Genomic surveillance and pandemic preparedness /
Genomic Surveillance and Pandemic Preparedness offers practical, in-depth instruction in where, how, and why genomic surveillance may be applied.Drawing heavily from the learnings during the COVID-19 pandemic, this book covers different aspects of microbes with a focus on viral genome sequencing and...
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| Format: | eBook |
| Language: | English |
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London, United Kingdom ; San Diego, CA :
Academic Press,
2023.
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| Online Access: | Connect to the full text of this electronic book |
Table of Contents:
- Front Cover
- Genomic Surveillance and Pandemic Preparedness
- Genomic Surveillance and Pandemic Preparedness
- Copyright
- Contents
- List of contributors
- Preface
- A
- Pathogens and host: genomics perspective
- 1
- Population-level differences in COVID-19 prevalence, severity, and clinical outcome
- Introduction
- Measuring the burden of disease: prevalence and incidence
- Prevalence
- Incidence
- Types of prevalence
- Factors affecting prevalence
- Seroprevalence: measuring infection status in the population
- Decoding COVID-19 prevalence: a population-based approach
- Spectrum of disease severity
- Populations-based deciphering of COVID-19 severity
- Comorbidities
- Sex
- Age
- Genetic
- Population-based understanding of COVID-19 clinical outcome
- Conclusions
- Future perspectives
- References
- 2
- Host genetics in disease susceptibility and protection
- Introduction
- Methods and technologies
- Tuberculosis
- HIV-1/AIDS
- Malaria
- Leprosy
- Viral hepatitis
- Inborn errors of immunity
- COVID-19
- Conclusions and future directions
- References
- 3
- RNA as modulators of infection outcome: potential usage for genomic surveillance
- Introduction
- Evolution of pathogenic RNA viruses
- Genome surveillance as a strategy to unravel viral pathogenicity and transmission
- Whole genome sequencing in RNA surveillance
- Evolution of WGS in genome surveillance
- Use of metagenomics in RNA surveillance
- Target-based genome sequencing
- Variation in RNA can modulate infection outcomes
- Impact of RNA structure variations on viral infections
- RNA interactions and infectivity
- Global initiatives for pathogen surveillance
- Acknowledgments
- References
- B
- Pathogen diversity
- 4
- Genomic surveillance of bacterial pathogens: expanding horizons
- Introduction.
- Genomic surveillance of bacterial pathogens
- Salmonella Typhi (S. Typhi)
- Mycobacterium tuberculosis (M.tb)
- Pseudomonas aeruginosa
- Neisseria gonorrhoeae
- Staphylococcus aureus
- Other pathogenic bacteria
- Role of machine learning (ML) and artificial intelligence (AI) in genomics surveillance
- Incorporating ML/AI methodologies in genomic surveillance
- Global surveillance efforts-data resource
- Conclusion
- References
- C
- Cofactors in addition to pathogen
- 5
- Host immune responses in COVID-19: implication for preexisting chronic systemic inflammation
- Introduction
- SARS-CoV-2 transmission and clinical features
- Immune response in SARS-CoV-2 pathogenesis
- The "cytokine storm"
- Chronic inflammatory disorders and associated cytokine profile
- Rheumatic disorders
- Inflammatory bowel disease
- Chronic obstructive pulmonary disorder (COPD)
- Atherosclerosis
- Diabetes mellitus
- Conclusion
- References
- 6
- Role of co-infections in modulating disease severities and clinical phenotypes
- Prelude to the chapter
- Preamble to the topic
- Opening pandora's box: explaining co-infections
- What happens when the primary pathogen infects?
- What co-infections have to do with disease severity and outcome?
- Are these co-infections advantageous or deleterious?
- Introducing transcriptionally active microbes (TAMs)
- Human gut microbiome and the SARS-CoV-2
- Dataset acquire and pre-processing
- Quality control analysis
- From reads to assembly
- From fragments to taxa (binning)
- Statistical analysis
- Probiotics
- Prebiotics
- Postbiotics
- FMT
- References
- Further reading
- 7
- Wastewater surveillance: a quick guide to check community health
- Introduction
- Wastewater surveillance
- The methodology employed in environmental and wastewater surveillance
- SARS-CoV-2 surveillance.
