The COVID-19 pandemic caused by the SARS-CoV-2 virus has affected nearly every country and territory in the world. Although worldwide vaccination efforts have reduced the risk of serious disease outcomes, disparities in distribution have led to multiple waves of SARS-CoV-2 outbreaks and the emergence of variants of concern, some of which have enhanced infectivity and ability to evade existing vaccines. Hence there is an increasing interest in understanding the evolution of viruses like SARS-CoV-2, as well as improving our capacity to effectively current and manage future pandemics.
This new volume reviews the most effective omic techniques for increasing our understanding of COVID-19, to improve diagnostics, prognostics, and genomic surveillance, and to facilitate development of effective treatments and vaccines. Chapters are written by an international team of experts and explore methods in the areas of genomics, transcriptomics, proteomics, and metabolomics. Techniques used to assess physiological function at the molecular level and artificial intelligence approaches used for more effective validation and translation of biomarker candidates into clinical use are also discussed. This book is an excellent resource for researchers studying biomarkers, virology, metabolic diseases, and infectious diseases, as well as clinical scientists, physicians, drug company scientists, and healthcare workers.
Author(s): Paul C. Guest
Series: Advances in Experimental Medicine and Biology, 1412
Publisher: Springer
Year: 2023
Language: English
Pages: 502
City: São Paulo
Preface
Contents
Part I: Background
Chapter 1: The COVID-19 Pandemic: SARS-CoV-2 Structure, Infection, Transmission, Symptomology, and Variants of Concern
1 Introduction
2 SARS-CoV-2 Structure
3 SARS-CoV-2 Infection of Host Cells
4 Symptomology
5 Variants of Concern
5.1 Alpha
5.2 Beta
5.3 Gamma
5.4 Delta
5.5 Omicron
6 Conclusions and Future Perspective
References
Chapter 2: Long-Term Vaccination and Treatment Strategies for COVID-19 Disease and Future Coronavirus Pandemics
1 Introduction
2 Current COVID-19 Vaccines
3 Treatments for COVID-19
3.1 Remdesivir
3.2 Anti-Spike Protein Monoclonal Antibodies
3.2.1 Regdanvimab
3.2.2 Casirivimab/Imdevimab Cocktail
3.2.3 Sotrovimab
3.2.4 Tixagevimab/Cilgavimab Cocktail
3.3 Tocilizumab
3.4 Anakinra
3.5 Ritonavir
4 Effect of SARS-CoV-2 Variants on the Efficacy of Vaccines and Monoclonal Antibody Therapeutics
5 Identification of Monoclonal Antibodies and Development of New Vaccines to Overcome the Immune Escape Capabilities of SARS-CoV-2 Variants
5.1 Monoclonal Antibodies
5.2 SARS-CoV-2 Vaccines
5.2.1 Updated Vaccines
5.2.2 Multivalent Vaccines
6 Natural Products for Improved Management of COVID-19 Patients
7 Conclusions and Future Perspectives
References
Part II: Neurological and Psychological Effects of the COVID-19 Pandemic
Chapter 3: Consequences of the Lockdown: Domestic Violence During the COVID-19 Pandemic
1 Introduction
2 Methods
2.1 Participants
2.2 Procedure
2.2.1 Demographic Information
2.2.2 Domestic Violence
2.2.3 Self-Report Measure for the Assessment of Emotion Regulation Skills
2.2.4 Commitment Score
2.2.5 Restrictions Due to Containment Measures
2.2.6 Contact Quality
2.3 Statistical Analyses
3 Results
3.1 Sociodemographic Data
3.2 Gender Differences Regarding Domestic Violence
3.3 Comparison of Domestic Violence Victims and Controls
3.4 Mediator Analyses
4 Discussion
5 Conclusions and Future Perspectives
References
