Search Results (163)

Point-of-care diagnostics are revolutionizing the detection of plant pathogens by enabling rapid, on-site identification without the need for specialized laboratories. One of the tools used for this purpose is loop-mediated isothermal amplification (LAMP). LAMP is a powerful molecular technique increasingly used in pathogen control for its rapid, sensitive, and specific detection of plant pathogens. The aim of this study was the development of a novel, easy-to-use portable colorimetric LAMP (cLAMP) assay that could be used by inexperienced personnel for the detection of the pathogen Clavibacter michiganensis. The assay was combined with a newly constructed device in which LAMP can be performed in 30 min. Initially, a new set of LAMP primers targeting the micA gene was designed and evaluated the sensitivity (100 fg/reaction) and specificity of the assay. Next, the limit of detection (LoD) of two different commercial LAMP kits was compared with common laboratory detection techniques (DAS-ELISA, immunofluorescence, quantitative PCR, and PCR) using the same samples. Additionally, the LoD of the developed cLAMP assay was evaluated in bacterial suspensions and plant extracts spiked with C. michiganensis and validated the effect on the LoD of plant extracts from different tomato varieties. Lastly, its efficacy for C. michiganensis detection was assessed in experimentally inoculated tomato seedlings. The developed method for C. michiganensis detection can be used as a reliable tool for the early detection of the pathogen for field-based applications by untrained personnel. Full article

Human immunodeficiency virus type 1 (HIV-1) continues to be a major global health burden. Combination antiretroviral therapy (cART) effectively abrogates HIV-1 replication and has transformed HIV-1 infection from a fatal to chronic disease. While ART can suppress viremia to undetectable levels in people living with HIV-1 (PWH), a small reservoir of cells infected with replication-competent HIV-1 persists and can lead to viral rebound upon ART interruption. This persistent HIV-1 reservoir can be quantified and characterized by measuring replication of infectious HIV-1 using a quantitative viral outgrowth assay (qVOA), or by measuring HIV-1 DNA, RNA, or protein levels as a proxy for the reservoir. Tools to quantify the reservoir in these distinct molecular compartments have been developed for HIV-1 subtype B, which is predominant in the Global North. However, non-B subtypes constitute the majority of HIV-1 infections worldwide. Here, we discuss the wide range of reservoir quantitation and characterization tools, explore their limitations, and, where applicable, their adaptations to non-B subtypes. We conclude that standardized tools should be used to characterize reservoir dynamics of HIV-1 B and non-B subtypes. These tests should be well-validated and accessible to all laboratories world-wide to be able to draw conclusions about subtype-specific reservoir dynamics. Full article

The overlapping circulation of influenza (Flu), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; SC2), and respiratory syncytial virus (RSV) continues to challenge clinical laboratories, particularly in settings with limited automation and fragmented healthcare coverage. This study expanded the CDC Flu-SC2 assay by incorporating a laboratory-developed test (LDT) for RSV A/B detection into a fully automated quadruplex RT-qPCR (LDRA) on the Panther Fusion^® Open Access™ system. The design, based on more than 8000 RSV genomic sequences targeting the conserved M gene, achieved optimal amplification efficiencies (97–105%) and full multiplex compatibility. Analytical assessment established limits of detection between 9.6 and 37.8 copies per reaction, absence of cross-reactivity with 30 respiratory pathogens, and inclusivity for 32 viral variants. Commutability and diagnostic performance among the LDRA, CE IVD-marked Allplex™ SARS-CoV-2/FluA/FluB/RSV, and US IVD-marked Panther Fusion^® SARS-CoV-2/Flu A/B/RSV Assays were evaluated using 405 nasopharyngeal UTM-preserved swabs. The LDRA demonstrated excellent concordance (overall agreement ≥ 98%, κ > 0.95), strong diagnostic accuracy, and reliable detection of mixed infections. This quadruplex provides a fully automated, rapid, and accurate solution for the simultaneous detection of influenza A, influenza B, SARS-CoV-2, and RSV viruses, enhancing molecular diagnostic capacity and supporting equitable, timely clinical decision-making in middle-income healthcare systems such as that of the Dominican Republic. Full article

