Pyrococcus furiosus Argonaute-mediated porcine epidemic diarrhea virus detection

Argonaute protein powered biosensing for pathogenic biosafety

The food safety and medical health issues caused by pathogen are particularly prominent. The development of biosensing technologies is urgent to ensure pathogenic biosafety. Argonaute system, as a promising and cutting-edged next-generation nucleic acid test technology, has the potential to address the challenges faced by CRISPR/Cas system. In this review, we focused on the current state-of-art Argonaute-powered biosensing for pathogenic biosafety. First, we introduced current methods for nucleic acid testing and programmable nucleases, followed by the working principle of Argonaute system (PfAgo, TtAgo, CbAgo, etc). Then Argonaute-medicated nucleic acid biosensing was highlighted through amplification and amplification-free manners. In addition, we summarized the application of Argonaute tools in detecting bacteria, virus, mycoplasma, etc. Finally, we pointed out the challenges and perspectives. Current pathogen methods demonstrate low sensitivity and specificity, as well as lack capabilities for multiple and point-of-care testing. Recent studies have shown that Argonaute-powered biosensing is an innovative and rapidly growing technology that could significantly enhance detection capabilities for pathogen-related issues, addressing the limitations of current methods. The application of Argonaute-powered biosensing is both promising and desirable due to the potential to offer "customized" and streamlined detection in the field of pathogenic biosafety monitoring.

LAMP Assay Coupled with a Pyrococcus furiosus Argonaute System for the Rapid Detection of Porcine Epidemic Diarrhea Virus

Porcine epidemic diarrhea virus (PEDV) infection can lead to serious acute intestinal infectious disease, bringing huge economic losses to the pig industry. In addition to triggering an extremely high mortality rate for lactating piglets, there is currently a lack of effective treatments and vaccines. Therefore, rapid, accurate, sensitive, and specific detection of PEDV is critical for timely control. In this study, a nucleic acid detection method combining reverse transcription loop-mediated isothermal amplification (RT-LAMP) and Pyrococcus furiosus Argonaute (PfAgo) was established for the detection of PEDV and performed after optimizing the system (mainly for the design and screening of the LAMP primers and PfAgo gDNA). The optimized system had a detection limit as low as 2.4 copies/μL. To reach more timely on-site detection of PEDV and overcome the reliance on bulky and complex equipment, a lateral flow strip was introduced into the system, which could detect the target as low as 24 copies/μL. This RT-LAMP-PfAgo system took about 35 min to react, and the results could be observed and clarified with the naked eyes. Moreover, the method was highly specific and had no cross-reactivity with other swine pathogens. The detection results for the clinical samples were consistent with those obtained by the gold standard method, reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), proving its applicability. In conclusion, the established RT-LAMP-PfAgo system can provide a new solution for the development of a portable, visual PEDV testing platform.

Advances in porcine epidemic diarrhea virus research: genome, epidemiology, vaccines, and detection methods

Porcine epidemic diarrhea (PED) is a highly contagious intestinal disease caused by the porcine epidemic diarrhea virus (PEDV). The economic impact of PEDV on the global pig industry has been significant, resulting in considerable losses. This paper presents a review of the latest research progress on PEDV genome, molecular epidemiology, vaccine development, and molecular detection methods. It was determined that the genetic diversity of the PEDV spike (S) gene was closely associated with the epidemiological trend of PEDV. The prevalence of S gene variants of different genotypes exhibited variability across regions and pig populations. Epidemiological analyses have demonstrated that PEDV can be transmitted via multiple routes, including direct contact, airborne aerosol, and water source contamination. With regard to vaccine research, the available vaccines can be classified into several categories, including live-attenuated vaccines, inactivated vaccines, subunit vaccines, bacterial vector vaccines, viral vector vaccines, mRNA vaccines, etc. Each of these has distinctive characteristics in terms of immunogenicity, protection efficiency, and safety. Molecular detection methods, including PCR-based methods, isothermal amplification techniques, immunological assays, and biosensors, play an important role in the diagnosis and monitoring of PEDV. Furthermore, this paper examines the current developments in PEDV research and identifies the key areas of future investigation. The objective of this paper is to establish a theoretical foundation for the prevention and control strategies of PED, and to provide a point of reference for further research on the genomics, epidemiology, vaccine development and detection methods of PEDV.

