Dipstick-based rapid nucleic acids purification and CRISPR/Cas12a-mediated isothermal amplification for visual detection of African swine fever virus

Pathogenicity and virulence of African swine fever virus

African swine fever (ASF) is a devastating disease with a high impact on the pork industry worldwide. ASF virus (ASFV) is a very complex pathogen, the sole member of the family Asfaviridae, which induces a state of immune suppression in the host through infection of myeloid cells and apoptosis of lymphocytes. Moreover, haemorrhages are the other main pathogenic effect of ASFV infection in pigs, related to the infection of endothelial cells, as well as the activation and structural changes of this cell population by proinflammatory cytokine upregulation within bystander monocytes and macrophages. There are still many gaps in the knowledge of the role of proteins produced by the ASFV, which is related to the difficulty in producing a safe and effective vaccine to combat the disease, although few candidates have been approved for use in Southeast Asia in the past couple of years.

"Blue-red-purple" multicolored lateral flow immunoassay for simultaneous detection of GM crops utilizing RPA and CRISPR/Cas12a

Advanced multiplexed testing techniques should be designed and developed to ensure an accurate and reliable evaluation for unknown samples. In this study, an efficient platform coupled with the "Blue-Red-Purple" strategy based on recombinant polymerase amplification (RPA), CRISPR/Cas12a and lateral flow strip was established, which could realize the dual-target detection of CP4-EPSPS and Cry1Ab/Ac in genetically modified crops. The lateral flow immunoassay was developed using different colored microspheres to label the antibodies to realize the visualization of results and avoid cross-reactions. The proposed method exhibits high specificity, sensitivity and stability. The visual detection limits of standard plasmids and real samples reached 10 copies/μL and 0.5 %, respectively, which could be stored at 4 °C for 12 months with high detection ability. Moreover, the entire detection process could be completed within 50 min without any complex instruments or professional operators. These findings indicated that a sensitive, specific, rapid and accurate method was established for on-site detection of GM crops.

Strategic nucleic acid detection approaches for diagnosing African swine fever (ASF): navigating disease dynamics

African swine fever (ASF) is a devastating disease caused by African swine fever virus (ASFV) and leads to significant economic losses in the pig farming industry. Given the absence of an effective vaccine or treatment, the mortality rate of ASF is alarmingly close to 100%. Consequently, the ability to rapidly and accurately detect ASFV on site and promptly identify infected pigs is critical for controlling the spread of this pandemic. The dynamics of the ASF virus load and antibody response necessitate the adoption of various detection strategies at different stages of infection, a topic that has received limited attention to date. This review offers detailed guidance for choosing appropriate ASF diagnostic techniques tailored to the clinical manifestations observed from the acute to chronic phases, including asymptomatic cases. We comprehensively summarize and evaluate the latest advancements in ASFV detection methods, such as CRISPR-based diagnostics, biosensors, and microfluidics. Additionally, we address the challenges of false negatives or positives due to ASF variants or the use of injected live attenuated vaccines. This review provides an exhaustive list of diagnostic tests suitable for detecting each stage of symptoms and potential target genes for developing new detection methods. In conclusion, we highlight the current challenges and future directions in ASFV detection, underscoring the need for continued research and innovation in this field.

Advances, challenges, and opportunities for food safety analysis in the isothermal nucleic acid amplification/CRISPR-Cas12a era

Global food safety stands out as a prominent public concern, affecting populations worldwide. The recurrent challenge of food safety incidents reveals the need for a robust inspection framework. In recent years, the integration of isothermal nucleic acid amplification with CRISPR-Cas12a techniques has emerged as a promising tool for molecular detection of food hazards, presenting next generation of biosensing for food safety detection. This paper provides a comprehensive review of the current state of research on the synergistic application of isothermal nucleic acid amplification and CRISPR-Cas12a technology in the field of food safety. This innovative combination not only enriches the analytical tools, but also improving assay performance such as sensitivity and specificity, addressing the limitations of traditional methods. The review summarized various detection methodologies by the integration of isothermal nucleic acid amplification and CRISPR-Cas12a technology for diverse food safety concerns, including pathogenic bacterium, viruses, mycotoxins, food adulteration, and genetically modified foods. Each section elucidates the specific strategies employed and highlights the advantages conferred. Furthermore, the paper discussed the challenges faced by this technology in the context of food safety, offering insightful discussions on potential solutions and future prospects.