Chapter 4: Psychological Distress Impact of Coronavirus Disease (COVID-19) Outbreak on Three Continents: A Systematic Review and Meta-analysis
1 Introduction
2 Materials and Methods
2.1 Database and Search Strategy
2.2 Eligibility Criteria
2.3 Introducing the CPDI
2.4 Data Extraction
2.5 Quality Assessment
2.6 Statistical Analysis
3 Results
3.1 Search Outcomes
3.2 Study Characteristics
3.3 Pooled Prevalence of Psychological Distress
3.4 Pooled Prevalence of Psychological Distress According to Continents
3.5 Pooled Prevalence of Psychological Distress According to Gender
3.6 Publication Bias
4 Discussion
5 Conclusions and Future Perspectives
References
Chapter 5: A Molecular Biomarker-Based Triage Approach for Targeted Treatment of Post-COVID-19 Syndrome Patients with Persistent Neurological or Neuropsychiatric Symptoms
1 Introduction
2 The SARS-CoV-2 Structure and Molecular Mimicry
3 Autoantibodies in PCS
4 Autoantibody Screening and Treatment Options for PCS
5 The Case for More Studies on PCS
5.1 The Need for Dedicated PCS Outpatient Clinics: Using Saxony-Anhalt as an Example
5.2 Proposed Methodology for Interdisciplinary PCS Outpatient Clinic
5.3 Methodologies for Autoimmune-Associated Neuronal, Vascular, or Thrombotic Dysregulation
6 Conclusions and Future Perspectives
References
Part III: Omic Techniques for COVID-19 Diagnostics
Chapter 6: Genetic Associations with Coronavirus Susceptibility and Disease Severity
1 Introduction
2 Global Response to COVID-19 Host Genetics
3 Genetic Findings
3.1 Chromosome 1
3.2 Chromosome 3
3.3 Chromosome 6
3.4 Chromosome 9
3.5 Chromosome 12
3.6 Chromosome 16
3.7 Chromosome 17
3.8 Chromosome 19
3.9 Chromosome 21
3.10 Chromosome X
4 Potentially Relevant Loci/Genes
5 Global Approach to COVID-19 Host Genetics
6 Conclusion
References
Chapter 7: COVID Diagnostics: From Molecules to Omics
1 Introduction
2 Transmission and Pathogenesis
3 COVID-19 Diagnosis
3.1 Traditional Diagnostic Methods
4 COVID-19 Risk Biomarkers
4.1 Risk Stratification and Prognostication of COVID-19 Patients
4.2 Cytokine Testing
5 The Use of Multiomics in Understanding SARS-CoV-2 Infection
6 Conclusions and Future Perspectives
References
Chapter 8: Assessing Biomarkers in Viral Infection
1 Introduction
2 Inflammatory Cytokines in Viral Infections
3 Coagulation as a Biomarker of Viral Infection
4 Traditional Biomarkers of Severe Viral Disease
4.1 CRP
4.2 PCT
5 Conclusions and Future Perspectives
References
Chapter 9: Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai
1 Introduction
2 Materials and Methods
2.1 Sample Collection and Processing
2.2 Mass Spectrometry Settings and Data Analysis
2.3 Statistical Analyses
2.4 Multiple Reaction Monitoring Validation
2.5 In Silico Pathway Analysis
2.6 In Silico Molecular Docking
2.7 Data Availability
3 Results
3.1 Analysis of Significantly Altered Proteins in COVID-19 Severe Samples
3.2 Anti-microbial Peptide Pathway as a Host Response to COVID-19 Infection
3.3 Validation of Severity Markers by MRM Analysis
3.4 Virtual Screening of Drugs for Selected Proteins
4 Discussion
4.1 Limitations
4.2 Conclusions
References
Chapter 10: NMR-Metabolomics in COVID-19 Research
1 Introduction
2 Biomarkers of COVID-19 Severity
3 Principal Risks Caused by COVID-19
4 Conclusions and Perspectives
References
Chapter 11: Potential Biomarkers of Mitochondrial Dysfunction Associated with COVID-19 Infection
1 Introduction
2 Assessment of Mitochondrial Respiratory Function
3 Pyruvate and Lactate
4 Amino Acids