Rapid and Sensitive One-Tube Detection of Getah Virus Using RT-LAMP Combined with Pyrococcus furiosus Argonaute

Getah virus (GETV) is a mosquito-borne virus that poses a significant threat to both animal and public health. Traditional diagnostic methods for GETV, such as RT-PCR and RT-qPCR, require expensive equipment and complex procedures, making them unsuitable for rapid, on-site detection. The combination of RT-LAMP and PfAgo offers a novel approach for nucleic acid detection, providing high specificity and effective without the need for sophisticated instruments. Herein, we developed a RT-LAMP combined with PfAgo assay for GETV detection. The RT-LAMP assay was conducted at 60~65 °C, and then the RT-LAMP product was cleaved, together with a fluorescent probe, mediated by PfAgo at 95 °C. After optimizing the primary reaction conditions, the detection limit of the RT-LAMP-PfAgo assay was 100 copies/µL. Importantly, there was no cross-reactivity with other viruses, including PEDV, PDCoV, PoRV, PRRSV, and CSFV. Compared to qPCR, analysis of 86 clinical samples showed that LAMP-PfAgo had a consistent positive rate with the qPCR method. In conclusion, we developed a valuable diagnostic tool for the rapid detection of GETV, enabling timely surveillance and control measures to mitigate the impact of GETV outbreaks.

Near zero background noise photoelectrochemical sensor based on sensitized signal probe CdS QDs-Dox intercalating double-stranded DNA for PEDV detection

The highly sensitive detection method for porcine epidemic diarrhea virus (PEDV) is crucial for promptly identify infected pigs and effectively control the spread of the virus. In this study, the sensitization enhancement of organic photoactive material was combined with near zero background noise strategy for PEDV sensitive detection. A novel sensitized signal probe CdS quantum dots-doxycycline complex (CdS QDs-Dox) was prepared serving as a photoelectrochemical (PEC) probe embedded in dsDNA. Subsequently, a thiol-modified upstream inner primer (SH-FIP) was immobilized on the surface of electrode modified with gold nanoparticles (Au NPs) via Au-S bonding, enabling the loop-mediated isothermal amplification (LAMP) of PEDV on the electrode surface. The PEC probe (CdS QDs-Dox) embedded in the amplified dsDNA groove showed an increasing photocurrent signal with the rise of PEDV concentration, establishing a near-zero background LAMP-PEC sensing platform for PEDV detection. Under optimized conditions, the photocurrent intensity of this platform exhibited a good linear relationship with PEDV concentrations ranging from 0.0005 pg/μL to 10 pg/μL, achieving a detection limit as low as 0.17 fg/μL. This platform demonstrates outstanding specificity and sensitivity, thereby enabling precise quantitative detection of diverse pathogens.

Polysaccharides of natural products alleviate antibiotic-associated diarrhea by regulating gut microbiota: a review

Antibiotic-associated diarrhea (AAD) is diarrhea caused by disturbances in intestinal microbiota and metabolism following inappropriate use of antibiotics. With the over-reliance on antibiotics, the incidence of AAD is increasing worldwide. Recently, the role of probiotics and prebiotic preparations in the prevention and treatment of AAD has received increasing attention. Various prebiotics can not only reduce the incidence of AAD, but also effectively shorten the course of the disease and alleviate the symptoms. Notably, many polysaccharides derived from plants and fungi are a class of biologically active and rich prebiotics with great potential to alleviate AAD. Therefore, this review aims to summarize the latest research on natural product polysaccharides to alleviate antibiotic-associated diarrhea by modulating the gut microbiota. It provides a theoretical basis for exploring the mechanism of natural product modulation of gut microbiota to alleviate AAD, and provides a reference for further development of active prebiotics.

A rapid and visual detection assay for Senecavirus A based on recombinase-aided amplification and lateral flow dipstick

Background

Senecavirus A (SVA) is a newly pathogenic virus correlated with the acute death of piglets and vesicular lesions in pigs. The further prevalence of SVA will cause considerable economic damage to the global pig farming industry. Therefore, rapid and accurate diagnostic tools for SVA are crucial for preventing and controlling the disease.

Methods

We designed multiple primer pairs targeting the most conserved region of the SVA 3D gene and selected those with the highest specificity. Nfo-probes were subsequently developed based on the highest specificity primer pairs. Subsequently, the recombinase-assisted amplification (RAA) reaction was completed, and the reaction temperature and duration were optimized. The RAA amplicons were detected using a lateral flow device (LFD). Finally, a rapid and intuitive RAA-LFD assay was established against SVA.

Results

The SVA RAA-LFD assay can be performed under reaction conditions of 35°C within 17 minutes, with results observable to the naked eye. We then evaluated the performance of this method. It exhibited high specificity and no cross-reaction with the other common swine pathogens. The lowest detectable limits of this method for the plasmid of pMD18-SVA-3D, DNA amplification product, and viral were 3.86×101 copies/µL, 8.76×10-7 ng/µL, and 1×100.25 TCID50/mL, respectively. A total of 44 clinical samples were then tested using the RAA-LFD, PCR, and RT-qPCR methods. The results demonstrated a consistent detection rate between the RAA-LFD and RT-qPCR assays.

