Covid-19: Biomedical Perspectives

Description

Covid-19: Biomedical Perspectives, Volume 50 in the Methods in Microbiology series highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors. Individual chapters in this new release include Sensitive methods for detection of SARS-CoV-2 RNA, Treatment of COVID-19 using Chinese herbal medicine, Understanding how SARS-CoV-2 is evolving and its impact on COVID-19 animal models and vaccine evaluation, Methods in machine learning to identify COVID-19 literature, COVID-19 seasonal behavior and the mutational landscape of the SARS-CoV-2 virus, CRISPR use in Diagnosis and Therapy for COVID-19, and much more.

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Front Cover 2
Covid-19: Biomedical Perspectives 5
Copyright 6
Dedication 7
Contents 9
Contributors 15
Preface 19
Chapter 1: Sensitive methods for detection of SARS-CoV-2 RNA 21
- 1. Introduction 21
- 2. General approaches for the detection of SARS-CoV-2 23
- 3. Isothermal amplification methods for sensitive detection of SARS-CoV-2 24
- 4. Sensitive detection of SARS-CoV-2 via RT-RPA 25
- 5. General considerations for designing an ultrasensitive RT-RPA assay 31
  - 5.1. Primer design 31
  - 5.2. Probe design 32

Front Cover 2
Covid-19: Biomedical Perspectives 5
Copyright 6
Dedication 7
Contents 9
Contributors 15
Preface 19
Chapter 1: Sensitive methods for detection of SARS-CoV-2 RNA 21
- 1. Introduction 21
- 2. General approaches for the detection of SARS-CoV-2 23
- 3. Isothermal amplification methods for sensitive detection of SARS-CoV-2 24
- 4. Sensitive detection of SARS-CoV-2 via RT-RPA 25
- 5. General considerations for designing an ultrasensitive RT-RPA assay 31
  - 5.1. Primer design 31
  - 5.2. Probe design 32
  - 5.3. Reaction temperature 32
- 6. Comparative reviews of recently published RT-RPA assays for SARS-CoV-2 detection 32
- 9. Key resources table 37
- 7. Methods section 37
- 8. Before you begin 37
- 11. Step-by-step method details 39
  - 11.1. Detection of SARS-CoV-2 N- or S-gene using exo probes and primers 39
  - 11.2. Detection of SARS-CoV-2 N- or S-gene using nfo probes and lateral flow strips 41
  - 11.3. Optional steps 42
  - 11.4. Simultaneous dual N- and S-gene detection using paired exo probe and primers for N-gene and exo probe and primers f ... 42
- 10. Materials and equipment 39
- 12. Summary 43
- Acknowledgement 44
- References 44
Chapter 2: The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike 47
- 1. Introduction 47
- 2. The seasonal behaviour of viruses 48
  - 2.1. Seasonality of viral diseases 48
  - 2.2. Drivers of seasonality in trade-off performance spaces 51
  - 2.3. Finding significant correlations 56
  - 2.4. Distinguishing error from chaos in time series 57
- 3. The seasonal behaviour of COVID-19 60
  - 3.1. Spatial distribution approaches 62
  - 3.2. Temporal distribution approaches 65
- 4. Viral genomic make up and seasonality 66
  - 4.1. Mutational change in rapidly expanding viral populations 69
  - 4.2. A structuring quasispecies as paradigm of viral mutational change 71
  - 4.3. The mutational landscape of evolving SARS-CoV-2 viruses 73
  - 4.4. Viral genomic change and seasonal behaviour 80
  - 4.5. Genomic change levels appear unlinked to temperature or latitude 83
  - 4.6. Galectin homologues appear likely molecular culprits 84
- 5. Conclusions and prospects 88
- Financial disclosures and conflicts of interest 89
- References 89
- Acknowledgements 89
- Further reading 99
Chapter 3: Current molecular diagnostics assays for SARS-CoV-2 and emerging variants 103
- 1. Introduction 104
- 2. SARS-CoV-2 variants of concern 105
  - 2.1. B.1.1.7 (Alpha) variant 108
  - 2.2. B.1.351 (Beta) variant 108
  - 2.3. P.1 (Gamma) variant 110
  - 2.4. B.1.617.2 (Delta) variant 110
- 3. COVID-19 diagnostics 111
  - 3.1. Real-time PCR diagnostics 112
    - 3.1.1. RT-PCR and COVID-19 detection 113
    - 3.1.2. RT-PCR and COVID-19 variants 116
  - 3.2. Serology based COVID-19 diagnostics 117
  - 3.3. CRISPR diagnostics 121
    - 3.3.1. CRISPR and COVID-19 detection 122
  - 3.4. Biosensor diagnostics 123
    - 3.4.2. Electrochemical biosensors 124
    - 3.4.1. Optical biosensors 124
    - 3.4.4. Next generation sensors 128
    - 3.4.3. Piezoelectric biosensors 128
  - 4. Diagnostics in the era of COVID-19 vaccination 129
  - 5. Conclusion 131
  - References 132
  - Further reading 140
- Chapter 4: CRISPR use in diagnosis and therapy for COVID-19 143
  - 1. Introduction 144
  - 2. Diagnostics and therapeutics for SARS-CoV-2 145
  - 3. CRISPR/Cas systems 147
    - 3.1. Cas12 148
      - 3.1.1. Cas12a 148
        