5 Organic Acid Profiles
6 Coenzyme Q10
7 Reduced Glutathione
8 FGF-21/GDF-15
9 Conclusion
References
Chapter 12: Red Cell Distribution Width as a Prognostic Indicator for Mortality and ICU Admission in Patients with COVID-19
1 Introduction
2 Materials and Methods
2.1 Study Design
2.2 Statistical Analysis
3 Results
4 Discussion
References
Chapter 13: Predicting the COVID-19 Patients Status Using Chest CT Scan Findings: A Risk Assessment Model Based on Decision Tree Analysis
1 Introduction
2 Methods
2.1 Study Design and Patients
2.2 CT Protocol and Evaluation of Chest CT
2.3 Statistical Analysis
3 Results
4 Discussion
4.1 Strengths and Limitations
4.2 Conclusion
References
Part IV: Tracking SARS-CoV-2 Variants
Chapter 14: Inferring Recombination Events in SARS-CoV-2 Variants In Silico
1 Introduction
2 Methods
2.1 Datasets
2.2 Structural Interpretation and Docking
2.3 Selection of Ligands
2.4 Phylogenetic and Pangolin Analyses
2.5 LncRNA Analysis
3 Results and Discussion
3.1 Sequence Similarities and Dissimilarities for All SARS-CoV-2 Variants
3.2 Pangolin Outbreak Lineages of 38 Different Variants
3.3 Noncoding RNA Sequences Known to Be Trespassed
3.4 Molecular Interaction Studies
4 Conclusions
References
Chapter 15: Amplicon-Based Nanopore Sequencing of Patients Infected by the SARS-CoV-2 Omicron (B.1.1.529) Variant in India
1 Introduction
2 Methods
3 Results and Discussion
References
Chapter 16: Perspectives on Rapid Antigen Tests for Downstream Validation and Development of Theranostics
1 Introduction
2 Methods
3 Results and Discussion
References
Chapter 17: Machine Learning and COVID-19: Lessons from SARS-CoV-2
1 Introduction
2 Databases
3 High-Throughput Technologies in COVID-19
3.1 Genome of SARS-CoV-2
3.2 Single-Cell RNASeq (sc-RNASeq)
3.3 Metabolomics and Machine Learning
3.4 Microbiome and Machine Learning
4 Neural Networks on COVID-19
4.1 Neural Networks in ODE
4.2 Deep Learning Applied in Image Classification
5 Towards Construction of Mechanistic Explanations: When Systems Biology Meets Machine Learning
5.1 Regulatory Mechanisms of Immunological Cells
5.2 Microbiome and COVID-19
6 Conclusions and Future Perspectives
References
Part V: Omic Approaches in the Development of New Treatments and Vaccines for COVID-19
Chapter 18: The Relationship Between Psoriasis, COVID-19 Infection and Vaccination During Treatment of Patients
1 Introduction
2 Methods
3 Psoriasis and Correlation with COVID-19
4 Efficacy and Safety of COVID-19 Vaccines in Patients with Psoriasis
5 Psoriasis After COVID-19 Vaccination
5.1 COVID-19 Vaccination Leading to De Novo Psoriasis
5.2 COVID-19 Vaccinations Which Exacerbates Psoriasis
5.2.1 Pfizer-BioNTech mRNA Vaccine
5.2.2 Oxford/AstraZeneca Vaccine
5.2.3 Studies Carried Out at Single Centres
5.3 COVID-19 Vaccination Changing Type of Psoriasis
6 Conclusions and Future Perspectives
References
Chapter 19: Immunogenicity of Inactivated SARS-CoV-2 Vaccine (BBIBP-CorV; Sinopharm) and Short-Term Clinical Outcomes in Vaccinated Solid Organ Transplant Recipients: A Prospective Cohort Study
1 Introduction
2 Material and Methods
2.1 Study Design and Participants
2.2 Immunogenicity Assay
2.3 Patients Follow-Up
2.4 Statistical Methods
3 Results
3.1 Participant Characteristics
3.2 SARS-CoV-2 Vaccination Immunogenicity
3.3 Clinical Outcomes 6 Months Post-Vaccination
3.4 Adverse Events
4 Discussion
4.1 Limitations
4.2 Conclusion
References
Chapter 20: Spices and Biomarkers of COVID-19: A Mechanistic and Therapeutic Perspective
