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16 pages, 1194 KB  
Article
A Multiplex One-Tube Nested Real-Time PCR Assay for the Point-of-Care Testing of Infectious Meningitis
by Duoxiao Zhang, Jie Wang, Zijin Zhao, Yanqing Tie, Jianing Wu, Shihao Jiao, Xingyu Liu, Yuxin Wang, Shijue Gao, Mengchuan Zhao, Pei Zhao, Zhiqiang Han, Xiaona Lyu, Xinxin Shen, Xuejun Ma and Zhishan Feng
Pathogens 2026, 15(5), 456; https://doi.org/10.3390/pathogens15050456 - 22 Apr 2026
Abstract
In this study, we developed a multiplex one-tube nested real-time fluorescent quantitative PCR (mONRT-PCR) assay integrated with a portable, fully automated nucleic acid point-of-care testing (POCT) platform for the detection of Haemophilus influenzae (H. influenzae), Listeria monocytogenes (L. monocytogenes), [...] Read more.
In this study, we developed a multiplex one-tube nested real-time fluorescent quantitative PCR (mONRT-PCR) assay integrated with a portable, fully automated nucleic acid point-of-care testing (POCT) platform for the detection of Haemophilus influenzae (H. influenzae), Listeria monocytogenes (L. monocytogenes), and Cryptococcus neoformans (C. neoformans) in cerebrospinal fluid (CSF). The assay enables nested amplification within a closed system using conventional primers and probes, thereby reducing operational complexity and minimizing contamination risk. Analytical evaluation demonstrated limits of detection of 100 copies/μL for H. influenzae and L. monocytogenes, and 101 copies/μL for C. neoformans using recombinant plasmids, as well as 10−7 to 10−6 ng/μL using genomic DNA. No cross-reactivity was observed when tested against a panel of 17 common non-target microorganisms encountered in clinical microbiology laboratories. In simulated CSF samples, the assay maintained detectable amplification at low pathogen concentrations. When implemented on the POCT platform, detection limits reached 5, 10, and 50 CFU/mL for the three pathogens, respectively. Clinical evaluation using 43 CSF samples showed almost perfect agreement with conventional qPCR (κ = 0.861, p < 0.001). Notably, additional C. neoformans detections were observed by mONRT-PCR-POCT compared with qPCR, suggesting improved sensitivity under clinical conditions. The assay yielded results within approximately 1 h and 47 min. These findings indicate that the proposed assay provides a rapid, sensitive, and integrated approach for meningitis pathogen detection, while maintaining a practical balance between analytical performance and operational simplicity. Further validation in larger cohorts is warranted. Full article
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12 pages, 780 KB  
Article
Disease-Relevant Preoperative Serum miRNA Levels in Papillary Thyroid Cancer
by Olga Bourogianni, Eliza Tsitoura, Konstantinos Sifakis, Nikolaos Kapsoritakis, Alexander Karatzanis, Maria Doulaptsi, Katerina Antoniou, Sophia Koukouraki and Emmanuel Prokopakis
Biology 2026, 15(8), 626; https://doi.org/10.3390/biology15080626 - 16 Apr 2026
Viewed by 193
Abstract
Background: Papillary thyroid cancer (PTC) is the most common form of thyroid malignancy, with an incidence that has been steadily rising globally. Early and accurate diagnosis remains crucial for effective treatment and improved outcomes. MicroRNAs (miRNAs), small non-coding RNA molecules that regulate gene [...] Read more.