        3.1.1.1. DNA endonuclease-targeted CRISPR trans reporter (DETECTR) 149
        
        3.1.1.2. All-in-one dual CRISPR-Cas12a (AIOD-CRISPR) assay 149
        
        3.1.1.4. iSCAN (in vitro specific CRISPR-based assay for nucleic acids detection) 150
        
        3.1.1.3. CRISPR/Cas12a-NER (naked eye readout) 150
        
        3.1.1.5. Variant nucleotide guard (VaNGuard) assay 151
      - 3.1.2. Cas12b 151
        
        3.1.2.1. STOP (SHERLOCK testing in one pot) 152
        
        3.1.2.2. CASdetect (CRISPR-assisted detection) 152
      - 3.1.3. Cas13 152
        
        3.1.3.1. Specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) 152
        
        3.1.3.3. SHINE (SHERLOCK and HUDSON integration to navigate epidemics) 154
        
        3.1.3.2. CREST (Cas13-based, rugged, equitable, scalable testing) 154
        
        3.1.3.4. CARVER (Cas13-assisted restriction of viral expression and readout) 155
      - 3.1.4. Cas3 155
        
        3.1.4.1. Cas3-operated nucleic acid detection (CONAN) 155
      - 3.1.5. Cas9 155
        
        3.1.5.1. FnCas9 editor linked uniform detection assay (FELUDA) 155
      - 4. CRISPR-based therapeutics for SARS-Cov-2 156
        
        4.1. Disrupting the viral RNA genome 157
        
        4.1.1. Overview of Crispr/Cas13 system 157
        
        4.1.3. Applications of Cas13 variants as potential antivirals 158
        
        4.1.3.1. Cas13a 158
        
        4.1.3.2. Cas13b 159
        
        4.1.3.3. Cas13d 160
        
        4.1.2. Mechanism of action of CRISPR/Cas13 system 158
        
        4.2. Disrupting the host cell factors essential for SARS-CoV-2 infection 163
        
        6. Limitations of CRISPR/Cas system 164
        
        5. Delivery of CRISPR/Cas components 164
        
        7. Summary 165
        
        References 166
      - Chapter 5: Recent and advanced nano-technological strategies for COVID-19 vaccine development 171
        
