COVID-19: From Basics To Clinical Practice

Contents
Foreword
Preface
List of Contributors
Acknowledgments
Part 1 Epidemiology
Chapter 1 Epidemiology Review
1.1 Naming the Disease and Its Pathogen
1.2 Overview of the Epidemic in China
1.2.1 Early cases and transmission
1.2.2 Stages of community transmission
1.2.3 After implementing containment measures
1.3 The Epidemic Outside of China
1.3.1 Overview of the epidemic outside of China
1.3.2 The outbreak on the Diamond Princess cruise ship
Chapter 2 Epidemiological Characteristics
2.1 Sources of Transmission
2.1.1 Origin of the virus
2.1.2 Animal host
2.1.3 Types of transmission sources
2.1.4 Mutations in the virus
2.2 Routes of Transmission
2.2.1 Respiratory droplet transmission
2.2.2 Transmission by indirect contact
2.2.3 Fecal-oral transmission
2.2.4 Aerosol transmission
2.2.5 Mother-to-child transmission
2.3 Susceptible Population
2.3.1 Universal susceptibility
2.3.2 High-risk population
2.4 Transmission Dynamics
References
Part 2 Etiology and Pathogenesis
Chapter 3 Morphology, Systematics, and Structure
3.1 Position in Systematics
3.2 Evolutionary Analyses of the Genome
3.2.1 Evolutionary analysis based on whole viral genomes
3.2.2 Based on single genes in the viral genome
3.2.3 Comparative genomics analysis based on amino acid sequences
3.2.4 Time series analysis
3.3 Structure of the Viral Genome
Chapter 4 SARS-CoV-2 Natural Origins and Genomic Mutation
4.1 Origins of SARS-CoV-2
4.1.1 Natural host
4.1.2 Intermediate host
4.2 Genomic Mutations
4.2.1 Rate of evolution in SARS-CoV-2
4.2.2 Types and proportions of mutations in SARS-CoV-2
4.3 Impact of Mutations on Clinical Pathogenic Diagnoses
4.4 Impact of Mutations on Antigen Epitopes
Chapter 5 Mechanism of Infecting Host Cells
5.1 Targets and Mechanism of Viral Entry
5.2 Structural Analysis of the S Protein
5.3 Expression of the ACE2 Gene and Infection Sites
5.4 Life Cycle of the Coronaviruses
5.4.1 Viral entry
5.4.2 Replication–transcription
5.4.3 Viral shedding
References
Part 3 Immunology and Vaccine Development
Chapter 6 Progress in Immunology Research
6.1 Research Targeting the S Protein
6.2 Antigen Epitope Prediction
6.3 ACE2 Fusion Protein
6.4 T-Cell Exhaustion and Cytokine Storm
Chapter 7 Research on Coronavirus Vaccines
7.1 The Research Strategy for Coronavirus Vaccines
7.1.1 Recombinant vector vaccine
7.1.2 RBD subunit vaccine
7.1.3 Adjuvant vaccine
7.2 Research and Development of Vaccines against SARS-CoV-2
7.3 Animal Models
7.3.1 Mouse models
7.3.2 Hamster models
7.3.3 Ferret models
7.3.4 Dromedary models
7.3.5 Nonhuman primate models
7.4 Summary and Outlook
References
Part 4 Clinical Characteristics
Chapter 8 Clinical Manifestations
8.1 Incubation Period
8.2 Clinical Manifestations
8.2.1 Systemic symptoms
8.2.2 Respiratory symptoms
8.2.3 Gastrointestinal symptoms
8.2.4 Other rare clinical manifestations
8.2.5 Asymptomatic infections
8.3 Clinical Classification
Chapter 9 Chest Imaging
9.1 Common CT Manifestations
9.2 Stages of CT Manifestations
9.2.1 Early stage
9.2.2 Progressive stage
9.2.3 Severe stage
9.2.4 Recovery stage
9.3 Atypical CT Manifestation
Chapter 10 Laboratory Diagnosis
10.1 Laboratory Test Results
10.2 Specimen Types and Collection Methods for Etiology Diagnosis
10.2.1 Respiratory tract specimen collection
10.2.2 Blood specimen collection
10.2.3 Collection of other specimens
10.3 Testing Laboratory Biosafety Guidelines
10.3.1 Transport in the hospital
10.3.2 Transport out of the hospital
10.3.3 Specimen acceptance
10.3.4 Laboratory practice and environmental disinfection
10.4 RT-PCR Test
10.4.1 Introduction of RT-PCR test method
10.4.2 Recommended primers and probes and result interpretation
10.4.3 Causes for false negative results in RT-PCR test
10.5 Metagenomic Sequencing
10.6 Serological Test
10.7 Viral Culture In Vitro