Background: Papillary thyroid cancer (PTC) is the most common form of thyroid malignancy, with an incidence that has been steadily rising globally. Early and accurate diagnosis remains crucial for effective treatment and improved outcomes. MicroRNAs (miRNAs), small non-coding RNA molecules that regulate gene expression, have emerged as promising biomarkers in cancer research due to their stability and accessibility in serum. In this pilot study we compared the expression of 84 consistently reported, malignancy-associated serum miRNAs in patients with PTC (PTC group) and benign thyroid disease (Control group) as potential PTC markers. Methods: A focused panel containing primer assays for 84 human miRNAs that are consistently reported in the literature as being detectable and differentially expressed in serum in various organ-specific cancers was used to measure miRNA levels in serum samples from PTC (n = 8) and benign thyroid disease (n = 6) patients prior to thyroidectomy. Results: Among the 84 miRNAs analyzed, a panel of ten miRNAs showed numerical trends of differential expression between the two groups, including three upregulated (hsa-miR-150-5p, hsa-miR-21-5p, hsa-miR-23a-3p) and seven downregulated miRNAs (hsa-miR-17-5p, hsa-miR-17-3p, hsa-miR-200c-3p, hsa-miR-296-5p, hsa-miR-574-3p, hsa-miR-885-5p, hsa-miR-130-3p). The serum expression levels of hsa-miR-23a-3p were markedly elevated in patients with malignant nodules compared with those with benign lesions, while hsa-miR-574-3p was significantly downregulated in the PTC group. Conclusions: These findings warrant further investigation of hsa-miR-23a-3p and hsa-miR-574-3p in larger cohorts of patients with PTC to validate their potential clinical relevance. Full article
(This article belongs to the Special Issue Signalling Pathways in Cancer and Disease)
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18 pages, 1584 KB  
Article
Development and Validation of a Quantitative RT-qPCR Panel for the Detection and Monitoring of Polioviruses in Wastewater Samples
by Linnet Immaraj, Judy Y. Qiu, Logan A. Brand, Tiejun Gao, Bonita Lee, Michael Parkins, Casey Hubert, Christine O’Grady and Xiaoli Pang
Microorganisms 2026, 14(3), 709; https://doi.org/10.3390/microorganisms14030709 - 21 Mar 2026
Viewed by 446
Abstract
Clusters of acute flaccid paralysis (AFP) caused by oral vaccine-derived poliovirus (VDPV) in 2022 and sporadic outbreaks in New York and Gaza highlight the ongoing risk of polio, alongside the persistent global threat posed by wild-type poliovirus. This study aims to develop and [...] Read more.
Clusters of acute flaccid paralysis (AFP) caused by oral vaccine-derived poliovirus (VDPV) in 2022 and sporadic outbreaks in New York and Gaza highlight the ongoing risk of polio, alongside the persistent global threat posed by wild-type poliovirus. This study aims to develop and validate a quantitative reverse transcription PCR (RT-qPCR) panel that employs different primer–probe sets to simultaneously detect vaccine and wild-type poliovirus (WPV) in wastewater. Using an inactivated poliovirus vaccine (IPV) and engineered DNA fragments (eDNAf), the qPCR master mix (MM) performance, assay specificity, sensitivity (limit of detection, LOD), and recovery from IPV-spiked wastewater were evaluated. Compared with two-step RT-qPCR and qScript MM, one-step RT-qPCR with TaqMan MM improved sensitivity for the following polioviruses (PV): Sabin 1 in IPV and the eDNAf of Sabin 1, 2, and 3; WPV1 and WPV3; and poliovirus type 2 (any serotype 2). The LOD for Sabin 1 in IPV was 2.49 copies/PCR, while LODs for eDNAf of polio targets ranged from 1.06 to 3.12 copies/PCR. Sabin 1 recovery from IPV-spiked wastewater ranged from 10.26% to 57.27%. The RT-qPCR panel for poliovirus exhibited good specificity and sensitivity, with moderate viral recovery, enabling rapid implementation of wastewater monitoring for PV as needed. Full article
(This article belongs to the Special Issue Pathogen Surveillance in Wastewater)
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15 pages, 6570 KB  
Article
Development and Validation of a Multienzyme Isothermal Rapid Amplification Combined with Lateral-Flow Dipstick (MIRA-LFD) Assay for Trypanosoma Strains Circulating in Large Yellow Croaker (Larimichthys crocea)
by You Zuo, Bichai Liao, Luoxuan Lin, Tong Wu, Jiahao Yuan, Qianxi Xue, Haiyun Wei, Shuming Liu, Guangliang Huang, Xinhua Chen and Pan Qin
Fishes 2026, 11(2), 107; https://doi.org/10.3390/fishes11020107 - 10 Feb 2026
Viewed by 418
Abstract
Trypanosomiasis, caused by flagellated protozoa of the genus Trypanosoma, has recently emerged as a major threat to aquaculture in China, particularly in farmed large yellow croaker (Larimichthys crocea). Outbreaks lead to high mortality rates and severe economic losses. Conventional diagnostic [...] Read more.
