Current FMD diagnostic technologies used in Australia

Australia’s preparedness for Foot and Mouth Disease (FMD) is underpinned by continued investment in advanced diagnostic technologies designed to provide rapid, accurate, and scalable detection capabilities, which are critical for an effective biosecurity response and rapid restoration of trade status in the event of an incursion. In recent years, multiple approaches—ranging from molecular assays and serological methods to point-of-care devices and digital surveillance infrastructures—have been developed, validated, and implemented within the Australian context.
 
Molecular Diagnostic Techniques: Real-Time PCR and Beyond
 
One of the core advancements is the comprehensive implementation of molecular diagnostic techniques—especially quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays—for routine diagnostic and surveillance purposes. The Australian Animal Health Laboratory (AAHL) has deployed two TaqMan PCR assays targeting independent sections of the FMD viral genome: the internal ribosome entry site (IRES) and the 3D polymerase coding region. These molecular tests can detect a wide array of FMDV serotypes with high sensitivity and specificity, and are routinely run in parallel for suspect cases, providing robust confirmation or exclusion of FMD infection. This dual-target approach increases confidence in diagnosis because the assays amplify different genetic regions, reducing the chance of false negatives due to sequence variation. The established protocols allow detection of FMDV in multiple sample types, supporting both outbreak response and proof-of-freedom testing.
 
In tandem, Australia has adopted and continues to refine other nucleic acid–based detection platforms, such as reverse transcription loop-mediated isothermal amplification (RT-LAMP), which enables rapid amplification at a constant temperature. RT-LAMP assays are particularly notable for their speed and robustness, completing detection typically within an hour and potentially offering sensitivity on par with, or even exceeding, certain conventional PCR protocols, particularly when coupled with innovations such as swarm primers.
 
Rapid Point-of-Care and Field Deployable Diagnostic Tools
 
Recognizing the need for faster field testing, Australia has validated and started deploying rapid point-of-care tests (POCTs) suitable for in-field or pen-side diagnosis. RT-LAMP, as previously mentioned, can be adapted for field deployment, given its simple, portable equipment and minimal infrastructure requirements. Additional POCTs in the form of lateral flow immunochromatographic (LFI) test strips have also been developed and assessed for their utility in Australia. These LFI assays enable on-site detection of either viral antigens or specific antibodies, allowing for straightforward visual interpretation of results without the need for sophisticated laboratory processing. Their ease of use and speed (often yielding results in under an hour) facilitate rapid decision-making and containment measures in the field.
 
Serological Innovations: Advanced ELISA Platforms for Surveillance and DIVA
 
Australia leads in the development and implementation of refined serological assays, particularly enzyme-linked immunosorbent assay (ELISA) technologies. Central to FMD surveillance strategies is the Australian-developed 3ABC non-structural protein (NSP) ELISA, specifically tailored to differentiate infected from vaccinated animals (DIVA). This assay has undergone extensive validation for diagnostic sensitivity (91.5%) and specificity (96.4%), with particular relevance for herd-level screening and confirmation of absence of FMDV infection across diverse livestock populations. The 3ABC NSP-ELISA also aids substantiation of freedom from infection post-vaccination or post-outbreak, which is crucial for resuming export markets following control activities.
 
Parallel serological platforms based on recombinant proteins and monoclonal antibodies, such as solid-phase competition (SPC)-ELISA and liquid-phase blocking (LPB)-ELISA, are utilized for both broad surveillance and precise serotyping, with demonstrated high reproducibility and rapid turnaround. Notably, recombinant antigen ELISAs enhance safety and uniformity by circumventing the need to handle live virus, thus addressing Australian biosecurity restrictions on direct FMDV work in-country.
 
Integration of Next-Generation Sequencing (NGS) and Digital Surveillance
 
Australia has piloted and incorporated next-generation sequencing (NGS) methods into FMD diagnostic workflows to provide comprehensive genotypic characterization of circulating FMDV strains during outbreaks. NGS enables rapid whole-genome sequencing from clinical samples, fundamental for molecular epidemiology, tracing of outbreak sources, and informed selection of appropriate vaccine strains. This incorporation of genomics complements molecular and serological surveillance and enhances the ability to track viral evolution.
 
Supporting these technical advancements is the implementation of national digital surveillance and laboratory information management systems. These platforms allow real-time data integration from laboratory diagnostics, POCTs, and field surveillance, optimizing the detection-response continuum and facilitating rapid information flow between laboratories, government, and industry. Advanced decision-support tools, including outbreak simulation models such as the Australian Animal Disease spread model (AADIS), are integrated for scenario analysis and for guiding resource allocation, vaccination, and movement control strategies during emergencies.

Comparative Evaluation of Diagnostic Platforms
 
Recent studies and critical appraisals have emphasized that novel diagnostics—such as RT-LAMP and POCTs—offer substantial improvements in efficiency over traditional methods like qRT-PCR, particularly in time-to-result and field-deployability, without compromising sensitivity or specificity in most use cases. For example, comparative evaluations indicate that multiplexed RT-LAMP (mRT-LAMP) can produce diagnostic results in less than half the time of RT-qPCR, which is vital for high-throughput or remote-surveillance contexts. However, during laboratory-based incident investigations, qRT-PCR remains the gold standard due to its high analytical sensitivity and established validation.
 
Investment, Collaboration, and Continued Development
 
Australia’s government and livestock industry have jointly invested in ambitious, multidisciplinary projects such as the FMD Ready Project, which is designed to ensure the continuous improvement, validation, and deployment of state-of-the-art diagnostics. These initiatives include funding from Meat & Livestock Australia, the Department of Agriculture, Water and the Environment, Animal Health Australia, and other partners to both drive technological advancement and guarantee knowledge transfer into the field through training, proficiency testing, and simulation exercises. Significant collaboration with international laboratories ensures that diagnostic innovations are rapidly assessed against emerging strains and global best practices.
 
Practical Implementation and “Fit-for-Purpose” Diagnostics
 
Australia’s diagnostic landscape is characterized by a layered approach, combining central reference laboratory capabilities with deployable rapid tests and integrating molecular, serological, and digital data streams. Diagnostic platforms are selected based on end-use: qRT-PCR and comprehensive ELISAs for confirmation and surveillance, field-deployable RT-LAMP and LFI strips for on-site exclusion or preliminary diagnosis, and NGS for characterization and trace-back. All diagnostic technologies are supported by ongoing proficiency testing and regulatory oversight to ensure reliability and “fit-for-purpose” application in the Australian context.
 
Conclusion
 
Australia’s latest advancements in FMD diagnostic technologies reflect a strategic investment in molecular, serological, and digital solutions that collectively bolster national biosecurity preparedness. These innovations provide rapid, sensitive, and specific detection tools, enable scalable deployment from laboratory to field, and support integrated surveillance and outbreak management systems. Ongoing research, international collaboration, and multidisciplinary partnerships ensure that Australian FMD diagnostics remain at the global forefront, safeguarding the livestock industries and supporting a swift and confident response to potential incursions.