• Foot-and-mouth disease (FMD)
• Goats
• Laboratory data
• Retrospective analysis
• Sheep
• Small ruminants

• Animals
• Foot-and-Mouth Disease/epidemiology
• Foot-and-Mouth Disease/virology
• Retrospective Studies
• Foot-and-Mouth Disease Virus/isolation & purification
• Foot-and-Mouth Disease Virus/physiology
• Sheep Diseases/epidemiology
• Sheep Diseases/virology
• Goat Diseases/epidemiology
• Goat Diseases/virology
• Swine
• Swine Diseases/epidemiology
• Swine Diseases/virology
• Sheep
• Goats
• Ruminants
• Cattle
• Cattle Diseases/epidemiology
• Cattle Diseases/virology
• Animals, Wild

• 2B-NSP
• Colorimetric assay
• FMDV
• Pan-serotype
• RT-LAMP

• FMD
• MolEpidPred
• machine learning
• molecular epidemiology
• nucleotide
• web-server

• Foot-and-Mouth Disease Virus/genetics
• Foot-and-Mouth Disease Virus/classification
• Foot-and-Mouth Disease/epidemiology
• Foot-and-Mouth Disease/virology
• Computational Biology/methods
• Algorithms
• Molecular Epidemiology/methods
• Animals
• Serogroup
• Software
• Capsid Proteins/genetics
• Base Sequence

• ST-SCST-MISC-0011-2023 Science and Technology Department, Government of Odisha, India
• Indian Council of Agricultural Research
• CRG/2021/004960 Core Research Grant of Science & Engineering Research Board, New Delhi
• Core Research Grant of Science & Engineering Research Board, New Delhi

• Combined vaccine
• Concurrent infections
• Diagnosis
• FMD
• Immune suppression
• Serotypes

• Animals
• Asia/epidemiology
• Foot-and-Mouth Disease/epidemiology
• Foot-and-Mouth Disease/prevention & control
• Foot-and-Mouth Disease/transmission
• Foot-and-Mouth Disease/virology
• Foot-and-Mouth Disease Virus/immunology
• Foot-and-Mouth Disease Virus/classification
• Foot-and-Mouth Disease Virus/genetics
• Foot-and-Mouth Disease Virus/pathogenicity
• Prevalence
• Serogroup
• Vaccination/veterinary
• Viral Vaccines/administration & dosage
• Viral Vaccines/immunology

• LAMP
• bioengineering
• diagnosis
• foot-and-mouth disease
• loop-mediated amplification
• point-of-need
• virus

• Isothermal amplification
• Molecular techniques
• PCR
• Plant virus detection
• Virus diagnosis

• Science and Engineering Research Board (SERB), Department of Science and Technology, Govt. of India

• Loop-mediated isothermal amplification
• Photochromic sensing chip
• Transmissible gastroenteritis virus
• Visual detection

• Swine
• Animals
• Transmissible gastroenteritis virus/genetics
• Zinc Oxide
• Sensitivity and Specificity
• Biosensing Techniques
• Nucleic Acid Amplification Techniques/methods
• Nucleic Acids

• Animals
• Dogs
• Antigens, Viral
• Astroviridae/genetics
• Real-Time Polymerase Chain Reaction/veterinary
• Reproducibility of Results
• RNA Viruses

• feline immunodeficiency virus
• loop-mediated isothermal amplification
• molecular diagnosis
• neutral red

• H5N1 subtype
• avian influenza virus
• detection technology

• Animals
• Humans
• Influenza in Birds/diagnosis
• Influenza A Virus, H5N1 Subtype/genetics
• Poultry
• Influenza A virus
• Agriculture
• Mammals

• 2021YFF0602801 and 2022YFF1101000 National Key Research and Development Program of China
• LTGN23B050001 Natural Fund Exploration Project of Zhejiang Province
• LQ23C200006 Zhejiang Provincial Natural Science Foundation of China

• Infectious diseases
• Isothermal nucleic acid amplification
• Pen-side testing
• Veterinary diagnostics