An instrument-free, integrated micro-platform for rapid and multiplexed detection of dairy adulteration in resource-limited environments

In dairy industry, expensive yak's milk, camel's milk, and other specialty dairy products are often adulterated with low-cost cow's milk, goat's milk and so on. Currently, the detection of specialty dairy products typically requires laboratory settings and relies on skilled operators. Therefore, there is an urgent need to develop a multi-detection technology and on-site rapid detection technique to enhance the efficiency and accuracy of the detection of specialty dairy products. In this study, we introduced a fully integrated and portable microfluidic detection platform called Sector Self-Driving Microfluidics (SDM), designed to simultaneously detect eight common species-specific components in milk. SDM integrated nucleic acid extraction, purification, loop-mediated isothermal amplification (LAMP), and lateral flow strip (LFS) detection functions into a closed microfluidic system, enabling contamination-free visual detection. The SDM platform used a constant-temperature heating plate, powered by a mobile battery, eliminated the need for additional power support. The SDM platform achieved nucleic acid enrichment and transfer through magnetic force and liquid flow driven by capillary forces, operating without external pumps. The standalone SDM platform could detect dairy components with as low as 1% content within 1 h. Validation with 35 commercially available samples demonstrated 100% specificity and accuracy compared to the gold standard real-time PCR. The SDM platform provided the dairy industry with an efficient, convenient, and accurate detection tool, enabling rapid on-site testing at production facilities or sales points. This facilitated real-time monitoring of quality issues during the production process, quickly identifying potential risks and preventing substandard products from entering the market.

Rapid Nucleic Acid Diagnostic Technology for Pandemic Diseases

The recent global pandemic of coronavirus disease 2019 (COVID-19) has enormously promoted the development of diagnostic technology. To control the spread of pandemic diseases and achieve rapid screening of the population, ensuring that patients receive timely treatment, rapid diagnosis has become the top priority in the development of clinical technology. This review article aims to summarize the current rapid nucleic acid diagnostic technologies applied to pandemic disease diagnosis, from rapid extraction and rapid amplification to rapid detection. We also discuss future prospects in the development of rapid nucleic acid diagnostic technologies.

Current detection methods of African swine fever virus

African swine fever (ASF), caused by the African swine fever virus (ASFV), is a highly contagious and notifiable animal disease in domestic pigs and wild boars, as designated by the World Organization for Animal Health (WOAH). The effective diagnosis of ASF holds great importance in promptly controlling its spread due to its increasing prevalence and the continuous emergence of variant strains. This paper offers a comprehensive review of the most common and up-to-date methods established for various genes/proteins associated with ASFV. The discussed methods primarily focus on the detection of viral genomes or particles, as well as the detection of ASFV associated antibodies. It is anticipated that this paper will serve as a reference for choosing appropriate diagnostic methods in diverse application scenarios, while also provide direction for the development of innovative technologies in the future.

Advanced Strategies for Developing Vaccines and Diagnostic Tools for African Swine Fever

African swine fever (ASF) is one of the most lethal infectious diseases affecting domestic pigs and wild boars of all ages. Over a span of 100 years, ASF has continued to spread over continents and adversely affects the global pig industry. To date, no vaccine or treatment has been approved. The complex genome structure and diverse variants facilitate the immune evasion of the ASF virus (ASFV). Recently, advanced technologies have been used to design various potential vaccine candidates and effective diagnostic tools. This review updates vaccine platforms that are currently being used worldwide, with a focus on genetically modified live attenuated vaccines, including an understanding of their potential efficacy and limitations of safety and stability. Furthermore, advanced ASFV detection technologies are presented that discuss and incorporate the challenges that remain to be addressed for conventional detection methods. We also highlight a nano-bio-based system that enhances sensitivity and specificity. A combination of prophylactic vaccines and point-of-care diagnostics can help effectively control the spread of ASFV.

