Advances in Animal Disease Diagnosis

Suresh Kumar Gahlawat, Ph.D. is presently working as Professor, Department of Biotechnology Chaudhary Devi Lal University (CDLU), Sirsa, India. He also worked in various capacities such as Dean, Research, Dean, Faculty of Life Sciences, Dean of Colleges, Dean Student’s Welfare and Chairperson, Department of Biotechnology in the same university. He received postdoctoral BOYSCAST fellowship and DBT Overseas Associateship from the Ministry of Science & Technology, Government of India for carrying out research at FRS Marine Laboratory, Aberdeen, UK. His research interests include the development of molecular diagnostic methods for bacterial and viral diseases. He published more than 70 research papers in journals of national and international repute, authored more than 06 books and supervised M.Phil and Ph.D research work of 14 students. He is active member of various international scientific organizations and societies including Association Microbiologist of India.Sushila Maan, Ph.D. Professor & Head at Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India. She did her Ph.D. from Royal Veterinary College, University of London, UK. She had been Post-Doctoral Fellow within the Arbovirus Molecular Research Group at the Institute for Animal Health (IAH), Pirbright, UK from 2006 – 2011. Dr Sushila Maan has made vital contributions to the extraordinary high impact success of bluetongue virus (BTV) and other pathogens’ research and surveillance including the development of innovative next generation sequencing techniques, identification of seven new Orbivirus species and the 26th serotype of BTV. Dr Maan has developed and commercialized advanced molecular diagnostic systems for detection of pathogens of livestock and wildlife importance, during twenty-four years of her research career since 1995, she has published 122 peer reviewed research articles, out of which 76 are in various international journals of repute and 46 in national journals. She has also presented her research findings at several international conferences in the U.K., France, Portugal, Italy, Holland, Australia, South Africa, China and USA. She is on scientific panel (as a referee) of various International and National journals viz. Virus Research, Plos One, Virology, Vaccine, Journal of Virology, Transboundary and emerging diseases, Indian Journal of Virology etc.

• Biosensor: an advanced system for infectious disease diagnosis1.1 Introduction1.2 Principle of biosensors1.3 Composition of biosensors1.3.1. Enzymes1.3.2 Microbes1.3.3 Cells and Tissues1.3.4 Organelles1.3.5 Antibodies1.3.6 Nucleic Acids1.3.7 Aptamers1.4 Classification of biosensors1.4.1. Electrochemical Transducers1.4.1.1 Potentiometric transducers.1.4.1.2 Voltammetric transducers1.4.1.3 Conductometric transducers1.4.1.4 Impedimetric transducers1.4.2 Thermometric Transducers1.4.3 Optical Transducers1.4.4 Piezoelectric Devices1.4.5Others biosensors1.4.5.1 Enzymatic Sensors1.4.5.1.1 Substrate biosensors1.4.5.1.2 Inhibitor biosensors1.4.5.2 Immunosensors1.4.5.3 DNA Sensors1.4.5.4 Microbial Biosensors1.5 Biosensors in diagnosis of infectious diseases1.5.1 Acquired Immunodeficiency Syndrome (AIDS)1.5.2 Ebola Virus Disease1.5.3 Zika virus disease1.5.4 Influenza1.5.5 Hepatitis1.5.6 Dengue1.5.7 Salmonellosis1.5.8 Shigellosis1.5.9 Tuberculosis1.5.10 Food borne diseases caused by Enterococcus faecalis and Staphylococcus aureus1.5.11 Listerosis1.5.12 Leismaniasis1.6 Future perspective1.7 ConclusionViral Pseudotyping: A novel tool to study emerging and transboundary virusesAdvanced Sensors for Animal Disease Diagnosis3.1 Introduction to animal diseases3.2 Common animal diseases3.3 Sensors as new generation diagnostic platforms for animal disease diagnosis3.3.1 Bovine3.3.2 Canine3.3.3 Equine3.3.4 Swine3.3.5 Avian3.3.6 Fish3.4 Bacteriophage based sensors for detection of bacterial pathogens3.5 ConclusionApplications of metagenomics and viral genomics to investigating diseases of livestock4.1 Introduction4.2 Obtaining