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Genomic Surveillance and Pandemic Preparedness
- 1st Edition - June 28, 2023
- Editor: Rajesh Pandey
- Language: English
- Paperback ISBN:9 7 8 - 0 - 4 4 3 - 1 8 7 6 9 - 8
- eBook ISBN:9 7 8 - 0 - 4 4 3 - 1 8 7 6 8 - 1
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… Read more
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Request a sales quoteGenomic 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 analysis, implementation and inference of genomic surveillance, and global data sharing best practices for future pandemic preparedness. Here, more than a dozen international authors consider host and pathogen genome interaction, population-level prevalence, individual disease susceptibility and gene protection, pathogen mutation evolutionary dynamics, RNA modulation of infection, pathogen diversity, and the role of coinfections and comorbidities in disease severity. A wide range of examples, from bacterial pathogens to fungal and viral infections, with an emphasis on recent COVID-19 analysis, are discussed. Finally, the authors provide step-by-step instruction in experimental and computational approaches for genomic surveillance, including nucleic acid isolation, sequencing library preparation, functional sequencing analysis, and bioinformatics pipelines. Throughout this book, importance is placed on inference—moving from genomic sequencing to meaningful genomic surveillance that bolsters pandemic preparedness.
- Highlights different aspects of genomic surveillance, from theory to implementation to inferences
- Covers a broad range of infectious diseases, with emphasis on recent COVID-19 studies
- Shares methods and approaches for sequencing-based pathogen detection, diagnostics, and surveillance
- Facilitates international collaboration in drug and vaccine development
- Cover image
- Title page
- Table of Contents
- Copyright
- List of contributors
- Preface
- Section 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
- Seroprevalence: measuring infection status in the population
- Decoding COVID-19 prevalence: a population-based approach
- Spectrum of disease severity
- Population-based understanding of COVID-19 clinical outcome
- Conclusions
- Future perspectives
- 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
- 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
- Variation in RNA can modulate infection outcomes
- Global initiatives for pathogen surveillance
- Section B. Pathogen diversity
- 4. Genomic surveillance of bacterial pathogens: expanding horizons
- Introduction
- Genomic surveillance of bacterial pathogens
- Role of machine learning (ML) and artificial intelligence (AI) in genomics surveillance
- Conclusion
- Section 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
- 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
- Introducing transcriptionally active microbes (TAMs)
- 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
- Section 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
- Understanding the host response through genomics and transcriptomics
- Summary
- 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
- Discussions and future scopes
- Conclusion
- 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
- Information gateway (IG)
- Data security
- Section E. Roadmap ahead
- 11. Interactions shaping the interactome: genome surveillance inclusive of host–pathogen
- Introduction
- 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)
- Tools to study HPI
- HPI in infectious diseases
- Mycobacterium tuberculosis (mTB)
- Influenza
- COVID-19
- 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
- Future perspectives of host–pathogen interaction studies
- 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
- 13. Harsh environmental stressors of high altitude on pathogens susceptibility
- Background
- HA exposure on T and B lymphocytes
- Neurological system
- Respiratory system
- Dermatological system
- Gastrointestinal system
- Concluding remark
- 14. Implications of antibiotics and antimicrobial resistance development during COVID-19: questing genomic surveillance for a balancing act
- COVID-19 pandemic: a wakeup call for future pandemics
- Positive implication of antibiotics for COVID-19 and future pandemic
- Negative implication of antibiotics during COVID-19 and the need for genomic surveillance
- Conclusion
- Index
- No. of pages: 450
- Language: English
- Edition: 1
- Published: June 28, 2023
- Imprint: Academic Press
- Paperback ISBN: 9780443187698
- eBook ISBN: 9780443187681
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