Heterocapsa bohaiensis is an emerging harmful dinoflagellate increasingly reported from coastal regions of the Pacific. However, an available molecular assay offering rapid and sensitive detection is still lacking. This study developed a SYBR Green real-time quantitative PCR (qPCR) assay for the identification and quantification of H. bohaiensis. Species-specific primers (F: 5′-CCATCGAACCAGAACTCCGT-3′; R: 5′-AGTGTAGTGCACCGCATGTC-3′) were designed and the assay was optimized and evaluated using laboratory cultures for specificity, sensitivity, and quantitative performance. Primer screening and melt-curve analysis confirmed that the selected primer pair produced a single, specific amplification peak for H. bohaiensis, with no cross-reactivity observed in non-target species (Chlorella pyrenoidosa, Phaeocystis globosa, Skeletonema costatum, Alexandrium tamarense) or mixed algal communities. The standard curve displayed strong linearity (R² = 0.9868) and a high amplification efficiency (102.5%). The limit of detection (LOD) was approximately 2–3 cells per reaction, as determined from 24 replicates of 5-cell equivalents and verified at ~2.7-cell equivalents. This sensitivity was comparable to or exceeded that reported for assays targeting other HABs forming dinoflagellates. Quantitative results derived from the qPCR assay closely matched microscopic cell counts, with a relative error of 10.79%, falling within the acceptable threshold for phytoplankton surveys. In summary, this study established and validates a species-specific qPCR assay for H. bohaiensis under controlled laboratory conditions. The method shows strong potential for incorporation into HAB monitoring programs, early-warning systems, and future ecological investigations of this emerging species. Full article

African Swine Fever (ASF) control is severely hampered by the reliance on slow, laboratory-bound diagnostics. While rapid, field-deployable lateral flow assays (LFAs) are urgently needed, the comparative performance of key single-antigen targets remains poorly characterized. This study aimed to develop and systematically evaluate the diagnostic performance of three in-house single-antigen LFAs targeting ASF virus P30, P54, and P72, using swine field samples from Thailand, including a panel of 143 quantitative polymerase chain reaction-negative swine serum samples. The performance of each LFA was compared against a commercial multi-antigen (P32/P62/P72) indirect ELISA, which served as the reference standard, classifying 64 samples as positive and 79 as negative. The P72-based LFA demonstrated perfect diagnostic performance (100% sensitivity, 100% specificity) and perfect agreement (κ = 1.0) with the enzyme-linked immunosorbent assay (ELISA). Similarly, the P30 LFA demonstrated high performance (100% sensitivity, 98.7% specificity) with ‘Almost Perfect’ agreement (κ = 0.9859). In contrast, the P54 LFA was unsuitable, achieving 100% sensitivity but unacceptably low specificity (88.6%) due to a high rate of false positives. Overall, the single-antigen P72 and P30 LFAs demonstrated excellent concordance with the multi-antigen ELISA, supporting their reliable for detecting antibodies against ASFV. Although these assays do not replace molecular methods for acute infection detection, they represent valuable complementary tools for serosurveillance. Full article

Bovine coronavirus(BCoV) is a significant pathogen causing substantial economic losses in the cattle industry through increased calf mortality, reduced growth performance, and decreased milk yield. Rapid and accurate diagnostic methods are therefore essential for controlling BCoV transmission. Current diagnostic methods comprise two primary categories: conventional techniques and cutting-edge innovations. Conventional approaches, including molecular methods like RT-PCR/qRT-PCR and immunological assays such as ELISA and neutralization tests, remain the main diagnostic methods. However, they are limited by laboratory dependency as well as the necessary balance between speed and sensitivity. These limitations have promoted the development of innovative methods, including isothermal amplification, CRISPR/Cas systems, droplet digital PCR, and integrated platforms. This review comprehensively analyzes the advantages, limitations, and applications of current diagnostic methods, highlighting integrated platforms such as RPA-CRISPR-LFA and microfluidics-based LFA. These innovations bridge critical performance gaps by enhancing sensitivity and specificity while enabling field application, demonstrating significant potential as next-generation point-of-care diagnostics for managing this economically critical pathogen. Full article