• Animals
• Humans
• Virus Diseases/diagnosis
• Virus Diseases/veterinary
• Nucleic Acid Amplification Techniques/methods
• Communicable Diseases/diagnosis
• Ruminants
• Sensitivity and Specificity

• 2210597 Türkiye Bilimsel ve Teknolojik Araştırma Kurumu

• Foot-and-mouth disease
• pen-side diagnosis
• portable real-time PCR device

• RT-LAMP
• porcine epidemic diarrhea virus
• visual detection

• FMD
• PCR
• PPR
• RNA extraction
• foot and mouth disease
• pen-side PCR
• peste des petits ruminants

• Animals
• Cattle
• Foot-and-Mouth Disease/diagnosis
• Goat Diseases
• Goats
• Peste-des-Petits-Ruminants
• Peste-des-petits-ruminants virus/genetics
• RNA, Viral/genetics

• BBS/E/I/00007036 Biotechnology and Biological Sciences Research Council
• BBS/E/I/00007037 Biotechnology and Biological Sciences Research Council
• BBS/E/I/00007030, BBS/E/I/00007031, BBS/E/I/00007036, BBS/E/I/00007037 Biotechnology and Biological Sciences Research Council

• D. nodosus
• Duplex PCR
• F. necrophorum
• Footrot
• LAMP
• Sheep and goat

• SARS-CoV-2 detection
• decentralized diagnostics
• loop-mediated isothermal amplification
• low-cost molecular diagnostics
• point of care diagnostics
• rapid diagnostic test

• bovine respiratory disease
• diagnostics
• loop-mediated isothermal amplification
• pen-side

• Animals
• Cattle
• Cattle Diseases/diagnosis
• Cattle Diseases/microbiology
• Colorimetry/instrumentation
• Colorimetry/veterinary
• Diagnostic Tests, Routine/instrumentation
• Diagnostic Tests, Routine/veterinary
• Mannheimia haemolytica/isolation & purification
• Molecular Diagnostic Techniques/instrumentation
• Molecular Diagnostic Techniques/veterinary
• Nose/microbiology
• Nucleic Acid Amplification Techniques/instrumentation
• Nucleic Acid Amplification Techniques/veterinary
• Pasteurella Infections/diagnosis
• Pasteurella Infections/microbiology
• Pasteurella Infections/veterinary
• Pasteurella multocida/isolation & purification
• Pasteurellaceae/isolation & purification
• Pasteurellaceae Infections/diagnosis
• Pasteurellaceae Infections/microbiology
• Pasteurellaceae Infections/veterinary

• 2020-68014-31302 National Institute of Food and Agriculture
• Purdue University

• bovine respiratory disease
• diagnostics
• loop-mediated isothermal amplification
• pen-side

• Animals
• Cattle
• Cattle Diseases/diagnosis
• Cattle Diseases/microbiology
• Colorimetry/instrumentation
• Colorimetry/veterinary
• Diagnostic Tests, Routine/instrumentation
• Diagnostic Tests, Routine/veterinary
• Mannheimia haemolytica/isolation & purification
• Molecular Diagnostic Techniques/instrumentation
• Molecular Diagnostic Techniques/veterinary
• Nose/microbiology
• Nucleic Acid Amplification Techniques/instrumentation
• Nucleic Acid Amplification Techniques/veterinary
• Pasteurella Infections/diagnosis
• Pasteurella Infections/microbiology
• Pasteurella Infections/veterinary
• Pasteurella multocida/isolation & purification
• Pasteurellaceae/isolation & purification
• Pasteurellaceae Infections/diagnosis
• Pasteurellaceae Infections/microbiology
• Pasteurellaceae Infections/veterinary

• Amide additives
• Bst 3.0
• Foot-and-Mouth disease Virus (FMDV)
• Loop-Mediated Isothermal Amplification (LAMP)
• Reverse transcriptase

• LAMP method
• SARS-CoV-2 detection
• isothermal amplification

• COVID-19/diagnosis
• Humans
• Molecular Diagnostic Techniques/methods
• Nucleic Acid Amplification Techniques/methods
• SARS-CoV-2/isolation & purification