1 Introduction
2 Immunopathology
3 Herbal Remedies
4 Spices
4.1 Turmeric (Curcuma longa L.)
4.1.1 Safety of Curcumin
4.2 Ginger (Zingiber officinale)
4.2.1 Safety of Ginger
4.3 Cinnamon (Cinnamomum cassia)
4.3.1 Safety of Cinnamon
4.4 Other Spices
4.4.1 Black Pepper
4.4.2 Saffron
4.4.3 Capsaicin
4.4.4 Cumin
5 Conclusion and Future Perspectives
References
Chapter 21: Antiviral Mechanisms of Curcumin and Its Derivatives in Prevention and Treatment of COVID-19: A Review
1 Introduction
2 Methods
3 Results
3.1 Cellular Entry of SARS-CoV-2 and Curcumin
3.2 SARS-CoV-2 Proliferation and Curcumin
3.3 COVID-19, the Cytokine Storm, and Curcumin
3.4 Renin-Angiotensin System, SARS-CoV-2, and Curcumin
4 Cellular and Molecular Profiling Techniques Used in the Assessment of Curcumin Efficacy in the Treatment of COVID-19 Disease
5 Conclusions and Future Perspectives
References
Chapter 22: Evaluation of Curcumin-Piperine Supplementation in COVID-19 Patients Admitted to the Intensive Care: A Double-Blind, Randomized Controlled Trial
1 Introduction
2 Material and Methods
2.1 Study Design and Participants
2.2 Randomization and Blinding
2.3 Intervention
2.4 Outcome Measures and Data Collection
2.5 Statistical Analysis
3 Results
4 Discussion
References
Chapter 23: Chronobiological Efficacy of Combined Therapy of Pelargonium Sidoides and Melatonin in Acute and Persistent Cases of COVID-19: A Hypothetical Approach
1 Introduction
2 The Possible Chronobiological Efficiency of Melatonin in Acute and Long COVID-19 Period
3 Melatonin and Its Effect on the Immune System
4 The Antiviral Effects of Melatonin and Its Use Against COVID-19
5 Anti-Inflammatory Effect of Melatonin in SARS-CoV-2 Infection
6 Pelargonium sidoides Root Extract as an Adjuvant for the Treatment of Acute and Long COVID-19
7 The Role of Clinical Pharmacists in Adjuvant Chronotherapy for Acute and Ongoing COVID-19
7.1 The Role of the Pharmacist
8 Conclusions and Future Perspectives
References
Chapter 24: The Potential Effect of Royal Jelly on Biomarkers Related to COVID-19 Infection and Severe Progression
1 Introduction
2 Inflammatory Biomarkers
3 Hematological Biomarkers
4 Coagulation Biomarkers
5 Renal Biomarkers
6 Cardiac Biomarkers
7 Liver Biomarkers
8 Brain Biomarkers
9 Conclusion
References
Chapter 25: Statins: Beneficial Effects in Treatment of COVID-19
1 Introduction
2 Search Methods
3 SARS-CoV-2 and COVID-19
3.1 Biology
3.2 Structure
3.3 Variants
4 Pathogenesis of COVID-19: The Role of Inflammation
5 Statins
5.1 Anti-Inflammatory Effects of Statins
6 Statins in COVID-19: New Possibility for COVID-19 Treatment
6.1 Clinical Evidence
6.2 In Vivo/In Vitro Evidence
7 Conclusions and Future Perspectives
References
Part VI: Genomic Surveillance and Future Pandemics
Chapter 26: Multiplex Immunoassay Approaches Using Luminex® xMAP® Technology for the Study of COVID-19 Disease
1 Introduction
2 xMAP Technology
3 Applications of xMAP Technology During the Pandemic
3.1 Diagnosis
3.2 Vaccine Research
3.3 Epidemiology and Surveillance
3.4 Biomarker Analysis
4 Conclusion
References
Chapter 27: Rapid Detection of SARS-CoV-2 Variants of Concern by Genomic Surveillance Techniques
1 Introduction
2 The Omicron Variant
3 Genomic Surveillance
3.1 Next-Generation Sequencing
3.2 Real-Time PCR
4 Machine Learning
5 Lab-on-a-Chip Devices
5.1 LOC Devices for Diagnosis of COVID-19
5.2 LOC Devices for Detection of SARS-CoV-2 Antibodies
5.3 SARS-CoV-2 Disease-associated Effects
5.4 LOC Devices for Detection of SARS-CoV-2 Variants
6 Conclusions and Future Perspectives
References
Index
