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At least 19 recordsLinked to original sources
PubMed2026

First molecular detection and partial ORF1 characterization of psittacine beak and feather disease virus (PBFDV) in domesticated parrots of Northern Vietnam.

Psittacine beak and feather disease virus (PBFDV), currently classified within the species Circovirus parrot, is an infectious agent in avian species, particularly psittacine birds. PBFDV is the causative agent of psittacine beak and feather disease (PBFD), leading to feather loss, deformed beaks and nails, immunosuppression, and high mortality. However, there is limited information on PBFDV in Vietnam, particularly in domesticated parrots. This study aims to detect and molecularly characterize PBFDV in psittacine birds in Northern Vietnam. Among the 193 psittacine birds tested by conventional PCR, 48 were PBFDV-positive, corresponding to a positivity rate of 24.87%. Based on partial ORF1 characterization, phylogenetic tree analysis of the ten PBFDV sequences showed that genotype I, which exhibits genetic diversity, is circulating in Vietnam. This study highlights the importance of genomic characterization of PBFDV in domesticated exotic psittacine birds in Vietnam. Together with the recent cases of PBFD in domestic parrots, further surveillance is needed to elucidate the host specificity, transmission, and pathophysiology of PBFDV.

Animals↗
PubMed2025

Molecular Detection and Characterization of Bovine Diarrhea Virus (BVDV) in Aborted Fetuses and Semen Samples from Paraguay.

Bovine viral diarrhea virus (BVDV) is the most prevalent pathogen in cattle and causes significant economic losses due to its severe clinical manifestations. It belongs to the family Flaviviridae and is distributed in species A, B, and H within the genus Pestivirus. The objective of this study was to detect and characterize BVDV using molecular techniques (RT-PCR) in semen and aborted fetuses samples that were sent to the CEDIVEP (Veterinary Diagnostic Center of Paraguay) laboratory. Seventy-three samples of semen from bulls were analyzed, and 54.7% of the samples were positive for Pestivirus A. The presence of Pestivirus A and H was detected in 2/8 spontaneously aborted fetuses. The genotypes of four individual samples of type A and four samples of type H organs were confirmed by partial sequencing of the 5-UTR region. The presence of BVDV was confirmed by molecular techniques for the first time in our country through its detection in different types of samples, as well as the presence of two genotypes. This suggests that the circulation of this virus can cause significant losses in cattle production in Paraguay.

Diarrhea Viruses, Bovine Viral↗
PubMed2026

First molecular detection and genomic characterization of West Nile virus associated with a naturally aborted sheep in Tunisia.

In September 2025, West Nile virus (WNV) RNA was detected for the first time in a sheep in Zaghouan Governorate, Tunisia. Following sheep abortions, fetal specimens were analyzed and one tested positive for WNV by RT-qPCR. The generated near-complete WNV genome sequence by Oxford Nanopore Technologies belonged to Lineage 1a, previously associated with locally reported human neuroinvasive cases in the same area. Amino acid analysis of the envelope (E) protein confirmed the presence of the conserved NYS glycosylation motif (E154-E156), a characteristic feature of Euro-Mediterranean Lineage 1 WNV strains. These findings further support the endemic circulation of WNV in Tunisia and underline its significance for both animal and public health.

Abortion↗
PubMed2025

MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection.

Molecular residual disease (MRD) detection, initially developed for hematologic malignancies, has become a critical biomarker for monitoring solid tumors. MRD detection primarily relies on circulating tumor DNA (ctDNA) analysis using next-generation sequencing, offering high sensitivity and broad genomic coverage. However, challenges remain in designing cost-effective panels that maximize mutation detection while maintaining biological relevance. Fixed panels often lack sufficient patient-specific mutation coverage, while WES-based personalized MRD assays, despite their high sensitivity, are costly and less accessible. We developed a tumor comprehensive genomic profiling (CGP)-informed personalized MRD assay to detect tumor-derived mutations, which allowed us to design patient-specific personalized panels and meanwhile, provide a cost-effective alternative to whole exome sequencing (WES). To address these limitations, we developed MRDtarget, a heuristic multivariate Gaussian model-based targeted capture region selection method. By expanding beyond traditional hotspot regions, MRDtarget optimizes variant tracking for MRD detection, significantly improving sensitivity. Using a Bayesian inference-based heuristic approach, MRDtarget integrates multi-feature informativeness rates to identify optimal genomic regions for capture. Experimental results demonstrate that MRDtarget enables the detection of more variants per patient. This study underscores the importance of rational panel design to improve MRD sensitivity and provides a novel approach to enhance precision diagnostics and treatment for solid tumor patients.