Equine viral diseases remain a prominent concern for human and equine health globally. Many of these viruses are of primary biosecurity concern to countries that import equines where these viruses are not present. In addition, several equine viruses are zoonotic, which can have a significant impact on human health. Current diagnostic techniques are both time consuming and laboratory-based. The ability to accurately detect diseases will lead to better management, treatment strategies, and health outcomes. This review outlines the current modern isothermal techniques for diagnostics, such as loop-mediated isothermal amplification and insulated isothermal polymerase chain reaction, and their application as point-of-care diagnostics for the equine industry.

The global equine industry provides significant economic contributions worldwide, producing approximately USD $300 billion annually. However, with the continuous national and international movement and importation of horses, there is an ongoing threat of a viral outbreak causing large epidemics and subsequent significant economic losses. Additionally, horses serve as a host for several zoonotic diseases that could cause significant human health problems. The ability to rapidly diagnose equine viral diseases early could lead to better management, treatment, and biosecurity strategies. Current serological and molecular methods cannot be field-deployable and are not suitable for resource-poor laboratories due to the requirement of expensive equipment and trained personnel. Recently, isothermal nucleic acid amplification technologies, such as loop-mediated isothermal amplification (LAMP) and insulated isothermal polymerase chain reaction (iiPCR), have been developed to be utilized in-field, and provide rapid results within an hour. We will review current isothermal diagnostic techniques available to diagnose equine viruses of biosecurity and zoonotic concern and provide insight into their potential for in-field deployment.

• equine
• field-deployable
• insulated isothermal polymerase chain reaction
• loop-mediated isothermal amplification
• point-of-care testing
• viruses

Foot-and-mouth disease virus (FMDV) is a highly contagious disease that affects cloven-hoofed animals. The traditional diagnostic methods for FMDV have several drawbacks such as cross-reactivity, low sensitivity, and low selectivity. To overcome these drawbacks, we present an optical and electrochemical dual-modal approach for the specific detection of FMDV serotypes O and A by utilizing a magnetic nanoparticle labeling technique with resorufin β-d-glucopyranoside (res-β-glc) and β-glucosidase (β-glc), without the use of typical lateral flow assay or polymerase chain reaction. FMDV serotypes O and A were reacted with pan-FMDV antibodies that recognize all seven FMDV serotypes (O, A, C, Asia 1, SAT 1, SAT 2, and SAT 3). The antigen–antibody complex was then immobilized on magnetic nanoparticles and reacted with β-glc-conjugated FMDV type O or type A antibodies. Subsequently, the addition of res-β-glc resulted in the release of fluorescent resorufin and glucose owing to catalytic hydrolysis by β-glc. The detection limit of fluorescent signals using a fluorescence spectrophotometer was estimated to be log(6.7) and log(5.9) copies/mL for FMDV type O and A, respectively, while that of electrochemical signals using a glucometer was estimated to be log(6.9) and log(6.1) copies/mL for FMDV type O and A, respectively. Compared with a commercially available lateral flow assay diagnostic kit for immunochromatographic detection of FMDV type O and A, this dual-modal detection platform offers approximately four-fold greater sensitivity. This highly sensitive and accurate dual-modal detection method can be used for effective disease diagnosis and treatment, and will find application in the early-stage diagnosis of viral diseases and next-generation diagnostic platforms.

• dual-modality
• electrochemical
• foot-and-mouth disease virus (FMDV)
• optical

• ASFV
• Asfarviridae
• diagnostics
• neutral red
• one-step
• penside
• visual LAMP

• ASFV
• LAMP
• Timor-Leste
• colourmetric LAMP
• qPCR

• African Swine Fever/diagnosis
• African Swine Fever/epidemiology
• African Swine Fever/virology
• African Swine Fever Virus/genetics
• African Swine Fever Virus/isolation & purification
• Animals
• Disease Outbreaks
• Female
• Male
• Molecular Diagnostic Techniques/methods
• Molecular Diagnostic Techniques/standards
• Nucleic Acid Amplification Techniques/methods
• Nucleic Acid Amplification Techniques/standards
• Real-Time Polymerase Chain Reaction
• Sensitivity and Specificity
• Swine
• Viremia