Photocatalytic oxidation of microorganisms is a powerful alternative to established disinfection approaches, applicable to a variety of water matrices. Bacterial vegetative cells, spores, fungi, and viruses, represent potential biopathogens and photocatalysis targets. Inactivation efficiency is usually evaluated by assessing viability through culture. However, additional inactivation assessment approaches are needed, as some microbes, despite being unculturable, remain metabolically active and pathogenic. Nucleic acid quantification approaches (qPCR) can assess nucleic acid release and degradation during photocatalysis. We developed a novel multiplex qPCR assay for simultaneous detection/quantification of genomic DNA from different bacterial and fungal species and of MS2 bacteriophage load. Following small-scale solar titanium dioxide photocatalysis on a microbial suspension mixture containing different biopathogen classes, we assessed photocatalytic efficiency by conventional microbiological assays (culture) and our novel molecular assay. Microbiological assays show a significant reduction in microbe viability within one hour of processing, following previously reported patterns of microbial species resistance. Molecular analysis data show that nucleic acids released in solution due to microbial oxidative damage were significantly reduced due to oxidative degradation within six hours. Through targeting different biopathogen classes, our assay could be a useful tool for assessment of photocatalytic microbe inactivation both in laboratory and real-wastewater applications. Full article

Malaria remains a considerable challenge to international health, especially in returning travelers from endemic regions where exposure risk may be downplayed. Prompt and accurate diagnosis is crucial, especially when conventional diagnostic techniques are insufficient. This case report presents a 59-year-old man who developed fever, rash, and myalgia after returning from the Amazon rainforest. Initial laboratory tests demonstrated leukopenia, thrombocytopenia, transaminitis, and hyperbilirubinemia. Despite these abnormal results and a clinically suspicious presentation, malaria smears were negative. Since the symptoms did not resolve, a Karius test—a plasma-based microbial cell-free DNA sequencing assay—successfully detected the presence of Plasmodium vivax, thus establishing the diagnosis. The patient needed several treatment regimens for the recurrent attacks, including chloroquine and primaquine, artemether-lumefantrine, and eventually a combination of quinine and doxycycline together with a prolonged course of primaquine. His symptoms resolved completely after the last treatment regimen, along with the normalization of the blood counts and liver function tests. This case demonstrates the limitations of smear microscopy diagnosis in P. vivax infections, highlights the role of molecular diagnostics like the Karius test, and stresses the importance of preventing relapses with adequate hypnozoite clearance. It further highlights the importance of clinician awareness and diligent follow-up in cases of travel-related Malaria, especially those with unusual presentations or recurrent symptoms. Full article

Accurate differentiation between Coilia brachygnathus and Coilia nasus is imperative for the effective management of fisheries, the conservation of aquatic ecosystems, and the mitigation of commercial fraud. Current morphological identification remains challenging due to their high morphological similarity—particularly for processed samples—while conventional molecular methods often lack the speed or specificity required for field applications or high-throughput screening. In this study, a novel integrated approach was developed and validated, combining TaqMan quantitative real-time PCR (qPCR). for precise genotyping of C. brachygnathus and C. nasus with Recombinase Polymerase Amplification coupled with Lateral Flow Dipstick (RPA-LFD) for rapid on-site screening. First, species-specific RPA-LFD assays were designed to target the mitochondrial COI gene sequence. This enabled visual detection within 10 min at 37 °C, with a sensitivity of 10² copies/μL, and required no complex equipment. A dual TaqMan MGB qPCR assay was further developed by validating stable differentiating SNPs (chr21:3798155, C/T) between C. brachygnathus and C. nasus, using FAM/VIC dual-labeled MGB probes. Results showed that this assay could distinguish the two species in a single tube: for C. brachygnathus, Ct values in the FAM channel were significantly earlier than those in the VIC channel (ΔCt ≥ 1), with a FAM detection limit of 125 copies/reaction; for C. nasus, only VIC channel amplification was observed, with a detection limit as low as 12.5 copies/reaction. Validation with 171 known tissue samples demonstrated 100% concordance with expected species identities. This integrated approach effectively combines the high accuracy and quantitative capacity of TaqMan qPCR for confirmatory laboratory genotyping with the speed, simplicity, and portability of RPA-LFD for initial field or point-of-need screening. This reliable, efficient, and user-friendly technique provides a powerful tool for resource management, biodiversity monitoring, and ensuring the authenticity of high-quality C. brachygnathus and C. nasus. Full article