Conclusion

The SVA RAA-LFD assay developed in our study exhibits excellent specificity, sensitivity, and time-saving attributes, making it ideally suited for utilization in lack-instrumented laboratory and field settings.

Programmable and ultra-efficient Argonaute protein-mediated nucleic acid tests: A review

With the attributes of high sensitivity, single-base resolution, multiplex detection capability, and programmability upon nucleic acid recognition, Argonaute (Ago)-based biosensing assays are increasingly recognized as one of the most promising tools for precise identification and quantification of target analytes. Employed as highly specific sequence recognition elements of these robust diagnostic methods, Agos are revolutionizing how nucleic acid targets are detected. A systematic and comprehensive summary of this emerging and rapid-advancing technology is necessary to give play to the potential of Ago-based biosensing assays. The structure and function of Agos were briefly overviewed at the beginning of the work, followed by a review of the recent advancements in employing Agos sensing for detecting various targets with a comprehensive analysis such as viruses, tumor biomarkers, pathogens, mycoplasma, and parasite. The significance and benefits of these platforms were then deliberated. In addition, the authors shared subjective viewpoints on the existing challenges and offered relevant guidance for the future progress of Agos assays. Finally, the future research outlook regarding Ago-based sensing in this field was also outlined. As such, this review is expected to offer valuable information and fresh perspectives for a broader group of researchers.

Epitopes screening and vaccine molecular design of PEDV S protein based on immunoinformatics

Porcine epidemic diarrhea virus (PEDV) is a serious disease that poses a significant threat to the pig industry. This study focused on analyzing the Spike protein of PEDV, which harbors crucial antigenic determinants, in identifying dominant epitopes. Immunoinformatics tools were used to screen for B-cell, CD4+ and CD8+ predominance epitopes. These epitopes were then connected to the N-terminal of ferritin to form a self-assembled nanoparticle vaccine. Various physical and chemical properties of the candidate vaccine were analyzed, including secondary structure prediction, tertiary structure modeling, molecular docking, immune response simulation and computer cloning. The results demonstrated that the candidate vaccine was antigenic, soluble, stable, non-allergic, and formed a stable complex with the target receptor TLR-3. Immune simulation analysis showed that the candidate vaccine effectively stimulated both cellular and humoral reactions, leading to increased related cytokines production. Furthermore, efficient and stable expression of the candidate vaccine was achieved through reverse translation in the Escherichia coli K12 expression system following codon optimization and in silico cloning. The developed nanoparticle candidate vaccine in this study holds promise as an effective PEDV vaccine candidate, offering a new approach for the research, development and improvement of vaccines targeting porcine enteric diarrhea coronavirus.

Recombinase polymerase amplification combined with Pyrococcus furiosus Argonaute for fast Salmonella spp. testing in food safety

Foodborne illness caused by Salmonella spp. is one of the most prevalent public health problems globally, which have brought immeasurable economic burden and social impact to countries around the world. Neither current nucleic acid amplification detection method nor standard culture method (2-3 days) are suitable for field detection in areas with a heavy burden of Salmonella spp. Here, we developed a highly sensitive and accurate assay for Salmonella spp. detection in less than 40 min. Specifically, the invA gene of Salmonella spp. was amplified by recombinase polymerase amplification (RPA), followed by Pyrococcus furiosus Argonaute (PfAgo)-based target sequence cleavage, which could be observed by a fluorescence reader or the naked eye. The assay offered the lowest detectable concentration of 1.05 × 101 colony forming units/mL (CFU/mL). This assay had strong specificity and high sensitivity for the detection of Salmonella spp. in field samples, which indicated the feasibility of this assay.

Pyrococcus furiosus Argonaute Based Detection Assays for Porcine Deltacoronavirus

Porcine deltacoronavirus (PDCoV) is a major cause of diarrhea and diarrhea-related deaths among piglets and results in massive losses to the overall porcine industry. The clinical manifestations of porcine diarrhea brought on by the porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), and PDCoV are oddly similar to each other. Hence, the identification of different pathogens through molecular diagnosis and serological techniques is crucial. Three novel detection methods for identifying PDCoV have been developed utilizing recombinase-aided amplification (RAA) or reverse transcription recombinase-aided amplification (RT-RAA) in conjunction with Pyrococcus furiosus Argonaute (PfAgo): RAA-PfAgo, one-pot RT-RAA-PfAgo, and one-pot RT-RAA-PfAgo-LFD. The indicated approaches have a detection limit of around 60 copies/μL of PDCoV and do not cross-react with other viruses including PEDV, TGEV, RVA, PRV, PCV2, or PCV3. The applicability of one-pot RT-RAA-PfAgo and one-pot RT-RAA-PfAgo-LFD were examined using clinical samples and showed a positive rate comparable to the qPCR method. These techniques offer cutting-edge technical assistance for identifying, stopping, and managing PDCoV.