Covid-19: Biomedical Perspectives (Volume 50) (Methods in Microbiology, Volume 50)

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