10.8 Other Detection Methods
10.9 Pathogen Detection for Pneumonia of Unknown Causes
Chapter 11 Pathology
Chapter 12 Prognosis and Outcome
References
Part 5 Diagnosis and Differential Diagnosis
Chapter 13 Formulation and Evolution of China’s Diagnostic Criteria
13.1 The First Version: Released on January 15, 2020
13.2 The Second Version: Detailed Diagnostic Criteria
13.3 The Third Version: Focus on the Definition of Serious Cases
13.4 The Fourth Version: Expanded Scope of Contact History Outside Wuhan
13.5 The Fifth Version: Clinical Diagnosed Cases in Hubei Province
13.5.1 Cases outside Hubei province
13.5.2 Cases in Hubei province
13.6 The Sixth Version: Clinically Diagnosed Cases Cancelled
Chapter 14 Draft and Revision of WHO Interim Clinical Care Guidance
14.1 Definitions for nCoV (Jan 12, 2020)
14.2 Definitions for 2019-nCoV (Jan 28, 2020)
14.2.1 Suspect case
14.2.2 Confirmed case
Chapter 15 Differential Diagnosis
15.1 Influenza
15.2 Human Parainfluenza
15.3 Adenovirus Infection
15.4 RSV Infection
15.5 Rhinovirus Infection
15.6 Human Metapneumovirus Infection
15.7 SARS
15.8 Mycoplasma Pneumonia
15.9 Chlamydia Pneumonia
15.10 Bacterial Pneumonia
15.11 Vasculitis
15.12 Dermatomyositis
15.13 Cryptogenic Organizing Pneumonia
References
Part 6 Treatment Principles and Progress in Drug Research
Chapter 16 Treatment Principles
16.1 Determine the Treatment Site According to Patients’ Conditions
16.2 General Treatment Principles
16.3 Discharge Criteria
16.4 Health Management of Discharged Patients
Chapter 17 Progress in Research of Antiviral Drugs
17.1 Methods for Screening Anti-coronavirus Drugs
17.2 Potential Drugs for the Treatment of SARS-CoV-2
17.2.1.1 Ribavirin
17.2.1.2 Favipiravir (T-705)
17.2.1.3 Remdesivir (GS-5734)
17.2.1.4 Galidesivir (BCX4430 )
17.2.1.5 Lopinavir and Ritonavir
17.2.1.6 Griffithsin
17.2.1.7 Monoclonal antibodies
17.2.1.8 Targeted therapy based on CRISPR/Cas13d technology
17.2.2 Drugs targeting the host
17.2.2.1 Interferon (IFN )
17.2.2.2 Baricitinib
17.2.2.3 Chloroquine
17.2.2.4 Nitazoxanide
17.3. Limitations of Existing Drugs
17.4 Conclusion and Outlook
Chapter 18 Precautions for the Treatment of Special Population
18.1 Children
18.2 Pregnant Women
18.3 Newborns
References
Part 7 Treatment of Severe and Critical Patients
Chapter 19 Definition of Severe and Critical Patients
19.1 Serious Patients Match at Least One of the Following
19.2 Critical Patients Match at Least One of the Following
Chapter 20 Comprehensive Treatment of Severe and Critical Patients
Chapter 21 Treatment of Severe and Critical Patients
21.1 Warning Indicators of Clinical Deterioration
21.2 Treatment Principles
21.3 Oxygen Therapy and Respiratory Support
21.3.1 Ventilatory support in mild ARDS (200 mmHg ≤ PaO2/FiO2 < 300 mmHg)
21.3.2 Ventilatory support in mild–moderate ARDS (150 mmHg ≤ PaO2/FiO2 <200 mmHg)
21.3.3 Ventilatory support in moderate–severe ARDS (PaO2/FiO2 < 150 mmHg )
21.3.4 Prone positioning ventilation
21.4 Extracorporeal Membrane Oxygenation
21.4.1 Timing of starting ECMO
21.4.2 Contraindications
21.4.3 Modalities
21.5 Hemodynamic Management
21.6 Continuous Renal Replacement Therapy
21.6.1 Indications
21.6.2 Contraindications
21.6.3 Modalities
21.6.4 Anticoagulation
21.7 Nutritional Support
Chapter 22 Precautions for the Treatment of Severe Patients
22.1 Glucocorticoids
22.2 Immunotherapy
22.2.1 Intravenous immunoglobulin
22.2.2 Convalescent plasma
22.3 Targeted Antimicrobial Therapy Against Secondary Bacterial and Fungal Infection
22.3.1 Pathogen detection
22.3.2 The value of inflammatory biomarkers
22.3.3 Antimicrobial therapy
22.4 Criteria for Discharge from ICU
References
Part 8 Containment Strategy and Prevention and Control of Nosocomial Infection
Chapter 23 An Overview of the Containment Strategy
Chapter 24 Preventive Measures
24.1 Control of Infection Source
