .......................................................................................................................... 134 Convalescent Plasma .............................................................................................................. 134 Dexamethasone ....................................................................................................................... 134 IMMUNE RESPONSE IN COVID-19 .......................................................................................... 135 Innate Immune Response ........................................................................................................ 136 Adaptive Immune Response ................................................................................................... 136 Potential Immune Evasion ...................................................................................................... 137 PATHOGENESIS ........................................................................................................................... 137 CONCLUDING REMARKS ......................................................................................................... 139 CONSENT FOR PUBLICATION ................................................................................................ 140 CONFLICT OF INTEREST ......................................................................................................... 140 ACKNOWLEDGEMENTS ........................................................................................................... 140 REFERENCES ............................................................................................................................... 140 Comorbid Conditions .............................................................................................................. 113 Pre-natal Transmission ............................................................................................................ 117 CHAPTER 7 CLINICAL MANIFESTATIONS, TREATMENT, IMMUNE RESPONSE AND PATHOGENESIS OF COVID-19 ............................................................................... 123 Irshad H. Naqvi, Md. Imam Faizan, Mohammad Islamuddin, Mohd Abdullah Arpita Rai and Shama Parveen CHAPTER 8 COVID-19: CURRENT DIAGNOSTIC APPROACHES ......................................... 145 Anwar Ahmed, Fahad N. Almajhdi, Md. Imam Faizan, Tanveer Ahmad and Shama Parveen INTRODUCTION .......................................................................................................................... 146 LOOP-MEDIATED ISOTHERMAL AMPLIFICATION (LAMP) ......................................... 150 SEROLOGICAL DIAGNOSIS ..................................................................................................... 152 RAPID DIAGNOSTIC TEST (RDT) ............................................................................................ 154 ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA) .................................................... 156 CHEMILUMINESCENT IMMUNOASSAY (CLIA) ................................................................. 156 NEUTRALIZATION ASSAY (NA) .............................................................................................. 157 RAPID ANTIGEN DETECTION TEST (RADT) ....................................................................... 159 CONCLUDING REMARKS ......................................................................................................... 160 CONSENT FOR PUBLICATION ................................................................................................ 162 CONFLICT OF INTEREST ......................................................................................................... 162 ACKNOWLEDGEMENTS ........................................................................................................... 162 REFERENCES ............................................................................................................................... 162 INTRODUCTION .......................................................................................................................... 169 SIGNIFICANCE OF PLANTS DERIVED COMPOUNDS AS ANTIVIRALS ....................... 169 ANTIVIRAL ACTIVITY OF SELECTED NATURAL COMPOUNDS AGAINST SARSCOV- 2 .............................................................................................................................................. 170 FLAVONOIDS ................................................................................................................................ 171 Myricitrin ................................................................................................................................ 171 Baicalin ................................................................................................................................... 172 Hesperidin ............................................................................................................................... 173 Theaflavin ............................................................................................................................... 173 Quercetagetin .......................................................................................................................... 173 Apigenin .................................................................................................................................. 174 Glabridin ................................................................................................................................. 174 TERPENES AND TERPENOIDS ................................................................................................. 177 CURCUMINOIDS .......................................................................................................................... 179 TANNIN ........................................................................................................................................... 180 PROMISING ANTIVIRAL POTENTIALS OF PLANTS ......................................................... 188 Camellia Sinensis (Black/Oolong/Green Tea) ........................................................................ 188 Vitis vinifera (Grapevine or Black grapes) .............................................................................. 189 Malus domestica (Apple) ........................................................................................................ 189 Azadirachta indica (Neem) ..................................................................................................... 190 Glycyrrhiza glabra (Licorice) ................................................................................................. 191 Nigella sativa (Black Seed) ..................................................................................................... 191 CONCLUDING REMARKS ......................................................................................................... 192 CONSENT FOR PUBLICATION ................................................................................................ 193 CONFLICT OF INTEREST ......................................................................................................... 193 ACKNOWLEDGEMENT ............................................................................................................. 193 REFERENCES ............................................................................................................................... 193 197 197 INTRODUCTION .......................................................................................................................... 198 SAMPLE COLLECTION .............................................................................................................. 147 REAL-TIME REVERSE TRANSCRIPTASE-PCR (RT-PCR) ................................................ 147 CHAPTER 9 NATURAL COMPOUNDS AS POTENTIAL THERAPEUTIC AGENTS AGAINST COVID-19 ................................................................................................... 