Remote and rural communities in low‐ and middle‐income countries (LMICs) are disproportionately affected by infectious animal diseases due to their close contact with livestock and limited access to animal health personnel). However, animal disease surveillance and diagnosis in LMICs is often challenging, and turnaround times between sample submission and diagnosis can take days to weeks. This diagnostic gap and subsequent disease under‐reporting can allow emerging and transboundary animal pathogens to spread, with potentially serious and far‐reaching consequences. Point‐of‐care tests (POCTs), which allow for rapid diagnosis of infectious diseases in non‐laboratory settings, have the potential to significantly disrupt traditional animal health surveillance paradigms in LMICs. This literature review sought to identify POCTs currently available for diagnosing infectious animal diseases and to determine facilitators and barriers to their use and uptake in LMICs. Results indicated that some veterinary POCTs have been used for field‐based animal disease diagnosis in LMICs with good results. However, many POCTs target a small number of key agricultural and zoonotic animal diseases, while few exist for other important animal diseases. POCT evaluation is rarely taken beyond the laboratory and into the field where they are predicted to have the greatest impact, and where conditions can greatly affect test performance. A lack of mandated test validation regulations for veterinary POCTs has allowed tests of varying quality to enter the market, presenting challenges for potential customers. The use of substandard, improperly validated or unsuitable POCTs in LMICs can greatly undermine their true potential and can have far‐reaching negative impacts on disease control. To successfully implement novel rapid diagnostic pathways for animal disease in LMICs, technical, regulatory, socio‐political and economic challenges must be overcome, and further research is urgently needed before the potential of animal disease POCTs can be fully realized.

• communicable disease control
• developing countries
• livestock
• point-of-care testing
• public health
• validation and quality control
• zoonoses

The polymerase chain reaction (PCR) has become a powerful molecular diagnostic technique over the past few decades, but remains somewhat impaired due to low specificity, poor sensitivity, and false positive results. Metal and carbon nanomaterials, quantum dots, and metal oxides, can improve the quality and productivity of PCR assays. Here, we describe the ability of PCR assisted with nanomaterials (nano-PCR) comprising a nanocomposite of graphene oxide (GO) and gold nanoparticles (AuNPs) for sensitive detection of the foot-and-mouth disease virus (FMDV). Graphene oxide and AuNPs have been widely applied as biomedical materials for diagnosis, therapy, and drug delivery due to their unique chemical and physical properties. Foot-and-mouth disease (FMD) is highly contagious and fatal for cloven-hoofed animals including pigs, and it can thus seriously damage the swine industry. Therefore, a highly sensitive, specific, and practical method is needed to detect FMDV. The detection limit of real-time PCR improved by ~1000 fold when assisted by GO-AuNPs. We also designed a system of detecting serotypes in a single assay based on melting temperatures. Our sensitive and specific nano-PCR system can be applied to diagnose early FMDV infection, and thus may prove to be useful for clinical and biomedical applications.

• foot-and-mouth disease virus
• gold nanoparticle
• graphene oxide
• polymerase chain reaction