metagenomic next generating sequencing data for viruses4.2.1 Sample collection4.2.2 Sample preparation and viral enrichment4.2.3 Library preparation and sequencing4.3 Bioinformatic analysis of NGS sequence data4.3.1. Step 1: Quality assessment of the data produced4.3.2. Step 2: Assembly of reads (fragments)4.3.3. Step 3: Taxonomic classification4.4 Metagenomics and viral genomics can identify new viruses and foster understanding of emerging viruses4.5 Viral genomics and phylogenetics can identify disease transmission chains4.6 Viral genomics in monitoring vaccine matchingToll- like receptor of livestock species5.1 Toll-like receptors5.1.1 Structure of TLRs5.1.2. TLRs ligands5.1.3. Localization of TLR5.2 Localization of TLRs on mammalian chromosomes5.2.1. TLR signaling pathways5.3 Sequence characterization of livestock TLRs5.3.1. Polymorphism in TLRs of livestock species5.4 Phylogenetic analysis of buffalo TLR genes5.5. Role of TLRs in immune responses5.6 TLRs as therapeutic agentsCOVID-19: An emerging pandemic to mankind6.1 Introduction6.2 Virology6.2.1 Taxonomy6.2.2Virion structure6.2.3 Genome characteristics6.2.4 Recent genome wide studies6.2.5 Specificity of Spike protein6.3 Origin and evolution6.4 Pathogenesis6.4.1 Virus Entry6.4.2 Pathological Findings6.4.3 Immunopathology6.5 Epidemiology6.5.1 Route of transmission6.5.2 Transmissibility6.5.3 Viral shedding6.5.4 Environment viability6.5.5 Clinical manifestation6.6 Diagnosis6.6.1 Molecular diagnosis6.6.1.1 Real-time reverse transcriptase-PCR (RT-qPCR)6.6.1.2 SHERLOCK techniques6.6.2 Classical diagnosis6.6.3 Physical examination6.6.4 Virus isolation6.6.5 Serologic diagnosis6.7 Treatment6.8 Status of vaccine6.9 Prevention6.10 ConclusionsApplication of Proteomics and Metabolomics in disease Diagnosis7.1 Introduction7.2 Basic strategies and platforms of proteomics and metabolomics 7.2.1 Biological Specimens for proteomics and metabolomics 7.2.2 Proteomics workflow7.2.3 Quantitative proteomics7.2.4 Proteomics analytical platforms7.2.5 Metabolomics workflow7.2.6 Metabolomics analytical platform(s)7.3 Proteomics in animal disease diagnosis and biomarker discovery7.3.1 Proteomics biomarkers in infectious disease of farm animals7.3.2 Proteomics biomarkers in non-infectious disease of farm animals7.3.3 Proteomics in parasitic disease of animals7.4 Proteomics in companion animal disease biomarker discovery7.5 Metabolomics in animal disease diagnosis7.5.1 Metabolomics in canine diseases7.5.2 Metabolomics in farm animal disease diagnosis7.6 Proteomics and metabolomics in human disease diagnosis7.7 ConclusionImaging techniques in Veterinary Disease diagnosis8.1 Introduction8.2 MicroscopyOptical microscopy8.2.2 Dark field microscopy8.2.3 Phase contrast microscopy8.2.4 Polarized light microscopy8.2.5 Fluorescence microscopyConfocal Microscopy8.2.5.2 Two-Photon MicroscopyElectron microscopy (EM)8.6.1 Scanning electron microscopy (SEM)8.6.2 Transmission electron microscopy(TEM)Cryogenic Electron Microscopy (cryoEM)8.7 Scanning Probe Microscopy8.8 X-ray microscopy8.9 Raman microscopy8.10 Magnetic Resonance Microscopy (MRM)8.11 Super-resolution microscopy8.3 Ultrasonography/diagnostic sonography:8.4 Digital stethoscope8.5 Endoscopy8.6 Thermal imaging8.7 Radiographic ImagingContrast MediaRecent advancements in Radiographic Imaging8.8 Computed Tomography (CT)8.9 Magnetic Resonance Imaging (MRI)8.10 Radiopharmaceuticals and Nuclear Imaging8.11 Nuclear Scintigraphy or Gamma Scan8.12 Positron-emission tomography (PET)8.13 Single-Photon Emission Computed Tomography (SPECT)8.14 Electrical Impedance Tomography8.15 Nanoparticles in diagnostic imaging8.16 Future Prospect and ConclusionListeriosis in Animals: Prevalence and Detection9.1 Introduction9.2 Epidemiology, Transmission and Spread9.3 Organism Characteristics and Classification9.4 Life cycle9.4.1 L. monocytogenes virulence factors9.4.2 Factors for Adhesion9.4.3 Factors for Host Invasion9.4.4 Factors for escape From Phagocytic Vacuole9.4.5 Factors for Intracellular Survival and Multiplication9.4.6 