Table of Contents

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A Guide to SARS-CoV-2 and the COVID-19 Pandemic

    1 Background Information
        1.1 Introduction
        1.2 MolecularCharacteristics
            1.2.1 Characteristics of Coronaviruses
            1.2.2 Characteristics of SARS-CoV-2 Genome
            1.2.3 Characteristics of SARS-CoV-2 Proteins
       SARS-CoV-2 Spike (S) Protein
       SARS-CoV-2 Nucleocapsid (N) Protein
       SARS-CoV-2 Envelope (E) and Membrane (M)>
       SARS-CoV-2 Non-structural Proteins
        1.3 ACE2 Receptor
        1.4 Replication Cycle
        1.5 Interaction with the Immune System
        1.6 Epidemiology
            1.6.1 Natural Reservoirs
            1.6.2 Early Human Cases
       The Latham-Wilson Hypothesis
            1.6.3 Climate Factors of Disease Distribution
            1.6.4 Undocumented Cases
            1.6.5 Superspreaders and Seeding Events
            1.6.6 Mutations and Divergent Strains
       Early Lineages
       D614G Mutation
       Mink Variants
       Other Notable Mutations
            1.6.7 Infections in Non-human Species
        1.7 Previous Pandemics and Waves
        1.8 Viral Inactivation
            1.8.1 Oxygen, Heat, pH, and Radiation
            1.8.2 Soaps, Surfactants, and Detergents
            1.8.3 Electrokinetic Inactivation
    2 Chronology, Data, and Observations
        2.1 Chronology
        2.2 Current Data, Trends, and Models
            2.2.1 General Definitions
            2.2.2 Global Trend
            2.2.3 International Trends
       Sustained Exponential Growth
            2.2.4 Domestic Trends
       Nationwide Data
       Statewide Data
       Countywide Data
            2.2.5 A Modified SEIR Model
            2.2.6 Bayesian Inference / Convolution Model
        2.3 Symptoms of Infection
        2.4 Transmission Factors
            2.4.1 Incubation and Communicability Periods
            2.4.2 Basic Reproduction Number
            2.4.3 Contact and Droplet Transmission
       Face Masks and Other Methods for Limiting Droplet Transmission
            2.4.4 Evidence for Airborne and/or Fomite Transmission
            2.4.5 Asymptomatic Cases and Transmission
        2.5 Pathophysiology
            2.5.1 Pulmonary Pathophysiology
            2.5.2 Vascular Pathophysiology and Coagulopathy
            2.5.3 Central Nervous System Involvement
            2.5.4 Pathophysiology in Other Organs
        2.6 Immunity and Reinfection
            2.6.1 SARS-CoV-2 Epitope
            2.6.2 The Kinetics of SARS-CoV-2 Specific Antibodies and Memory Immune Cells
            2.6.3 Reinfection
            2.6.4 Pre-Existing Immunity
        2.7 Herd Immunity
            2.7.1 Effect of Population Heterogeneity
        2.8 Factors Concerning Severity
            2.8.1 Age, Pre-Existing Conditions, and Clinical Course
            2.8.2 Kawasaki-like Disease (MIS-C)
            2.8.3 Molecular and Cellular Factors
            2.8.4 Genetic Risk Factors
        2.9 Fatality, Recovery, and Potential for Lasting Damage
    3 Diagnosis, Treatment, and Vaccine Candidates
        3.1 Diagnostic Devices and Related Techniques
            3.1.1 Polymerase Chain Reaction
       SalivaDirect Testing
            3.1.2 Isothermal Amplification
            3.1.3 Radiological Methods
            3.1.4 Serological Assays
        3.2 Current Clinical Treatments
            3.2.1 Management of Patients with Cancer
            3.2.2 Cancer, Immune Checkpoint Inhibitors (ICI), and COVID-19
            3.2.3 Potential Impact of Delays in Cancer Diagnosis and Treatment on Prognosis
            3.2.4 Treatment of Cancer Patients on Cancer-Related Clinical Trials
            3.2.5 Management of Patients with Diabetes
            3.2.6 Management of Pregnant Patients
        3.3 Current and Proposed Clinical Trials
            3.3.1 Adaptive COVID-19 Treatment Trial
            3.3.2 RECOVERY Trial
            3.3.3 Solidarity Trial
        3.4 Proposed Repurposed Drugs
            3.4.1 Angiotensin Receptor Blocker
       Current Clinical Trials
       Study Results
            3.4.2 Chloroquines (with or without Azithromycin)
       Current Clinical Trials
       Results from Individual Trials
            3.4.3 Dexamethasone and Other Corticosteroids
       Current Clinical Trials
       Study Results
            3.4.4 Famotidine
            3.4.5 Favipiravir
            3.4.6 Interleukin-6 Receptor Antagonists
            3.4.7 Lopinavir and Ritonavir
            3.4.8 Remdesivir
            3.4.9 Other Pharmaceutical Drugs
        3.5 Current Vaccine Candidates
            3.5.1 RNA Vaccine Candidates
           Phase I U.S. Trial
           Phase II U.S. Trial
           Phase II/III U.S. Adolescent Trial
           Phase III U.S. Trial
           Phase I/II/III Global Trial
           Phase I/II German Trial
            3.5.2 DNA Vaccine Candidates
            3.5.3 Viral Vector-Based Vaccine Candidates
           Phase I Chinese Trial
           Phase II Chinese Trial
           Phase III Global Trial
       AZD1222 (ChAdOx1 nCoV-19)
           Pre-Clinical Trial Results
           Phase I/II U.K. Trial
           Phase II/III U.K. Trial
           Phase III U.S. Trial
           Phase III Brazil Trial
           Pre-Clinical Trial Results
           Phase I/II U.S. and Belgium Trial
           Phase III International Single Dose Trial
           Phase III International Two Dose Trial
       Sputnik V
           Phase I/II Trials
           Phase III Trial
            3.5.4 Inactivated Vaccine Candidates
           Phase II Chinese Trial
           Phase III Brazil Trial
           Pre-Clinical Results
           Phase I/II Chinese Trial
       Sinopharm-Wuhan Vaccine Candidate
           Phase I/II Chinese Trial
            3.5.5 Protein-Based Vaccine Candidates
           Phase II South Africa Trial
           Phase III U.K. Trial
           Phase III U.S. and Mexico Trial
       EpiVac Corona
       Other Protein-Based Vaccines
            3.5.6 DIY Vaccine Efforts
            3.5.7 Recommendations for Future Research
        3.6 Potential Experimental Treatments and Preventatives
            3.6.1 Monoclonal Antibodies
       Other Antibody Treatments
            3.6.2 ACE2 Peptides and Recombinant ACE2
            3.6.3 Other Experimental Compounds
            3.6.4 Cell Therapy
            3.6.5 Convalescent Plasma Transfusion
       U.S. Expanded Access Trial
            3.6.6 Gene Editing Therapy
            3.6.7 Radiation Therapy
        3.7 Potential Nutritional Supplements
    4 Summary and Outlook
    A Appendix
    R References and Hyperlinks