Humans↗
PubMed2026

Liquid Biopsy of HPV Cell-Free DNA Enables Blood-Based Early Detection and Molecular Stratification of HPV-Associated Cancer and Precancer Stages.

Liquid biopsies targeting circulating tumor DNA enable noninvasive cancer detection but lack sensitivity in pre- and early- cancer stages, where clinical benefits would be greatest. Human papillomavirus (HPV) causes six cancer types, accounting for 5% of all cancers worldwide. Targeting HPV cell-free (cf)DNA offers a compelling opportunity to overcome current liquid biopsy constraints due to its unique tumor-specific origin, lack of sequence homology to the human genome, and the high viral-to-human copy ratio per cell. Utilizing HPV-associated anal cancer and precancer as a model, here we applied a custom, multi-feature HPV whole-genome liquid biopsy to biobanked and prospective screening cohorts spanning the HPV infection-precancer-cancer continuum. HPV cfDNA was detected years before cancer diagnosis and as early as the infection stage, with increasing detection as stages advanced. Genomic hallmarks of HPV malignancy, including HPV integration, PIK3CA mutations, and 3q amplification, were detected exclusively in cancer, while precancers exhibited distinct HPV genotypes. Fragmentomics analysis of HPV cfDNA revealed stage-informative signatures reflecting viral epigenetic changes during carcinogenesis. A unified classifier incorporating genomic and fragmentomics features achieved a mean AUC of 0.77 for identifying cancer and high-grade precancer, stages requiring clinical intervention. Together, these findings demonstrate the feasibility of blood-based screening and molecular risk stratification for HPV-associated cancer and precancer.

Journal Article↗
PubMed1977

Detection and molecular characterization of the thymus-brain antigen in human brain.

Anti-human brain sera were found to contain antibodies reacting with determinants present on murine thymocyte plasma membranes. This determinant is borne by the thymocyte-brain antigen of mouse thymocytes. The non species-specific determinant of the thymocyte-brain system is detectable on the thymocyte-brain antigen of human and mouse brain in comparable amounts. In contrast to these findings, the allogenic Thy-1 and the species-specific determinant of this system were only found on the thymocyte-brain antigen of mouse brain but not on the corresponding antigen of human brain. The molecular weight, Stokes radius and diffusion coefficient of the thymocyte-brain antigen of human and mouse brain are in good accordance with the data estimated for the corresponding antigen of murine thymocytes.

Animals↗
PubMed2026

Serological and Molecular Prevalence of HCMV, HCV, HBV and Toxoplasma gondii Co-infection in Treatment-Naive HIV-Infected Individuals.

INTRODUCTION: Co-infections with human cytomegalovirus (HCMV), hepatitis B virus (HBV), hepatitis C virus (HCV), and Toxoplasma gondii (T. gondii) pose clinical challenges in human immunodeficiency virus-1 (HIV-1)-infected individuals by complicating disease progression and management. This study aimed to investigate the serological and molecular prevalence of HCMV, HBV, HCV, and T. gondii co-infections among treatment-naive HIV-infected individuals. METHODS: A cross-sectional study was conducted from March 2022 to August 2024 on 203 treatment- naive HIV-1-infected individuals. Plasma samples were analyzed using ELISA for serological markers and real-time PCR for molecular detection. Statistical analyses were performed to assess demographic and clinical variables associated with co-infections. RESULTS: Among the 203 participants, the prevalence of anti-HCV antibodies, HBsAg, HCMV IgM, and T. gondii IgM was 9.9%, 2.5%, 1.5%, and 0.5%, respectively. Molecular detection confirmed active HBV, HCV, and HCMV infections in 40%, 60%, and 66.7% of seropositive individuals, respectively, while T. gondii DNA was undetected. HCV genotyping revealed subtype 1a as the most common (50%), followed by 3a (37.5%) and 1b (12.5%). DISCUSSION: The findings indicate a moderate prevalence of HBV and HCV co-infections and a low prevalence of HCMV and T. gondii co-infections in treatment-naive HIV patients. CONCLUSION: These results highlight the need for targeted public health interventions, including vaccination and screening strategies, to reduce the risk of co-infections in HIV-infected individuals.

Humans↗
PubMed1978

Complement receptors: specific detection by molecular complexes.