Trypanosomiasis, caused by flagellated protozoa of the genus Trypanosoma, has recently emerged as a major threat to aquaculture in China, particularly in farmed large yellow croaker (Larimichthys crocea). Outbreaks lead to high mortality rates and severe economic losses. Conventional diagnostic tools, such as blood-smear microscopy and molecular assays including polymerase chain reaction or quantitative polymerase chain reaction (qPCR), are often limited by low sensitivity during early infection or by their dependence on sophisticated instruments and trained personnel, restricting their utility in field conditions. To address these challenges, a multienzyme isothermal rapid amplification (MIRA) assay coupled with a lateral-flow dipstick (LFD) was developed for the rapid detection of trypanosoma strains circulating in L. crocea targeting the 18S ribosomal ribonucleic acid gene. After optimizing primer-probe sets, the assay performance was evaluated using plasmid standards and a panel of common aquaculture pathogens. The MRA-LFD assay consistently detected plasmid DNA at concentrations as low as 0.01 fg/µL (≈2.1 copies/µL) and demonstrated no cross-reactivity with other pathogens. Using clinical DNA samples positive for Trypanosoma, the detection limit was 100 fg µL−1. Validation with 150 tissue samples from fish with and without clinical symptoms demonstrated high diagnostic consistency (94%) with qPCR results, confirming the reliability of the assay. This MIRA-LFD platform provides a sensitive, specific and portable diagnostic tool for early detection of Trypanosoma infections in large yellow croaker, offering valuable support for surveillance and disease management in aquaculture. Full article
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32 pages, 6380 KB  
Article
Identification and Development of Pathogen- and Pest-Specific Defense–Resistance-Associated SSR Marker Candidates Assisted by Machine Learning and Discovery of Putative QTL Hotspots in Camellia sinensis
by Ayşenur Eminoğlu
Plants 2026, 15(3), 454; https://doi.org/10.3390/plants15030454 - 2 Feb 2026
Viewed by 495
Abstract
In this study, a targeted SSR (Simple Sequence Repeat) marker resource was developed based on genes and protein families associated with pathogen- and pest-related defense–resistance mechanisms in Camellia sinensis. Forty-one genes and protein families reported to show upregulation, increased expression, or functional [...] Read more.
In this study, a targeted SSR (Simple Sequence Repeat) marker resource was developed based on genes and protein families associated with pathogen- and pest-related defense–resistance mechanisms in Camellia sinensis. Forty-one genes and protein families reported to show upregulation, increased expression, or functional validation under disease and pest stress were selected, and the corresponding 195 loci were mapped onto the Camellia sinensis cv. Shuchazao genome. SSR screening within gene bodies and gene-flanking regions (±5 kb) identified 5197 SSR loci. Putative QTL hotspot regions were defined using locus-based sliding-window analysis, Z-score calculations, and permutation tests, yielding 633 SSRs filtered at the 99% and 95% significance thresholds. Proteome-wide scans based on conserved amino acid motifs identified multiple loci within the WRKY, NAC, LRR, PRX, and CHI families, and Random Forest analysis was used to prioritize SSRs within these families. Finally, 386 SSR primer sets were designed and evaluated by in silico PCR across six tea genomes. Of these, 245 primers produced amplicons in more than one genome, and 124 exhibited polymorphic information content values greater than 0.500. Overall, the developed SSR panels represent a biologically contextualized and experimentally transferable marker resource targeting defense–resistance-associated genic and gene-proximal regions. Full article
(This article belongs to the Special Issue Genomics and Transcriptomics for Plant Development and Improvement)
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19 pages, 271 KB  
Article
MinION Adapted tNGS Panel for Carnivore Pathogens Including SARS-CoV-2
by Nelly O. Elshafie, Jobin J. Kattoor, Janetta Kelly and Rebecca P. Wilkes
Pathogens 2026, 15(1), 23; https://doi.org/10.3390/pathogens15010023 - 24 Dec 2025
Viewed by 681
Abstract
Affordable, flexible surveillance tools are needed to detect SARS-CoV-2 and other pathogens in wildlife. Standard nucleic acid amplification tests (NAATs) are reliable but restricted to predefined targets, limiting their ability to detect co-infections or emerging pathogens. To address this, we adapted a targeted [...] Read more.
Affordable, flexible surveillance tools are needed to detect SARS-CoV-2 and other pathogens in wildlife. Standard nucleic acid amplification tests (NAATs) are reliable but restricted to predefined targets, limiting their ability to detect co-infections or emerging pathogens. To address this, we adapted a targeted next-generation sequencing (tNGS) panel for mesocarnivores to the Oxford Nanopore Technologies (ONT) MinION platform and combined it with a SARS-CoV-2 whole-genome sequencing assay. Merging both assays before library preparation enables simultaneous SARS-CoV-2 detection, variant identification, and broader pathogen screening. The MinION platform also improves turnaround time because sequencing can begin immediately on small numbers of samples, reducing costs in low-volume workflows. We converted our validated carnivore tNGS panel from the Ion Torrent system to MinION, optimizing amplification conditions, primer pools, and barcoding for multiplexing. Analytical sensitivity was measured using contrived wildlife samples spiked with serial dilutions of SARS-CoV-2 and tested in parallel with a commercial NAAT. Diagnostic sensitivity was assessed using contrived positives, and specificity was evaluated using NAAT-negative wildlife samples and in silico analyses. All 161 wildlife samples were NAAT-negative. MinION tNGS detected SARS-CoV-2 down to Ct 34 and produced ≥ 99% genome coverage for Ct ≤ 24 while simultaneously identifying additional pathogens. Diagnostic sensitivity and specificity were 96.7% and 100%. This workflow offers a low-cost, scalable approach for comprehensive wildlife pathogen surveillance. Full article
(This article belongs to the Special Issue Diagnostics of Emerging and Re-Emerging Pathogens)
18 pages, 3328 KB  
Article
Influence of Primer Layer Configuration and Substrate Heterogeneity on the Overall Interfacial Performance of Waterborne Acrylic Coatings on Flattened Bamboo
by Yingyue Yu, Hong Chen, Shuangshuang Wu and Wei Xu
Coatings 2025, 15(11), 1307; https://doi.org/10.3390/coatings15111307 - 10 Nov 2025
Viewed by 645
Abstract
Flattened bamboo (FB) exhibits pronounced structural and chemical heterogeneity between outer and inner layers and between nodes and internodes. These variations critically influence its interfacial performance with waterborne acrylic coatings. This study aimed to clarify how primer layer configuration and substrate heterogeneity jointly [...] Read more.