Factors for Intracellular Motility and Intercellular Spread9.5 Clinical Manifestations9.6 Disease Diagnosis9.7 Pathogen Identification of Cultural Isolates9.7.1 Enzyme Based Assays9.7.2 Immunological Assays9.7.3 Nucleic Acid Based Molecular Assays9.7.4 Epidemiological Testing9.7.4.1 Phenotypic typing methods9.7.4.2 Molecular Typing MethodsPyroptosis Prevalence in Animal Diseases and Diagnosis10.1 Introduction10.2 Characteristic features of Pyroptosis10.3 Molecular Mechanism of Pyroptosis10.3.1 Canonical Inflammasome Pathway10.3.2 Non- Canonical Inflammasome pathway10.4 Pyroptosis Prevalence in Animal Diseases10.4.1 Neuro-inflammation and cognitive impairment in aged rodents10.4.2 Osteomyelitis10.4.3 Neonatal-onset multisystem inflammatory disease (NOMID)10.4.4 Sepsis10.4.5 Inflammatory Bowel Disease (IBD)10.4.6 Brucellosis10.4.7 Oxidative Stress in animals10.4.8 Viral Diseases in Animals10.5 Pyroptosis markers in Disease Diagnosis10.6 Conclusion and Future Prospects In DiagnosisCurrent diagnostic techniques for Influenza11.1 Introduction11.2 Influenza Diagnosis11.2.1 Cell Culture Approaches11.2.1.1 Virus Culture11.2.1.2 Virus Shell Culture11.2.2Direct Fluorescent Antibody Test11.2.3 Serological Assays11.2.3.1 Hemagglutination Inhibition Assay11.2.3.2 Virus Neutralization Assay11.2.3.3 Single Radial Hemolysis11.2.3.4 Complement Fixation11.2.4 Rapid Influenza Diagnostic Tests (RIDTs)11.2.5 Nucleic Acid-Based Tests (NATs)11.2.5.1 Reverse Transcription-Polymerase Chain Reaction (RT-PCR)11.2.5.2 Loop-Mediated Isothermal Amplification-Based Assay (LAMP)11.2.5.3 Simple Amplification-Based Assay11.2.5.4 Nucleic Acid Sequence-Based Amplification11.2.6 Microarray-Based Approaches11.2.7Modifications of Standard Methods11.3 ConclusionDiagnostic Tools for the Identification of Foot-and- Mouth Disease Virus12.1 Introduction12.2 Etiology12.3 Diagnostic techniques12.3.1 Virus isolation assay12.3.2 Serology-based assays12.3.2.1 Complement fixation test12.3.2.2 Virus neutralization test12.3.2.3 Enzyme-linked immunosorbent assay12.3.2.4 Virus infection associated gel immuno-diffusion test12.3.3 Nucleic acid-based assays12.3.3.1 Reverse transcriptase PCR12.3.3.2 Real-time RT-PCR12.3.3.3 Multiplex-PCR12.3.3.4 Reverse transcription loop-mediated isothermal amplification12.3.4 Novel and high-throughput assays12.3.4.1 Microarray12.3.4.2 Pen-side assay12.4 Prevention and treatment12.4.1 Attenuated vaccines12.4.2 Inactivated vaccinesSynthetic biology-based diagnostics for infectious animal diseases13.1 Introduction13.2 In vitro diagnostics13.2.1 Phage-Based Diagnostics13.2.2 Synthetic peptides-based diagnostics13.2.3 Synthetic peptide nucleic acid (PNA)-based diagnostics13.2.4 Aptamers-based diagnostics13.2.5 CRISPR/Cas-based biosensors13.2.5.1 Diagnostics using CRISPR-Cas913.2.5.2 CRISPR-Cas12- and CRISPR-Cas13-based diagnostics13.2.6 Synthetic RNA-based biosensors coupled with synthetic gene networks13.3 In vivo diagnostics13.4 Conclusions and Future perspectivesRecent Trends in Diagnosis of Campylobacter Infection14.1 Introduction14.2 Morphological characters of theCampylobacter14.3 PathogenesisofCampylobacter14.4 Diagnosis of Campylobacter infection (Campylobacteriosis)14.4.1 Conventional methods for detection of pathogen14.4.1.1 Direct demonstration of pathogen14.4.1.2 Culture and identification14.4.1.3 Selective media for Campylobacter isolation14.4.2 Confirmation of Campylobacter14.4.2.1 Colony characteristics14.4.2.2 Enzyme immune assay14.4.3 Molecular tools and techniques for Campylobacter diagnosis14.4.3.1 Phenotypic methods14.4.3.1.1 Bio-typing14.4.3.1.2 Phage-typing14.4.3.2 Genotyping methods14.4.3.2.1 Macro-restriction-mediated-analyses14.4.3.2.2 Polymerase Chain Reaction (PCR) based assays14.4.3.2.3 Ribotyping14.4.3.2.4 Fla-typing14.4.4 Metagenomics as a diagnostic tool14.4.4.1 Structural metagenomics14.4.4.2 Functional metagenomic14.5 Conclusion & Future perspectivesRecent trends in Bovine tuberculosis detection and control methods15.1 Introduction15.1.1. Bovine TB – The causative