- Polio surveillance in sewage samples
- Surveillance for Cryptosporidium and Giardia
- Surveillance of hepatitis E virus
- Environmental monitoring of Aichi virus, human bocavirus noroviruses, Adenoviruses, Sapoviruses, and Astroviruses
- Wastewater surveillance for typhoid transmission
- Wastewater surveillance for antibiotic-resistome and mobilome
- Multidrug-resistant Pseudomonas aeruginosa outbreaks and antimicrobial-resistant pathogens
- Surveillance of antibiotic-resistant Escherichia coli
- Role of environment surveillance in effective public health management
- Challenges in successful environmental/waste water surveillance
- Conclusion and future perspectives
- References
- D
- Future pandemic preparedness
- 8
- Experimental repertoire to elucidate the functional landscape of host-pathogen interactome
- Introduction
- Experimental approach to understand host-pathogen interaction
- Molecular, cell biology, model systems
- Immediate detection, diagnostics, surveillance, prognostic markers
- Building and aligning to the theme of "genomic surveillance and pandemic preparedness"
- Pathogen genomics: diagnosis, surveillance, and functional genomics
- Pathogen genomics for diagnosis and surveillance
- Choice of platform: high throughput or high priority?
- Functional genomics: mutations and genome architecture of pathogen
- Population, phylogenetic and, mutation studies
- Identifying and annotating mutations
- Associating mutations to clinical and phenotypic variables
- Statistical analysis
- Comparative genomic and metagenomic analysis
- Detecting or confirming a new microbe or similarity with previously known microbe/s
- Culturing-based detection technique
- Immunological-based detection technique
- Molecular-based detection technique
- Understanding the host response through genomics and transcriptomics.
- Multilayered understanding of host genome: genomic and transcriptomic knowledge
- Granularity of data, bulk or single-cell RNA sequencing: which one to use?
- Single-cell RNA sequencing: choice of platform
- Analytical approaches toward RNA-seq and single-cell RNA-seq data
- RNA-seq data repositories: where to find the files
- Counting method
- Differential gene expression methods for RNA-seq
- Analyzing the single-cell data: dos and don'ts
- WGS and array based techniques for detection
- Gene expression profiling
- Genotyping
- Host genetic variants: SNPs and haplotype associated risk factors
- Structural conformation of genome: 3D interaction and gene regulation
- Detection of TADs and interactions within TADs
- Summary
- References
- 9
- Computational means to understand and elucidate host-pathogen interaction and outcome
- Introduction
- Pathogen classification and invasion
- Elude host defenses and colonize
- Infection eradication
- Prediction algorithms for PHI
- Homology-based methods
- Structure-based methods
- Motif interaction methods
- Machine learning and artificial intelligence to predict PPI/PHI
- Host-pathogen interactions databases
- Discussions and future scopes
- Conclusion
- References
- 10
- Genomic surveillance system and technologies
- Genomic surveillance system
- Collection of clinical data, imaging data, and biological samples
- Generation of laboratory and sequencing data from biological samples
- Analysis of sequenced data
- Analysis of multimodal data
- Reporting insights
- Genomic surveillance architecture
- High performance compute and storage (HPCS) system
- Information gateway (IG)
- Genomic surveillance technologies
- Data security
- Anonymization
- Artificial intelligence (AI) and federated learning (FL)
- References
- E
- Roadmap ahead.
- 11
- Interactions shaping the interactome: genome surveillance inclusive of host-pathogen
- Introduction
- Understanding interactions in the context of host and pathogen
- Basic concepts of host-pathogen interaction-commensalism, colonization, infection, and disease
- Infectious diseases: high incidences, mortality rate, and population diversity
- An exploration of the host pathogen interactome (HPI)
- HPI: a multifaceted approach to understanding infectious diseases
- Host entry by the pathogen
- Evasion of host defenses by pathogens
- Pathogen replication in the host and host response
- Tools to study HPI
- HPI in infectious diseases
- Concepts of perennial and seasonal infections across viral, bacterial, and fungal infections
- Mycobacterium tuberculosis (mTB)
- Transmission and pathogenesis
- Genomics, HPI and tuberculosis
- Influenza
- Transmission and pathogenesis
- Genomics, HPI and influenza
- COVID-19
- Genome sequence and origin of the SARS-CoV-2
- Genomic insights into host-pathogen interaction in COVID-19
- Dengue
- Transmission and pathogenesis
- Genomics, HPI and dengue
- Tiered analysis of genomic surveillance for pathogen and host interactions
- Genomic surveillance in infectious diseases
- Multiomic technologies and NGS utilities (tools/techniques) to decipher HPI
- Conclusion
- Current advances in host-pathogen interaction studies aiding in clinical outcomes
- Future perspectives of host-pathogen interaction studies
- References
- 12
- Health informatics and data science for pandemic preparedness
- One Health and data as a public good
- Molecular surveillance and response
- Immune observatories
- Data science and social science
- References
- 13
- Harsh environmental stressors of high altitude on pathogens susceptibility
- Background
- HA exposure on T and B lymphocytes
- Neurological system.