Immune complexes of BSA-anti BSA (IgG F(ab')2) will activate human complement by the alternate pathway. The C3 bound to these complexes binds to human peripheral blood mononuclear cells which bear complement receptors. This interaction is visualized by fluoresceinated antigen (BSA-FITC) or fluorescein conjugated antisera directed at the C3 component of complement. The assay appears to be more sensitive than the usual IgMEAC rosette technique and correlates well with the rosette method.

Animals↗
PubMed2026

Comparative prevalence of the mercury resistance gene merA in human feces, food, and environmental water from Japan, Vietnam, and Ghana.

In this study, we investigated the prevalence and abundance of the mercury resistance gene merA in human feces, retail chicken meat, and environmental water samples collected from Japan, Vietnam, and Ghana. A real-time PCR assay developed in this study demonstrated high specificity toward merA sequences from more than 12 bacterial species. Using this assay, merA was detected in 6.8% of human fecal samples in Japan (n = 29), in contrast to significantly higher rates observed in Vietnam (70.2%, n = 47) and Ghana (97.4%, n = 39). Similar geographic trends were evident in the chicken meat samples: 18.5% in Japan (n = 27), 66% in Vietnam (n = 91), and 90% in Ghana (n = 10). Environmental water samples showed a consistently high merA detection rate across all countries (75-100%, n = 21), with substantially higher gene copy numbers in Vietnam and Ghana than in Japan. merA was detected in some water samples, even when total mercury concentrations were below the detection limit, indicating that molecular detection may offer greater sensitivity than traditional physicochemical methods. Mercury-resistant bacteria were successfully isolated and cultured, and Citrobacter freundii was identified as the representative strain. Genomic analysis revealed that merA was located on an IncFIB plasmid, flanked by insertion sequences, suggesting its potential for horizontal gene transfer. These findings highlight merA as a promising biomarker for environmental mercury exposure and support the utility of fecal merA analysis as a proxy for assessing mercury-related public health risks.

Humans↗
PubMedDate not supplied

[Metabolically stable classes of nuclear messenger-like RNA. I. Detection and molecular characterization].

Two discreet in size molecular classes of metabolically stable messenger-like RNA molecules with sedimentation coefficientes about 28S and 18S have been revealed in the nuclei of pigeon bone marrow cells. The structural pecularities of 28S RNA class were investigated more carefully. It was shown to constitute the largest fraction of nuclear messenger-like RNA and is characterized by a GC/AU ratio 1.13. As pulse-labeled nuclear RNA, 28S stable nuclear RNA hybridizes with the unique and rare repeated DNA, it does not contain poly(A)-sequences and is found in a form of RNP particles with density of 1.41 g/sm3, tightly bound to chromatin.

Animals↗
PubMed2026

Simultaneous detection of glyphosate and glufosinate target-site resistance in Eleusine indica via multiplex TaqMan qPCR.

BACKGROUND: Continuous use of glyphosate followed by glufosinate-ammonium has selected for multiple resistance to both herbicides in Eleusine indica worldwide. Managing such resistant weeds requires fast, accurate molecular detection assay. To address this critical need, we developed a robust multiplex TaqMan quantitative (q)PCR assay that simultaneously detects five well-characterized target-site resistance markers in E. indica: EPSPS copy number variation; T102I in EPSPS; P106A and P106S in EPSPS; and S59G in GS1-1. RESULTS: The multiplex qPCR assay showed analytical specificity when tested on genomic DNA from nine reference accessions: three susceptible, three glyphosate-resistant (with EPSPS CNV) and three multiple-resistant. Subsequent analysis of 56 field-collected samples demonstrated 98.2% concordance (55 of 56) with Sanger sequencing across all five resistance-associated markers: EPSPS CNV, T102I, P106A, P106S and GS1-1 S59G, confirming the reliability and practical value of the multiplex qPCR assay. Only samples 7-8 showed discordance at EPSPS position 102, where Sanger chromatograms showed overlapping peaks at this position, which is likely to be a result of heterozygous mutation distribution among amplified EPSPS gene copies. This case further underscores the advantages of the multiplex qPCR assay over Sanger sequencing in detection sensitivity and accuracy. Moreover, a strong correlation (R2 = 0.8935) in gene copy number estimation between the two methods across all samples further supports the reliability of the qPCR assay. CONCLUSIONS: In summary, this study delivers a simple, robust and high-throughput diagnostic tool for the rapid, simultaneous identification of dual herbicide target-site resistance in goosegrass, offering superior sensitivity, quantitative resolution and throughput compared with Sanger sequencing. © 2026 Society of Chemical Industry.