168 Ayesha Tazeen, Farah Deeba, Zoya Shafat, Md. Imam Faizan, Maryam Sarwat Mohammad Khalid Parvez and Shama Parveen CHAPTER 10 DRUG REPURPOSING CANDIDATES AND THERAPEUTIC APPROACHES TOWARDS THE TREATMENT OF COVID-19 .................................................... Arshi Islam, Nazish Parveen, Abu Hamza, Nazim Khan, Syed Naqui Kazim, Anwar Ahmed and Shama Parveen REMDESIVIR ................................................................................................................................ 200 LOPINAVIR/RITONAVIR (LPV/RTV) ..................................................................................... 201 CHLOROQUINE/HYDROXYCHLOROQUINE ....................................................................... 202 FAVIPIRAVIR ............................................................................................................................... 202 UMIFENOVIR (ARBIDOL) ......................................................................................................... 203 CONCLUDING REMARKS ......................................................................................................... 205 CONSENT FOR PUBLICATION ................................................................................................ 205 CONFLICT OF INTEREST ......................................................................................................... 205 ACKNOWLEDGEMENTS ........................................................................................................... 205 REFERENCES ............................................................................................................................... 205 210 210 INTRODUCTION .......................................................................................................................... 211 VACCINES ..................................................................................................................................... 212 OBSTACLES IN THE IMPLEMENTATION OF COVID-19 VACCINE .............................. 214 ANTIGEN SELECTION FOR VACCINE DEVELOPMENT .................................................. 214 ONGOING VACCINE DEVELOPMENT FOR COVID-19 ..................................................... 217 Viral Vector Vaccine .............................................................................................................. 222 Sputnik-V (Approved for Early Use) ............................................................................. 223 Ad5-nCoV (Approved for Limited Use) ......................................................................... 223 AZD1222 ....................................................................................................................... 223 Janssen Vaccine ............................................................................................................ 224 GRAd-COV2 .................................................................................................................. 224 LV-SMENP-DC ............................................................................................................. 224 aAPC ............................................................................................................................. 224 Whole Virus Vaccines ............................................................................................................ 225 CoronaVac (Approved for Limited Use) ....................................................................... 225 Inactivated Novel Coronavirus Pneumonia Vaccine .................................................... 225 BBIBP-CorV .................................................................................................................. 226 Inactivated SARS-CoV-2 Vaccine ......................................................................................... 226 COVAXIN ...................................................................................................................... 226 QazCovid ....................................................................................................................... 226 Nucleic acid vaccines .............................................................................................................. 226 mRNA-1273 ................................................................................................................... 227 BNT162 ......................................................................................................................... 227 Self-amplifying RNA Vaccine for COVID-19 ................................................................ 228 CVnCoV ......................................................................................................................... 228 GX-19 ............................................................................................................................ 228 INO-4800 DNA Vaccine ................................................................................................ 228 AG0301-COVID19 ........................................................................................................ 229 bacTRL-Spike ................................................................................................................ 229 Zydus Cadila DNA Vaccine .......................................................................................... 229 Subunit Vaccines .................................................................................................................... 230 Recombinant subunit vaccine for COVID-19 ............................................................... 230 NVX-CoV2373 ............................................................................................................... 230 COVAX-19 ..................................................................................................................... 231 The Available Therapeutic Options ........................................................................................ 198 Strategies for the Development of an Antiviral Drug ............................................................. 199 CHAPTER 11 COVID-19 VACCINE DEVELOPMENT: CHALLENGES AND CURRENT SCENARIOS ................................................................................................................ Nazish Parveen, Arshi Islam, Nazim Khan, Anwar Ahmed, Irshad H. Naqvi and Shama Parveen EpiVacCorona ............................................................................................................... 232 Virus Like Particle (VLP) Based Vaccine ..................................................................... 232 Tuberculosis Vaccine in Clinical Trial ................................................................................... 232 BCG vaccine .................................................................................................................. 232 VPM1002 Vaccine ......................................................................................................... 233 Vaccine Candidates in Preclinical Trial .................................................................................. 233 CONCLUDING REMARKS ......................................................................................................... 242 CONSENT FOR PUBLICATION ................................................................................................ 242 CONFLICT OF INTEREST ......................................................................................................... 243 ACKNOWLEDGEMENTS ........................................................................................................... 243 REFERENCES ............................................................................................................................... 243 SCB-2019 ...................................................................................................................... 231 Soberana1 ..................................................................................................................... 232 SUBJECT INDEX .................................................................................................................................... 248