Emergent Molecular Techniques Applied to the Detection of Porcine Viruses

Molecular diagnostic tests have evolved very rapidly in the field of human health, especially with the arrival of the recent pandemic caused by the SARS-CoV-2 virus. However, the animal sector is constantly neglected, even though accurate detection by molecular tools could represent economic advantages by preventing the spread of viruses. In this regard, the swine industry is of great interest. The main viruses that affect the swine industry are described in this review, including African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), and porcine circovirus (PCV), which have been effectively detected by different molecular tools in recent times. Here, we describe the rationale of molecular techniques such as multiplex PCR, isothermal methods (LAMP, NASBA, RPA, and PSR) and novel methods such as CRISPR-Cas and microfluidics platforms. Successful molecular diagnostic developments are presented by highlighting their most important findings. Finally, we describe the barriers that hinder the large-scale development of affordable, accessible, rapid, and easy-to-use molecular diagnostic tests. The evolution of diagnostic techniques is critical to prevent the spread of viruses and the development of viral reservoirs in the swine industry that impact the possible development of future pandemics and the world economy.

Bridging the Gap: Can COVID-19 Research Help Combat African Swine Fever?

African swine fever (ASF) is a highly contagious and economically devastating disease affecting domestic pigs and wild boar, caused by African swine fever virus (ASFV). Despite being harmless to humans, ASF poses significant challenges to the swine industry, due to sudden losses and trade restrictions. The ongoing COVID-19 pandemic has spurred an unparalleled global research effort, yielding remarkable advancements across scientific disciplines. In this review, we explore the potential technological spillover from COVID-19 research into ASF. Specifically, we assess the applicability of the diagnostic tools, vaccine development strategies, and biosecurity measures developed for COVID-19 for combating ASF. Additionally, we discuss the lessons learned from the pandemic in terms of surveillance systems and their implications for managing ASF. By bridging the gap between COVID-19 and ASF research, we highlight the potential for interdisciplinary collaboration and technological spillovers in the battle against ASF.

Microfluidics: the propellant of CRISPR-based nucleic acid detection

Since the discovery of collateral cleavage activity, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems have become the new generation of nucleic acid detection tools. However, their widespread application remains limited. A pre-amplification step is required to improve the sensitivity of CRISPR systems, complicating the operating procedure and limiting quantitative precision. In addition, nonspecific collateral cleavage activity makes it difficult to realize multiplex detection in a one-pot CRISPR reaction with a single Cas protein. Microfluidics, which can transfer nucleic acid analysis process to a chip, has the advantages of miniaturization, integration, and automation. Microfluidics coupled with CRISPR systems improves the detection ability of CRISPR, enabling fast, high-throughput, integrated, multiplex, and digital detection, which results in the further popularization of CRISPR for a range of scenarios.

Development of molecular and antigenic-based rapid tests for the identification of African swine fever virus in different tissues

African swine fever (ASF) is a severe haemorrhagic infectious disease affecting suids, thus representing a great economic concern. Considering the importance of the early diagnosis, rapid point of care testing (POCT) for ASF is highly demanded. In this work, we developed two strategies for the rapid onsite diagnosis of ASF, based on Lateral Flow Immunoassay (LFIA) and Recombinase Polymerase Amplification (RPA) techniques. The LFIA was a sandwich-type immunoassay exploiting a monoclonal antibody directed towards the p30 protein of the virus (Mab). The Mab was anchored onto the LFIA membrane to capture the ASFV and was also labelled with gold nanoparticles for staining the antibody-p30 complex. However, the use of the same antibody for capturing and as detector ligand showed a significant competitive effect for antigen binding, so required an experimental design to minimize reciprocal interference and maximize the response. The RPA assay, employing primers to the capsid protein p72 gene and an exonuclease III probe, was performed at 39 °C. The limit of detection of the method was assessed using a plasmid encoding the target gene and resulted in 5 copy/μL. The new LFIA and RPA were applied for ASFV detection in the animal tissues usually analysed by conventional assays (i.e., real-time PCR), such as kidney, spleen, and lymph nodes. A simple and universal virus extraction protocol was applied for sample preparation, followed by DNA extraction and purification for the RPA. The LFIA only required the addition of 3% H2O2 to limit matrix interference and prevent false positive results. The two rapid methods (25 min and 15 min were needed to complete the analysis for RPA and LFIA, respectively) showed high diagnostic specificity (100%) and sensitivity (93% and 87% for LFIA and RPA, respectively) for samples with high viral load (Ct < 27). False negative results were observed for samples with low viral load (Ct > 28) and/or also containing specific antibodies to ASFV, which decreased antigen availability and were indicative of a chronic, poorly transmissible infection. The simple and rapid sample preparation and the diagnostic performance of the LFIA suggested its large practical applicability for POC diagnosis of ASF.