Foot-and-mouth disease (FMD) is a devastating livestock disease caused by foot-and-mouth disease virus (FMDV). Outbreaks of this disease in a country always result in conspicuous economic losses to livestock industry and subsequently lead to serious socioeconomic damages due to the immediate imposition of trade embargo. Rapid and accurate diagnoses are imperative to control this infectious virus. In the current review, enzyme-linked immunosorbent assay (ELISA)-based methods used in FMD diagnosis are extensively reviewed, particularly the sandwich, liquid-phase blocking, and solid-phase competition ELISA. The differentiation of infected animals from vaccinated animals using ELISA-based methods is also highlighted, in which the role of 3ABC polyprotein as a marker is reviewed intensively. Recently, more studies are focusing on the molecular diagnostic methods, which detect the viral nucleic acids based on reverse transcription-polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplification (RT-LAMP). These methods are generally more sensitive because of their ability to amplify a minute amount of the viral nucleic acids. In this digital era, the RT-PCR and RT-LAMP are progressing toward the mobile versions, aiming for on-site FMDV diagnosis. Apart from RT-PCR and RT-LAMP, another diagnostic assay specifically designed for on-site diagnosis is the lateral flow immunochromatographic test strips. These test strips have some distinct advantages over other diagnostic methods, whereby the assay often does not require the aid of an external device, which greatly lowers the cost per test. In addition, the on-site diagnostic test can be easily performed by untrained personnel including farmers, and the results can be obtained in a few minutes. Lastly, the use of FMDV diagnostic assays for progressive control of the disease is also discussed critically.

• complement fixation test (CFT)
• enzyme-linked immunosorbent assay (ELISA)
• foot-and-mouth disease virus (FMDV) diagnosis
• lateral flow device (LFD)
• reverse transcription-loop-mediated isothermal amplification (RT-LAMP)
• reverse transcription-polymerase chain reaction (RT-PCR)
• reverse transcription-recombinase polymerase amplification (RT-RPA)
• virus neutralization test (VNT)

• assimilating probe
• foot-and-mouth disease virus
• real-time RT-LAMP

• RT-LAMP
• cattle
• detection and validation
• foot-and-mouth disease virus
• in-field test
• internal positive control

• Bst DNA polymerase
• LAMP
• loop-mediated isothermal amplification
• plant virology
• primers
• real-time monitoring
• viroids
• virus

• Bst DNA polymerase
• Citrus
• RT-LAMP
• SYBR Green I
• Tristeza disease

The application of innovative diagnostic technologies for the detection of animal pathogens at an early stage is essential in restricting the economic loss incurred due to emerging infectious animal diseases. The desirable characteristics of such diagnostic methods are easy to use, cost-effective, highly sensitive, and specific, coupled with the high-throughput detection capabilities. The enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are still the most common assays used for the detection of animal pathogens across the globe. However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Furthermore, animal disease diagnostics need to be updated regularly to capture new, emerging and divergent infectious pathogens, and biotechnological innovations are helpful in fulfilling the rising demand for such diagnostics for the welfare of the society. Therefore, this chapter primarily describes and discusses in detail the serological, molecular, novel high-throughput, and POC assays to detect pathogens affecting farm and companion animals.

• Bioassay
• Colorimetric detection
• Loop-mediated isothermal amplification (LAMP)
• Nanoparticle-based biosensors
• Virus

Loop mediated isothermal amplification (LAMP) is a nucleic acid amplification technique performed under isothermal conditions. The output of this amplification technique includes multiple different sizes of deoxyribonucleic acid (DNA) structures which are identified by a banding pattern on gel electrophoresis plots. Although this is a specific amplification technique, the complexity of the primer design and amplification still lead to the issue of obtaining false‐positive results, especially when a positive reading is determined solely by whether there is any banding pattern in the gel electrophoresis plot. Here, we first performed extensive LAMP experiments and evaluated the DNA structures using microchip electrophoresis. We then developed a mathematical model derived from the various components that make up an entire LAMP structure to predict the full LAMP structure size in base pairs. This model can be implemented by users to make predictions for specific, DNA size dependent, banding patterns on their gel electrophoresis plots. Each prediction is specific to the target sequence and primers used and therefore reduces incorrect diagnosis errors through identifying true‐positive and false‐positive results. This model was accurately tested with multiple primer sets in house and was also translatable to different DNA and RNA types in previously published literature. The mathematical model can ultimately be used to reduce false‐positive LAMP diagnosis errors for applications ranging from tuberculosis diagnostics to E. coli to numerous other infectious diseases.