Flattened bamboo (FB) exhibits pronounced structural and chemical heterogeneity between outer and inner layers and between nodes and internodes. These variations critically influence its interfacial performance with waterborne acrylic coatings. This study aimed to clarify how primer layer configuration and substrate heterogeneity jointly affect the coating adhesion, hardness, and abrasion resistance of FB. Three coating schemes—one primer and one topcoat (1P1T), two primers and one topcoat (2P1T), and three primers and one topcoat (3P1T)—were applied to four types of FB substrates defined by layer and structural position. Adhesion, pencil hardness, and abrasion resistance were measured according to GB/T standards, complemented by surface roughness, contact angle, XPS, and SEM analyses. Results showed that substrate heterogeneity dominated coating behavior. The parenchyma-rich inner-layer internodes, characterized by higher polarity (O/C = 0.296) and rougher texture, exhibited stronger adhesion and superior abrasion stability, whereas the fiber-dense outer layer nodes, with lower polarity (O/C = 0.262), showed weaker bonding. Increasing the number of primer layers improved film continuity only when the substrate microstructure allowed sufficient primer penetration. The combined findings indicate that coating adhesion and wear stability are primarily governed by substrate composition and surface polarity rather than by coating thickness. These results provide scientific and practical guidance for optimizing primer application and surface preparation in the industrial finishing of bamboo-based decorative panels, while also highlighting the environmental and economic advantages of waterborne coating optimization for sustainable bamboo manufacturing. Full article
(This article belongs to the Section Functional Polymer Coatings and Films)
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17 pages, 3897 KB  
Article
Physical–Mechanical and Corrosion Resistance Characterization of a Water-Based Epoxy Primer Applied to Galvanized Steel
by Rosalia Galiotto, Solidea Zanetti, Rocco Traini and Luca Pezzato
Metals 2025, 15(11), 1196; https://doi.org/10.3390/met15111196 - 27 Oct 2025
Viewed by 911
Abstract
This study presents a comprehensive characterization of a commercial water-based epoxy primer applied to galvanized steel sheets, which are commonly used in building and construction applications. The investigation focused on evaluating the primer’s adhesion, mechanical strength, chemical resistance, and corrosion protection under various [...] Read more.
This study presents a comprehensive characterization of a commercial water-based epoxy primer applied to galvanized steel sheets, which are commonly used in building and construction applications. The investigation focused on evaluating the primer’s adhesion, mechanical strength, chemical resistance, and corrosion protection under various environmental and thermal conditions. Particular attention was given to the effect of substrate sanding prior to application, which was found to influence the coating thickness and surface adaptation. The results demonstrated that the primer provides effective barrier properties and good adhesion to the metal surface, with average pull-off strengths remaining consistent across aged and unaged samples. Electrochemical impedance spectroscopy (EIS) confirmed high polarization resistance values, indicating strong corrosion protection, while SEM-EDS analysis revealed the presence of zinc phosphate and titanium dioxide fillers contributing to both passive and active inhibition mechanisms. However, the primer exhibited sensitivity to ultraviolet (UV) radiation, as evidenced by FT-IR spectra showing increased absorbance in the hydroxyl and carbonyl regions after prolonged exposure. A preliminary estimation of the photodegradation rate, based on FT-IR data at the carbonyl peak (1739 cm−1), yielded a value of approximately 2 × 10−6 absorbance units per hour between 3000 h and 5000 h of UV exposure. This value suggests a gradual degradation process, although further quantitative validation is required. Additional limitations were observed, including variability in coating thickness due to manual application and localized blistering at cut edges under salt spray conditions. These findings contribute to a deeper understanding of the primer’s behavior and suggest improvements for its practical use, such as the application of a protective topcoat and optimization of the coating process. Full article
(This article belongs to the Special Issue Surface Treatments and Coating of Metallic Materials)
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13 pages, 903 KB  
Article
A Validation Approach for Determining Fetal Blood Groups Non-Invasively by High-Sensitive Next-Generation Sequencing
by Sandra Wienzek-Lischka, Marion Soelter, Annika Froelich, Marion Ernst-Schlegel, Stefan Gattenloehner, Andreas Braeuninger and Ulrich J. Sachs
J. Clin. Med. 2025, 14(19), 6812; https://doi.org/10.3390/jcm14196812 - 26 Sep 2025
Cited by 1 | Viewed by 941
Abstract
Introduction: For pregnant women with a history of fetal and neonatal alloimmune thrombocytopenia (FNAIT) or hemolytic disease of the fetus and newborn (HDFN), prenatal intervention in subsequent pregnancies may be necessary to prevent complications for the fetus. A non-invasive prenatal diagnostic procedure (NIPD) [...] Read more.