Background/Objectives: The diagnosis of Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacterial (NTM) infections is accomplished by three main diagnostics methods: smear microscopy, culture, and molecular testing. Diagnostic algorithms used by laboratories can significantly impact clinical and infection control management. Current Canadian Tuberculosis Standards recommend the use of nucleic acid amplification testing (NAAT) for smear-positive patients and smear-negative patients upon request. An alternative algorithm is to utilize NAAT in the Panel approach on all samples, pulmonary and extrapulmonary, to potentially reduce time to diagnosis and treatment. This alternative approach was implemented in November 2019 at the Newfoundland and Labrador Public Health and Microbiology Laboratory (NL PHML) using a laboratory-developed multiplex real-time PCR (LDT m-qPCR) assay targeting Mycobacterium spp. (Myco spp.) and MTBC, performed in parallel with smear and culture. Methods: To investigate the impact of this alternate testing approach, we conducted an observational retrospective analysis of laboratory diagnostic and treatment data, recognizing that temporal changes in epidemiology, clinical practice, and laboratory workflow may also have influenced outcomes. To complete this, study data from three years before and four years after implementation were gathered. Results: The sensitivity/specificity of the smear, m-LDT qPCR-MTBC, m-LDT qPCR-Myco spp., and culture assays in this study were 18.1%/100%, 96.7%/99.8%, 47.6%/99.0%, and 96.8%/100%, respectively. The gold standard utilized for these calculations was clinical diagnosis for active MTBC disease and culture for NTM infections, recognizing that the use of clinical diagnosis may introduce subjectivity. The Panel approach reduced the time to diagnosis of tuberculosis MTBC by 29 days (p < 0.0001) for NL PHML, and when modelled for a laboratory with rapid culture identification, diagnosis was reduced by 14 days (p = 0.003). Among non-empirically treated tuberculosis patients, the time to treatment was decreased by 25.5 days (p < 0.001). For NTM infections, rapid diagnostics only affected one patient’s treatment. This finding agrees with clinical management guidelines, which do not routinely utilize rapid diagnostics for the diagnosis of disease or treatment decisions. The cost implications of additional NAAT testing were calculated to be an increase of CAD 23.62 per sample. Conclusions: Our findings support the adoption of a molecular assay for MTBC as an initial diagnostic tool to decrease time to diagnosis and time to treatment, depending on local epidemiology and irrespective of smear status. Utilizing a molecular assay for genus level identification of NTM had minimal impact on clinical management suggesting its limited diagnostic utility in a broad population setting. Full article

Liquid biopsies promise major advantages for cancer screening and diagnosis. By detecting biomarkers in peripheral blood samples, liquid biopsies reduce the need for invasive techniques and provide important genetic information integral to the emerging molecular classification of cancers. Unfortunately, the concentrations of most biomarkers, particularly circulating tumour nucleic acids, are vanishingly small—beyond the sensitivity and specificity of most assays. Clustered Regularly Interspaced Short Palindromic Repeats diagnostics (herein labelled ‘CRISPR-Dx’) use gene editing tools to detect, rather than modify, nucleic acids with extremely high specificity. These tools are commonly combined with isothermal nucleic acid amplification to also achieve sensitivities comparable to high-performance laboratory-based techniques, such as digital PCR. CRISPR assays, however, are inherently well suited to adaptation for point-of-care (POC) use, and unlike antigen-based POC assays, are significantly easier and faster to develop. In this review, we summarise current CRISPR-Dx platforms and their analytical potential for cancer biomarker discovery, with an emphasis on enhancing early diagnosis, disease monitoring, point-of-care testing, and supporting cancer therapy. Full article

Chrysotila dentata (Haptophyta), a harmful algal bloom (HAB) species frequently occurring in coastal waters of China, is one with strong environmental adaptability that poses a serious threat to marine ecosystems and fisheries. Current molecular detection techniques and early warning systems for this species remain limited. To address this, we developed a rapid and highly sensitive detection method for C. dentata. This method integrates recombinase polymerase amplification (RPA) with CRISPR-LbaCas12a and lateral flow dipstick (LFD) technologies, enabling visual readout of results. Key parameters, including the single-stranded DNA (ssDNA) reporter concentration, reaction time, and temperature, were systematically optimized. Field water sample testing demonstrated high specificity and sensitivity, achieving a detection limit of 5 × 10⁻⁶ pg μL⁻¹ for genomic DNA under laboratory conditions and 2.82 × 10¹ cells mL⁻¹ in simulated environmental samples. The entire detection process takes only 1 h (at a constant 39 °C), and results can be directly interpreted via LFD strips. For early warning and prevention of C. dentata outbreaks, this assay provides a powerful, reliable, and field-ready monitoring tool. Full article