Amino-modified silica membrane capable of DNA extraction and enrichment for facilitated isothermal amplification detection of Mycoplasma pneumoniae

Herein, we developed a facile integrated Mycoplasma pneumoniae diagnosis platform by combining amino-modified silica membrane (AMSM)-based nucleic acids fast extraction and enrichment with colorimetric isothermal amplification detection. AMSM demonstrates a strong ability to capture and enrich nucleic acids in complicated biological matrices, and the purified AMSM/nucleic acids composite could be directly used to perform isothermal amplification including denaturation bubble-mediated strand exchange amplification (SEA) and loop-mediated isothermal amplification (LAMP) reactions. Through comparing clinical specimens, excellent performance of AMSM-based SEA assay with 93.33% sensitivity and 100% specificity relative to real-time PCR was observed, and for AMSM-based LAMP was 96.67% and 100%, respectively. The diagnostic procedure could be completed within 55 min, and the colorimetric-based visual result further alleviates the use of sophisticated equipment. The proposed approach possesses great potential as a simple and time-saving alternative for point-of-care testing (POCT) of M. pneumoniae in resource-limited regions.

Integrated slip valve-assisted fluidic chip coupling with CRISPR/Cas12a system for nucleic acid analysis

Currently, some on-site nucleic acid detection platforms have been developed. However, these platforms still need to be improved in device integration and multiple detection capability. In this work, an integrated dual nucleic acid analysis platform was developed by slip valve-assisted fluidic chip coupled with CRISPR/Cas12a system. All the reagents, including nucleic acid extraction, air-dried loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a detection reagents, were preloaded on the fluidic chip. Liquids transfer and stirring could be controlled by a slip valve and a syringe. By combining duplex LAMP reaction with two CRISPR detection units, CRISPR/Cas12a-based dual nucleic acid analysis was successfully constructed. Benefiting from high-quality nucleic acid extraction on the chip, as low as 30 copies/reaction of Vibrio parahaemolyticus (V. parahaemolyticus) and 20 copies/reaction of Salmonella typhimurium (S. typhimurium) could be simultaneously detected. Detection results could be observed by the naked eye under a portable ultraviolet lamp. The whole detection procedure was finished within 60 min. This method with integrated nucleic acid analysis, dual detection capability and fluorescence visualized results provides a new solution for on-site nucleic acid analysis.

CRISPR/Cas12a-Assisted Dual Visualized Detection of SARS-CoV-2 on Frozen Shrimps

Given the possibility that food contaminated with SARS-CoV-2 might become an infection source, there is an urgent need for us to develop a rapid and accurate nucleic acid detection method for SARS-CoV-2 in food to ensure food safety. Here, we propose a sensitive, specific, and reliable molecular detection method for SARS-CoV-2. It has a mechanism to control amplicon contamination. Swabs from spiked frozen shrimps were used as detection samples, which were processed by heating at 95 °C for 30 s. These preprocessed samples served as the templates for subsequent amplification. A colorimetric LAMP reaction was carried out to amplify both the SARS-CoV-2 target and the MS2 phage simultaneously in one tube. MS2 phage was detected by colorimetric LAMP as the internal control, while SARS-CoV-2 was detected with a CRISPR/Cas12a system. The fluorescence results could be visually detected with an ultraviolet lamp. Meanwhile, uracil was incorporated during the LAMP reaction to provide an amplicon contamination proof mechanism. This test could detect as low as 20 copies of SARS-CoV-2 in one reaction. Additionally, the detection could be finished in 45 min. The test only needs a heating block and an ultraviolet lamp, which shows the potential for field detection.