Introduction: For pregnant women with a history of fetal and neonatal alloimmune thrombocytopenia (FNAIT) or hemolytic disease of the fetus and newborn (HDFN), prenatal intervention in subsequent pregnancies may be necessary to prevent complications for the fetus. A non-invasive prenatal diagnostic procedure (NIPD) is recommended for fetal blood group genotyping. RT-PCR is used for fetal RHD determination as a reliable screening method with high sensitivity and specificity. For other antigens with variants involving single-base substitutions, droplet digital PCR (ddPCR) and next-generation sequencing (NGS) are recommended to reduce the risk of false-negative results. Only NGS offers the possibility of determining the cell-free fetal DNA (cffDNA) fraction in maternal plasma by sequencing additional gene fragments in parallel, but no standard exists for assay validation. Material and Methods: A custom-made primer panel was designed to target the common platelet and red cell antigens involved in fetal red cell and platelet incompatibilities, as well as additional anonymous single-nucleotide polymorphism (SNP) targets for use as an internal control. Amplicon-based NGS was carried out using semiconductor sequencing. For HPA-1a (HPA*1A, ITGB3) and K (KEL*01.01, KEL) assay validation, the limit of detection (LOD) and limit of quantification (LOQ) were estimated, as were false-positive antithetic alleles, linearity, and inter-assay variation, using cell-free DNA (cfDNA) extracted from the blood samples of healthy blood donors. An additional analysis was performed using 23 diagnostic samples from 21 pregnant women. Results: Regression analysis of dilution series using HPA-1a- and K-positive cell-free plasma samples in antigen-negative donor plasma showed that recovery is definitely feasible up to an HPA*1A and KEL*01.01 allele frequency of 1%. Base calls of false-positive antithetic alleles were detected with a maximum of 0.25% using 21 healthy blood donors. The LOD was estimated to be 0.2057% (mean + 3 SD) for HPA*1A with a LOQ of 0.6298% (mean + 10 SD). For KEL*01.01, the LOD was 0.1706% (mean + 3 SD) and the LOQ was 0.5314% (mean + 10 SD). The analysis of 15 of 21 cases with diagnostic samples from pregnant women with neonatal blood available for confirmatory testing resulted in 100% concordant results. The fetal fraction of these samples was calculated with a median of 11.03% (95% CI: 8.89, 13.20). Conclusions: NGS for non-invasive fetal blood group genotyping is an accurate and reliable method. In-house validation of the used assays can be performed using healthy donors to determine the LOD, LOQ and sensitivity. The threshold for paternally inherited fetal HPA*1A and KEL*01.01 alleles could be set at 1% (i.e., 2% fetal fraction) to obtain reliable test results. Internal controls for assessing the fetal fraction are essential to avoid false-negative test results. Full article
(This article belongs to the Section Obstetrics & Gynecology)
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14 pages, 1026 KB  
Article
Targeted Whole Genome Sequencing of African Swine Fever Virus and Classical Swine Fever Virus on the MinION Portable Sequencing Platform
by Chester D. McDowell, Taeyong Kwon, Patricia Assato, Emily Mantlo, Jessie D. Trujillo, Natasha N. Gaudreault, Leonardo C. Caserta, Igor Morozov, Jayme A. Souza-Neto, Roman M. Pogranichniy, Diego G. Diel and Juergen A. Richt
Pathogens 2025, 14(8), 804; https://doi.org/10.3390/pathogens14080804 - 13 Aug 2025
Cited by 1 | Viewed by 2364
Abstract
African swine fever virus (ASFV) and classical swine fever virus (CSFV) are important transboundary animal diseases (TADs) affecting swine. ASFV is a large DNA virus with a genome size of 170–190+ kilobases (kB) belonging to the family Asfarviridae, genus Asfivirus. CSFV is [...] Read more.