Eel populations are globally threatened by overfishing and illegal trade, making accurate species identification essential for resource conservation and regulatory enforcement. Conventional molecular identification methods are generally applied in the laboratory, with limited rapid on-site application. This study developed a field-deployable assay to identify the Japanese eel (Anguilla japonica), by incorporating multienzyme isothermal rapid amplification (MIRA) technology with a visually readable lateral flow assay (LFA). Species-specific primers targeting a 286 bp region within the mitochondrial genome of A. japonica were designed and labeled with fluorescein amidite and biotin, respectively. The performance of the MIRA-LFA was validated by assessing its specificity against four other major eel species and its analytical sensitivity, i.e., limit of detection (LoD), under optimized temperature and reaction-time conditions. The MIRA-LFA demonstrated 100% specificity, generating a positive signal only for A. japonica, with no cross-reactivity. A clear visual result was obtained within 10 min at the optimal reaction temperature of 39 °C. Under these optimal conditions, the assay showed a high sensitivity, with an LoD of 0.1 ng/μL of genomic DNA. The proposed assay is an effective tool for the rapid, specific, and sensitive identification of A. japonica. The ability to obtain fast, equipment-free visual results makes this assay an ideal point-of-care testing solution to combat seafood fraud and support the sustainable management of this economically important and vulnerable species. Full article

Enteric viruses are a major cause of waterborne infections due to their high environmental stability and extremely low infectious dose. Current molecular diagnostic methods, while accurate, often depend on thermal cycling and centralized laboratory facilities, limiting their applicability in decentralized or resource-limited settings. In this study, we developed an isothermal biosensor based on a split deoxyribozyme that reconstitutes its catalytic core upon hybridization with a conserved sequence of enteroviral RNA. This activation leads to site-specific cleavage of a fluorogenic substrate, producing a quantifiable fluorescent signal. The system was experimentally validated using both synthetic enteroviral RNA and RNA extracted from environmental water samples. To enhance detection sensitivity, the DNAzyme-based assay was coupled with isothermal RNA amplification. The results demonstrate high selectivity and compatibility with real-world samples, supporting the sensor’s utility for field-deployable viral RNA detection. Overall, this study highlights the potential of the DNAzyme-based platform as a portable, sequence-specific, and amplification-assisted diagnostic tool for environmental surveillance of enteric viruses. Full article

Bovine viral diarrhea virus (BVDV) is a globally significant pathogen affecting both domestic livestock and wildlife, including white-tailed deer (WTD; Odocoileus virginianus). While experimental infections have demonstrated WTD susceptibility to BVDV, natural infections and associated reproductive outcomes remain scarcely documented. Here, we report the first confirmed case of naturally occurring BVDV-1 infection associated with fetal mummification in farmed WTD in Florida. A two-year-old doe experienced a stillbirth involving two mummified fetuses, which were submitted for necropsy and laboratory diagnostics. Gross findings included diarrhea and underdeveloped eyes in the fetuses, along with small white nodules indicative of amnion nodosum. While not harmful, this condition suggests underlying fetal compromise or intrauterine stress. Virus isolation using Vero E6 and bovine turbinate cell lines, along with a reverse transcription PCR (RT-PCR) assay specifically developed in this study, confirmed the presence of BVDV-1 (Pestivirus bovis) RNA in both maternal and fetal samples, suggesting vertical transmission. Sanger sequencing of RT-PCR amplicons further verified the virus species as BVDV-1. Differential diagnostics for other pathogens, including bluetongue virus, epizootic hemorrhagic disease virus, Mycobacterium spp., and Toxoplasma gondii, were negative. These findings underscore the importance of using biosecurity measures and including BVDV in the differential diagnosis of abortions to reduce the risk of BVDV transmission and potential outbreaks on deer farms, particularly those close to cattle operations. The molecular tools developed in this study provide a robust framework for improved detection and monitoring of BVDV in both wildlife and livestock populations. Full article