24.1.1. Setup of fever clinics in hospitals to accelerate the diagnosis of suspected cases
24.1.2 Isolation and classified treatment of confirmed cases based on the level of infection severity
24.1.3 Management of close contacts
24.1.4 Enhanced community management
24.2 Cutoff of Transmission Routes
24.2.1 Hospital measures
24.2.2 Community comprehensive preventive measures
24.2.3 Protection of susceptible population
Chapter 25 Prevention and Control of Nosocomial Infection
25.1 Principles of Personal Protective Equipment Selection
25.1.1 Goggles
25.1.2 Masks/protective face shields
25.1.3 Surgical masks
25.1.4 Medical protective masks
25.1.5 Latex examination gloves
25.1.6 Alcohol-containing hand sanitizer
25.1.7 Surgical gowns
25.1.8 Protective gown coveralls
25.2 Protection Levels
25.2.1 Level I protection
25.2.2 Level II protection
25.2.3 Level III protection
25.3 Self-Protection Requirements for Medical Personnel in Different Areas
25.3.1 Hospital entrance and outpatient department
25.3.2 Emergency
25.3.3 Fever clinics and observation wards
25.3.4 Other areas of medical institutions
25.4 Donning and Removing Procedures of Personal Protective Equipment
25.4.1 Surgical masks
25.4.2 Protective masks
25.4.3 Disposable surgical gowns
25.4.4 Protective gown coveralls
25.4.5 Goggles/protective face shields
25.4.6 The donning and removing process of personal protective equipment in fever clinics and AIIRs
25.4.7 Protection procedures during transfer of confirmed patients
25.5 Cleaning and Disinfection Process of Air, Environment and Surface
25.5.1 Air disinfection
25.5.2 Air conditioning management
25.5.3 Cleaning and disinfection of goggles, face shields, and powered air-purifying respirators (PAPRs)
25.5.4 Cleaning and disinfection of thermometers
25.5.5 Cleaning and disinfection of medical devices such as laryngoscope, bronchoscope, and negative pressure suction bottle
25.5.6 Cleaning and disinfection of clinic areas for suspected or confirmed cases
25.5.7 Cleaning and disinfection of reusable sanitary products
25.5.8 Cleaning and disinfection of medical fabrics
25.5.9 Cleaning and disinfection of bed unit in AIIRs after patients’ discharge
25.5.10 Infected operating room
25.5.11 Cleaning and disinfection of elevators
25.5.12 Precautions for cleaning and disinfection
25.6 Management of Relevant Departments
25.6.1 Outpatient and triage
25.6.2 Fever clinics
25.6.3 Emergency room
25.6.4 Outpatient clinics
25.6.5 Predelivery and delivery of pregnant women with COVID-19
25.6.6 Hemodialysis room
25.6.7 Operating room
26.6.8 General ward
25.6.9 Medical imaging department
25.6.10 Central sterile supply department (CSSD)
25.6.11 Sampling, transferring and laboratory testing of clinical specimens
25.6.12 Management of medical waste
25.6.13 Management of medical sewage
25.6.14 Postmortem disinfection
Chapter 26 Biosafety Guidance for Pathogenic Biology Laboratories
26.1 Viral Culture
26.2 Experimental Operations on Animal Infection
26.3 Experimental Operations on Uncultured Infectious Materials
26.4 Experimental Operations of Inactivating Agents
References
Appendix
Comprehensive Treatment and Management of COVID-19: Expert Consensus Statement from Shanghai
1. Etiology and Epidemiological Characteristics
2. Clinical Characteristics and Diagnostics
2.1 Clinical characteristics
2.2 Diagnostic criteria
2.3 Differential diagnosis
2.4 Clinical classifications
2.5 Clinical evaluation
3. Treatment
3.1 Antiviral treatment
3.2 Treatment of mild and ordinary patients
3.3 Treatment of organ function support for severe and critical patients
3.4 Treatment of organ function support for severe and critical patients
3.5 Integration of traditional Chinese and Western medicine treatment
3.6 Discharge standards
3.7 Health management of discharged patients
References
Translators’ Afterword