        1. Introduction 171
        
        2. The structure and infection mechanism of SARS-COV-2 172
        
        3. Pathogenesis and clinical presentation of COVID-19 173
        
        4. Vaccine development strategies and platforms 175
        
        4.1. Live attenuated viral vaccines 176
        
        4.2. Inactivated pathogen vaccines 178
        
        4.3. Protein subunit vaccines 183
        
        4.4. Virus-like particle vaccines 184
        
        4.5. Vectored vaccines 184
        
        4.6. Nucleic acid vaccines 185
        
        5. Relevant SARS-CoV-2 antigen explored in the design of vaccines 186
        
        5.2. Spike (S) protein 186
        
        5.1. Structural, sub-structural, and non-structural proteins 186
        
        5.4. Nucleocapsid (N) protein 189
        
        5.3. Membrane (M) protein 189
        
        5.5. Envelop (E) protein 190
        
        6. Nano-based strategies for COVID-19 vaccine development 190
        
        6.1. Nano-carriers for antigen delivery 191
        
        6.1.1. Polymeric nano-delivery systems 191
        
        6.1.2. Lipid-based nano-delivery systems 191
        
        6.1.3. Inorganic nano-delivery systems 193
        
        6.1.4. Carbon-based nanomaterials 194
        
        6.2. Nano-vaccine adjuvants 194
        
        6.3. Delivery devices 195
        
        6.4. Novel alternative routes of administration 196
        
        7. Benefits and challenges of nanotechnology in COVID-19 vaccine development 198
        
        8. Conclusion and future perspectives 199
        
        References 200
      - Chapter 6: A review of hypersensitivity methods to detect immune responses to SARS-CoV-2 209
        
        1. Historical perspective 210
        
        2. General overview, classification and description of hypersensitivity reactions 213
        
        2.1. Type I hypersensitivity-immediate/IgE mediated 213
        
        2.2. Type II hypersensitivity-IIa/IIb antibody mediated 216
        
        2.3. Type III hypersensitivity-immune complex-mediated 218
        
        2.4. Type IV hypersensitivity-IVa/IVb/IVc/IVd-T cell mediated 220
        
        3. Skin test application of hypersensitivity reactions: In vivo measurements of immune responses 225
        
        4. In vitro methods to measure immune responses after SARS-Cov-2 infection 226
        
        4.1. SARS-CoV-2 protein description 226
        
        4.2. Understanding the adaptive immune response in covid19 patients 227
        
        4.3. In vitro methods to measure SARS-CoV-2 cellular immune responses 229
        
        5. A novel application of a DTH method to measure immune responses after SARS-CoV-2 infection 231
        
        6. DTH to measure immunogenicity elicited by covid vaccines 233
        
        References 234
        
        7. Future prospects of DTH to study SARS-CoV-2 immunogenicity 234
        
        Acknowledgements 234
      - Chapter 7: Hesitancy to get vaccinated against COVID-19 and how it might be overcome 243
        
        References 251
      - Chapter 8: The emergence of SARS-CoV-2 variants of concern in Australia by haplotype coalescence reveals a contin 253
        
        1. Introduction 253
        
        2. Methods 255
        
        3. VOCs in Australia 256
        
        4. Prevalence of amino acid variants in Australia 260
        
        4.1. The emergence of first haplotypes 260
        
        4.2. Emergence of haplotypes associated with VOCs alpha, delta and omicron 263
        
        4.3. Amino acid variants and haplotypes shared by VOCs 265
        
        4.4. Amino acid variants that are not part of established VOC constellations 266
        
        5. A network view of haplotype diversity and VOC emergence 266
        
        5.1. Haplotype and variant reuse 266
        
        5.2. Haplotype size and coalescence 269
        
        5.3. Haplotypes and protein interactions 269
        
        5.4. VOC omicron haplotype variants cluster along the S-protein sequence 271
        
        5.5. Haplotypes follow the three phases of the COVID-19 pandemic 273
        
        6. Continental links to seasonality 274
        
        6.1. Core haplotypes of VOCs reveal latitude-linked patterns of seasonality 274
        
        6.2. Free-standing markers also support seasonal behavior in Australia 276
        
        7. Discussion 278
        
        7.1. Mutational landscapes of viral evolution 280
        
        7.2. VOC emergence by haplotype coalescence 281
        
        7.3. Haplotypes and seasonal behavior 282
        
        7.4. Conclusions 284
        
        References 285
      - Chapter 9: COVID-19 vaccines for high risk and immunocompromised patients 289
        
        1. Introduction 289
        
        2. Development of COVID-19 vaccines 290
        
        3. The use of COVID-19 vaccines for the high-risk patient population with the emphasis on HIV-infected patients 292
        
        References 297
        
        Author contribution 297
        
        Conflict of interest 297
        
        Funding 297
      - Back Cover 301

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