African swine fever virus (ASFV) and classical swine fever virus (CSFV) are important transboundary animal diseases (TADs) affecting swine. ASFV is a large DNA virus with a genome size of 170–190+ kilobases (kB) belonging to the family Asfarviridae, genus Asfivirus. CSFV is a single-stranded RNA virus with a genome size of approximately 12 kB, belonging to the family Flaviviridae, genus Pestivirus. Outbreaks involving either one of these viruses result in similar disease syndromes and significant economic impacts from: (i) high morbidity and mortality events; (ii) control measures which include culling and quarantine; and (iii) export restrictions of swine and pork products. Current detection methods during an outbreak provide minimal genetic information on the circulating virus strains/genotypes that are important for tracing and vaccine considerations. The increasing availability and reduced cost of next-generation sequencing (NGS) allow for the establishment of NGS protocols for the rapid identification and complete genetic characterization of outbreak strains during an investigation. NGS data provides a better understanding of viral spread and evolution, facilitating the development of novel and effective control measures. In this study, panels of primers spanning the genomes of ASFV and CSFV were independently developed to generate approximately 10 kB and 6 kB amplicons, respectively. The primer panels consisted of 19 primer pairs for ASFV and 2 primer pairs for CSFV, providing whole genome amplification of each pathogen. These primer pools were further optimized for batch pooling and thermocycling conditions, resulting in a total of 5 primer pools/reactions used for ASFV and 2 primer pairs/reactions for CSFV. The ASFV primer panel was tested on viral DNA extracted from blood collected from pigs experimentally infected with ASFV genotype I and genotype II viruses. The CSFV primer panel was tested on 11 different strains of CSFV representing the three known CSFV genotypes, and 21 clinical samples collected from pigs experimentally infected with two different genotype 1 CSF viruses. ASFV and CSFV amplicons from optimized PCR were subsequently sequenced on the Oxford Nanopore MinION platform. The targeted protocols for these viruses resulted in an average coverage greater than 1,000X for ASFV, with 99% of the genome covered, and 10,000X–20,000X for CSFV, with 97% to 99% of the genomes covered. The ASFV targeted whole genome sequencing protocol has been optimized for genotype II ASF viruses that have been responsible for the more recent outbreaks outside of Africa. The CSFV targeted whole genome sequencing protocol has universal applications for the detection of all CSFV genotypes. Protocols developed and evaluated here will be essential complementary tools for early pathogen detection and differentiation, as well as genetic characterization of these high-consequence swine viruses, globally and within the United States, should an outbreak occur. Full article
(This article belongs to the Section Viral Pathogens)
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12 pages, 1862 KB  
Article
A Novel Recurrent 200 kb CRYL1 Deletion Underlies DFNB1A Hearing Loss in Patients from Northwestern Spain
by Guadalupe A. Cifuentes, Marta Diñeiro, Alicia R. Huete, Raquel Capín, Adrián Santiago, Alberto A. R. Vargas, Dido Carrero, Esther López Martínez, Beatriz Aguiar, Anja Fischer, Roland Rad, María Costales, Rubén Cabanillas and Juan Cadiñanos
Genes 2025, 16(6), 670; https://doi.org/10.3390/genes16060670 - 30 May 2025
Cited by 3 | Viewed by 2262
Abstract
Background/Objectives: Pathogenic recessive GJB2 variants are the main genetic cause of non-syndromic sensorineural hearing loss. However, following GJB2 testing, a significant proportion of deaf patients are only found to be heterozygous carriers of pathogenic GJB2 alleles. Five large deletions not affecting GJB2 but [...] Read more.