• Electropherogram
• Loop mediated isothermal amplification
• Mathematical model
• Microchip electrophoresis

• Foot-and-mouth disease virus
• handheld
• polymerase chain reaction

• PCR
• detection
• loopmediated isothermal amplification
• tilapia lake virus

• Animals
• Aquaculture
• DNA Primers/genetics
• DNA Virus Infections/diagnosis
• DNA Virus Infections/veterinary
• DNA Viruses/isolation & purification
• Fish Diseases/diagnosis
• Fish Diseases/virology
• Lakes/virology
• Nucleic Acid Amplification Techniques/methods
• RNA, Viral/genetics
• Reverse Transcription
• Sensitivity and Specificity
• Temperature
• Tilapia/virology

• Loop mediated isothermal amplification (LAMP)
• Methyl green
• Mycobacterium tuberculosis
• Tuberculosis

• Coloring Agents
• DNA, Bacterial/analysis
• Developing Countries
• Humans
• Methyl Green
• Mycobacterium tuberculosis/genetics
• Mycobacterium tuberculosis/isolation & purification
• Nephelometry and Turbidimetry/methods
• Nucleic Acid Amplification Techniques/methods
• Point-of-Care Testing
• Retrospective Studies
• Sensitivity and Specificity
• Tuberculosis/diagnosis

Senecavirus A (SVA) is a critical pathogen causing vesicular lesions in sows and acute death of newborn piglets, resulting in very large economic losses in the pig industry. To restrict the transmission of SVA, an establishment of an effective diagnostic method is crucial for the prevention and control of the disease. However, traditional detection methods often have many drawbacks. In this study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) was combined with a lateral flow dipstick (LFD) to detect SVA. The resulting RT-LAMP-LFD assay was performed at 60°C for 50 min and then directly judged on an LFD visualization strip. This method shows high specificity and sensitivity to SVA. The detection limit of RT-LAMP was 4.56x10^-8 ng/μL RNA, approximately 11 copies/μL RNA, and it was 10 times more sensitive than RT-PCR. This detection method’s positive rate for clinical samples is comparable to that of RT-PCR. This method is time saving and highly efficient and is thus expected to be used to diagnose SVA infections in this field.

• Animals
• Molecular Diagnostic Techniques
• Nucleic Acid Amplification Techniques
• Picornaviridae/genetics
• RNA, Viral/genetics
• Reverse Transcription
• Sensitivity and Specificity
• Swine

• LAMP
• classical swine fever virus
• foot-and-mouth disease virus
• microfluidic disk
• multiplex detection
• porcine circovirus 2
• porcine parvovirus
• porcine reproductive and respiratory swine virus
• pseudorabies virus

• Seneca Valley virus-1
• point-of-care diagnostics
• rapid detection
• reverse transcription loop-mediated isothermal amplification

• 5' Untranslated Regions/genetics
• Animals
• Biological Assay
• Communicable Diseases, Emerging/diagnosis
• Communicable Diseases, Emerging/veterinary
• Communicable Diseases, Emerging/virology
• DNA Primers/chemistry
• Foot-and-Mouth Disease/virology
• Nucleic Acid Amplification Techniques/methods
• Picornaviridae/genetics
• Picornaviridae Infections/diagnosis
• Picornaviridae Infections/veterinary
• Real-Time Polymerase Chain Reaction
• Reverse Transcription
• Sensitivity and Specificity
• Swine
• Swine Diseases/diagnosis
• Viral Proteins/genetics

• 1646343 Biotechnology and Biological Sciences Research Council
• BB/M017273/1 Biotechnology and Biological Sciences Research Council

• Kenaf
• LAMP
• Mesta yellow vein mosaic virus
• PCR
• Roselle
• Virus detection

• Animals
• Australia
• Bacterial Proteins/genetics
• Dichelobacter nodosus/genetics
• Dichelobacter nodosus/pathogenicity
• Early Diagnosis
• Foot Rot/diagnosis
• Foot Rot/microbiology
• Gram-Negative Bacterial Infections/diagnosis
• Gram-Negative Bacterial Infections/veterinary
• Polymerase Chain Reaction/methods
• Sensitivity and Specificity
• Serine Endopeptidases/genetics
• Sheep
• Sheep Diseases/microbiology