organism and the disease15.1.2. Host genetics15.1.3. Surveillance Strategies,Prevention and Control Methods.15.2 Some basics of performance characteristics of Diagnostic tests15.2.1 Purpose of diagnostic tests15.2.2 Attributes of an Ideal diagnostic test15.3 Detection methods and strategies15.3.1 Direct Detection of the Pathogen15.3.1.1 Post-mortem examination15.3.1.2 Direct microscopic detection15.3.1.3 Bacteriological culture15.3.1.4 Nucleic Acid detection based molecular assays15.3.2. Detection of the cell-mediated immunity in host.15.3.2.1 Tuberculin DTH skin test15.3.2.2. Gamma-interferon assay15.3.2.3. Lymphocyte proliferation assay (LPA)15.3.2.4. Enzyme-linked immunosorbent spot (ELISPOT) assay15.3.3. Detection of the host antibody response to infection15.3.3. 1. Enzyme immunoassay (EIA) or Enzyme-linked immunosorbent assay (ELISA)15.3.3.2.Multi Antigen Print Immunoassay (MAPIA)15.3.3.3. Dual Path Platform (DPP) assay15.3.3.4. Fluorescent Polarisation Assay15.3.3.4.The SeraLyte-Mbv (PriTestInc) assay15.4 Futuristic Approaches 15.4.1. Detection of the host enzyme Adenosine deaminase enzyme(ADA)15.4.2. Detection of humoral response based on IgA (with or without IgG)15.4.3 Use of Recombinant molecule as markers15.4.4 High throughput technological advances for detection of conventional targets15.4.5 Combinatorial Approaches15.5 ConclusionLivestock Enteric Viruses: Latest Diagnostic Techniques for Their Easy and Rapid Identification16.1 Introduction16.2 Latest diagnostic techniques for identification of major enteric viruses affecting livestock16.2.1 Bovine corona viruses (BoCV)16.2.2 Bovine enterovirus (BEV)16.2.3 Rotaviruses16.2.4 Astroviruses16.2.5 Caliciviruses16.2.6 Picobirnaviruses16.3 ConclusionCoronaviruses: Recent trends and approaches in diagnosis and management17.1 Introduction17.2 Virus, Virology, and Pathogenesis17.3 Global Epidemiology17.4 Virus Diagnosis17.4.1 Virus Isolation17.4.2 Electron Microscopy17.4.3 Serology17.4.4 Molecular diagnosis17.5 Management of Coronaviruses17.5.1 Ribavirin17.5.2 Other antiviral Drug17.5.3 Monoclonal antibody therapy17.5.4 InterferonRecombinase Polymerase Amplification (RPA): A New Approach for Disease Diagnosis18.1 Introduction to Recombinase Polymerase Amplification18.2 Methodology and different parameters controlling RPA18.2.1 Primer and Probe design 18.2.2 Temperature18.3.3 Effect of crowding agent and mixing18.3.4 Incubation time18.3.5 Type of samples18.3 RPA reaction conditions18.3.1 Multiplexing in RPA18.4 Major applications of RPA technique18.4.1 Multiple target detection18.4.2 Seed testing and other agricultural assays18.4.3 On-site microbial testing18.4.4 Disease detection in animals18.4.5 Medical diagnostics18.5 Comparison with other isothermal technique18.6 Advantages over real time PCR18.7 ConclusionGlobal Rules, Regulations and Intellectual Property Rights on diagnostic methods19.1 Introduction19.1.1. Patenting19.1.2.Rationalization of patenting19.1.3.Patenting of Diagnostic methods19.1.4 What is a patent?19.2 Patent laws in India19.3 Patent Laws in USA19.4 Patent laws in Europe19.5 Analysis and Conclusion

"In this multi-authored text, contributing experts offer a broad overview of the most modern technologies—primarily molecular in scale but including an array of innovative microscopic and scanning techniques—for the detection and identification of infectious-disease organisms. In considering these novel diagnostic methods, authors generally emphasize overall utility and performance characteristics, notably sensitivity/specificity, accuracy/precision, rapidity, affordability, and ease of use. They also consider the direction of future efforts with respect to selected animal diseases. As shown in these pages, widespread application of modern technology has greatly changed the nature of animal disease diagnosis. This volume will be of considerable value to virologists, bacteriologists, molecular biologists, and others working in diagnostic facilities."— D. A. Brass, independent scholar, Choice December 2022