Background/Objectives: Pathogenic recessive GJB2 variants are the main genetic cause of non-syndromic sensorineural hearing loss. However, following GJB2 testing, a significant proportion of deaf patients are only found to be heterozygous carriers of pathogenic GJB2 alleles. Five large deletions not affecting GJB2 but encompassing a minimal common 62 kb region within the neighbouring CRYL1 gene have been described to cause loss of cis GJB2 expression and, as a result, produce hearing loss when in trans with pathogenic GJB2 variants. We describe the identification and characterization of a novel deletion of this type in deaf patients from northwestern Spain. Methods: We used panel NGS sequencing to detect the deletion, MLPA to validate it, whole-genome sequencing to map its breakpoints, PCR + Sanger sequencing to finely characterize it and triple-primer PCR to screen for it. Results: We identified a novel 200 kb deletion spanning the whole CRYL1 gene in two unrelated deaf patients from Asturias (in northwestern Spain) who were heterozygous for the pathogenic GJB2 c.35delG variant. Although the large deletion was absent from gnomAD v4.1.0 and 2052 local control alleles, screening for it in 20 additional deaf carriers of monoallelic pathogenic GJB2 variants detected it in another patient from Galicia (also in northwestern Spain). The novel deletion, termed del(200 kb)insATTATA, explained hearing loss in 3/43 (7%) deaf patients from our cohort that were otherwise heterozygous for pathogenic GJB2 variants. Conclusions: This work highlights the importance of comprehensively testing all genomic regions known to be clinically relevant for a given genetic condition, including thorough CRYL1 CNV screening for DFNB1A diagnostics. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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15 pages, 1251 KB  
Article
Benchmarking Nanopore Sequencing for CLN2 (TPP1) Mutation Detection: Integrating Rapid Genomics and Orthogonal Validation for Precision Diagnostics
by Betül Teker, Gökce Akan, Hasan Hüseyin Kazan, Özge Özgen, Suzin Tatonyan, Mehmet Cihan Balci, Meryem Karaca, Fulya Kurekci, Edibe Pembegül Yıldız, Olcay Güngor, Adnan Deniz, Asuman Gedikbasi, Fatmahan Atalar, Gülden Fatma Gokcay and Mehves Poda
Int. J. Mol. Sci. 2025, 26(11), 5037; https://doi.org/10.3390/ijms26115037 - 23 May 2025
Viewed by 1725
Abstract
CLN2 disease (neuronal ceroid lipofuscinosis type 2) is an ultra-rare lysosomal storage disorder caused by mutations in the TPP1/CLN2 gene, resulting in impaired tripeptidyl peptidase 1 (TPP1) activity. The timely initiation of enzyme replacement therapy is pivotal for attenuating progressive and irreversible neurodegeneration. [...] Read more.
CLN2 disease (neuronal ceroid lipofuscinosis type 2) is an ultra-rare lysosomal storage disorder caused by mutations in the TPP1/CLN2 gene, resulting in impaired tripeptidyl peptidase 1 (TPP1) activity. The timely initiation of enzyme replacement therapy is pivotal for attenuating progressive and irreversible neurodegeneration. This study aimed to benchmark the performance of Oxford Nanopore long-read sequencing (ONT-LRS) for targeted TPP1 mutation detection in a Turkish CLN2 cohort and to assess its concordance with orthogonal validation methods, including Sanger sequencing and enzymatic activity assays. Using a custom-designed primer panel, the entire TPP1 gene (6846 bp) was sequenced on the Oxford Nanopore (ONT) MinIon platform in seven clinically confirmed CLN2 index patients and sixteen unaffected family members. Detected variants were validated via Sanger sequencing and correlated with TPP1 enzyme activity in leucocytes and dried blood spots. Four pathogenic or likely pathogenic TPP1 variants were identified: c.622C>T (p.Arg208*), c.857A>G (p.Asn286Ser), c.1204G>T (p.Glu402*), and c.225A>G (p.Gln75=), along with fourteen additional benign variants. Variant allele frequencies were 50% for c.622C>T, 28.6% for c.1204G>T, 14.3% for c.857A>G, and 7.1% for c.225A>G. Notably, this is the first report to document the homozygous state of the c.857A>G variant and the compound heterozygous configuration of the c225A>G and c.622C>T variants in CLN2 patients, thereby expanding the known mutational landscape. In contrast, the globally common variant c.509-1G>C was not observed, suggesting regional variation in TPP1 mutation patterns. Consistent with the prior Turkish studies, c.622C>T (p.Arg208*) was the most prevalent variant, followed by c.1204G>T (p.Glu402*). TPP1 enzymatic activity was significantly reduced in all affected individuals (p < 0.0001), supporting the functional relevance of the identified variants. ONT-LRS offers a robust, cost-effective platform for high-resolution analysis of the TPP1 gene. Integrating molecular and biochemical data improves diagnostic precision and supports timely, targeted interventions for CLN2 disease, particularly in regions with high consanguinity and limited diagnostic infrastructure. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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24 pages, 3828 KB  
Article
Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63
by Tamila Musaeva, Artem Fadeev, Maria Pisareva, Veronika Eder, Andrey Ksenafontov, Margarita Korzhanova, Valery Tsvetkov, Alexander Perederiy, Irina Kiseleva, Daria Danilenko, Dmitry Lioznov and Andrey Komissarov
Viruses 2025, 17(1), 13; https://doi.org/10.3390/v17010013 - 25 Dec 2024
Cited by 2 | Viewed by 3140
Abstract
Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In [...] Read more.
Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900–1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with >70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses. Full article
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17 pages, 2953 KB  
Article
Loop-Mediated Isothermal Amplification-Based Workflow for the Detection and Serotyping of Salmonella spp. in Environmental Poultry Flock Samples
by Patricia Regal, Anne Doval, Iria García-Ramos, Alberto Cepeda, Alejandro Garrido-Maestu and Alexandre Lamas
Foods 2024, 13(24), 4069; https://doi.org/10.3390/foods13244069 - 17 Dec 2024
Cited by 5 | Viewed by 2630
Abstract
Salmonella spp. is one of the most important foodborne pathogens worldwide. Given the fact that poultry and poultry products are the main source of human infection, Salmonella control in these farms is of utmost importance. To better control this pathogen in farms, boot [...] Read more.
Salmonella spp. is one of the most important foodborne pathogens worldwide. Given the fact that poultry and poultry products are the main source of human infection, Salmonella control in these farms is of utmost importance. To better control this pathogen in farms, boot swabs are used to sample farm environments but the analysis of these swabs is mainly based on culture-dependent methods. In the present study, a novel loop-mediated isothermal amplification (LAMP) method was developed for the rapid screening of Salmonella spp. in boot swab samples from broiler flock environments. Four different DNA extraction protocols were evaluated in depth, including a simple thermal lysis, a chelex-based protocol and two thermal lysis protocols followed by the purification of magnetic beads made of silica (“glass milk”) in order to determine the most suitable alternative for potential on-site, farm analyses. The methodology evaluation included a blind interlaboratory assay and as a proof-of-concept, a naked-eye colorimetric assay was also included. Following the final methodology, it was possible to reach an LoD50 of 1.8 CFU/25 g of the samples, with a high relative sensitivity (95.7%), specificity (100%) and accuracy (96.6%) along with Cohen’s kappa of concordance with respect to the ISO standard 6579-1:2017 of 0.9, with an RLOD of 1.3. In addition to this, due to the relevance of certain serotypes with the genus Salmonella spp., a serotype LAMP panel for the specific identification of S. Typhimurium, S. Enteritidis, S. Infantis, S. Hadar and S. Virchow was also developed. Even though some degree of cross-reactivity among the primers developed was observed, all the serotypes could be accurately identified based on their melt curve analysis profile. Taken together, in the present study, a rapid Salmonella spp. screening method, suitable for farm applications, was developed, along with a serotyping panel that could be used in a laboratory setup for the identification of the most relevant serotypes of the genus, taking advantage of real-time amplification followed by melt curve analysis. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Foodborne Pathogenic Bacteria)
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22 pages, 9559 KB  
Article
Development of Primer Panels for Amplicon Sequencing of Human Parainfluenza Viruses Type 1 and 2
by Oula Mansour, Artem V. Fadeev, Alexander A. Perederiy, Daria M. Danilenko, Dmitry A. Lioznov and Andrey B. Komissarov
Int. J. Mol. Sci. 2024, 25(23), 13119; https://doi.org/10.3390/ijms252313119 - 6 Dec 2024
Cited by 2 | Viewed by 2857
Abstract
Human parainfluenza viruses (hPIVs) are major contributors to respiratory tract infections in young children worldwide. Despite their global significance, genomic surveillance of hPIV1 and hPIV2 had not previously been conducted in Russia. This study aimed to develop a robust amplicon-based sequencing protocol for [...] Read more.
Human parainfluenza viruses (hPIVs) are major contributors to respiratory tract infections in young children worldwide. Despite their global significance, genomic surveillance of hPIV1 and hPIV2 had not previously been conducted in Russia. This study aimed to develop a robust amplicon-based sequencing protocol for these viruses. The designed primer sets were tested on clinical samples containing hPIV RNA to evaluate their performance and efficiency. Sequencing results demonstrated high-quality genome data and efficient amplification across various Ct values. As a result, 41 hPIV1 and 13 hPIV2 near-complete genome sequences were successfully obtained from clinical specimens collected in Saint Petersburg (Russia). Phylogenetic analysis of the HN gene sequences showed that Russian hPIV1 strains clustered into clades II and III, while hPIV2 strains were distributed between clusters G1a and G3. The whole-genome-based trees confirmed the same distribution of the strains. These findings highlight the potential of our primer panels and contribute to a better understanding of the molecular characteristics and phylogenetic diversity of circulating hPIV strains. Notably, this study presents the first evolutionary analysis of hPIVs in Russia. Full article
(This article belongs to the Special Issue New Advances in Medical Microbiology)
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