Herbicides↗
PubMed2027

RT-RPA-Assisted CRISPR/Cas12a-Based Isothermal Detection of Chikungunya Virus.

Chikungunya virus (CHIKV) is transmitted through the bite of Aedes mosquitoes, specifically A. aegypti and A. albopictus. CHIKV belongs to the alphavirus with a positive-sense ssRNA genome of 11-12 kb size. The virus has been reported from various geographical regions across the globe. Chikungunya fever is an acute febrile illness, which, if left untreated, may develop into chronic arthralgia that may persist for several months or acute encephalitis syndrome. Therefore, early diagnosis of CHIKV is crucial to initiate prompt supportive treatment. Laboratory diagnosis of CHIKV typically relies on serological tests such as IgM antigen capture ELISA and molecular methods including RT-PCR or qRT-PCR. However, both these methods are not viable in peripheral settings. This chapter highlights recent advancements in molecular detection techniques for CHIKV, specifically isothermal detection methods that eliminate the requirement for complex instruments. The detection is facilitated by RT-RPA and CRISPR/Cas12a endonuclease. The assay offers advantages over existing methods such as rapid and early detection, and eliminates cross-over contamination, ultra-sensitivity, high specificity, and ease of result interpretation.

Chikungunya virus↗
PubMed2026

Global molecular and serological evidence of dengue and chikungunya infection: a systematic review and meta-analysis of 158,608 tested participants.

INTRODUCTION: Dengue virus (DENV) and chikungunya virus (CHIKV) are Aedes-borne arboviruses with overlapping clinical manifestations, shared vectors, and substantial diagnostic challenges in co-endemic settings. This systematic review and meta-analysis synthesized published evidence on molecular detection, serological positivity, and DENV-CHIKV dual positivity/co-infection in human clinical, surveillance, and community-based study populations. CONTENT: Following PRISMA 2020 guidance, five bibliographic databases (PubMed/MEDLINE, Scopus, Web of Science, ScienceDirect, and Google Scholar) and supplementary grey-literature/preprint sources were searched for English-language studies published from 1 January 1980 to 31 December 2024. No prospective PROSPERO or OSF protocol registration was available. Eligible records reported extractable numerators and denominators for DENV and/or CHIKV in humans using recognized molecular or serological assays. A total of 196 studies comprising 158,608 tested or suspected participants were included in the extraction table. The pooled CHIKV estimate was 14.0 % (95 % CI: 12.0-16.4; I2=97.5 %), with molecular and serological estimates of 9.8 and 15.7 %, respectively. The pooled DENV estimate was 13.8 % (95 % CI: 10.9-17.3; I2=99.0 %), with molecular and serological estimates of 13.1 % (95 % CI: 7.9-21.0) and 14.3 % (95 % CI: 10.2-19.8), respectively. DENV-CHIKV dual positivity/co-infection was 52.9 % (95 % CI: 48.7-57.1) among studies that tested and reported both outcomes. Country-level estimates varied widely and should be interpreted as summaries of available studies rather than nationally representative burden estimates. Funnel-plot asymmetry was statistically significant in DENV analyses but not in the overall CHIKV analysis. SUMMARY: Available evidence indicates extensive but highly heterogeneous DENV and CHIKV positivity across selected clinical and surveillance populations. The pooled estimates should be interpreted cautiously because of substantial between-study heterogeneity, diagnostic variability, outbreak-period sampling, and uneven geographic representation. OUTLOOK: The findings support integrated arboviral surveillance, multiplex diagnostics, and vector-control preparedness in co-endemic regions.

Humans↗
PubMed2027

Protocol for Detecting and Sequencing Chikungunya Virus from Field-Collected Mosquitoes.

Arboviral diseases represent a major public health challenge, especially in tropical regions where environmental conditions may favor the proliferation and spread of mosquito vectors. Thus, early and accurate detection of chikungunya virus (CHIKV) in mosquito populations can be a valuable tool for effective surveillance of circulating variants and for identifying new viral introductions. Given the challenges of detecting arboviruses in field-captured mosquitoes, we describe an integrated workflow for CHIKV molecular detection and whole-genome sequencing. This protocol includes mosquito homogenization using a bead-based mechanical disruptor, RNA extraction using TRIzol reagent with minor modifications, molecular screening using CHIKV-specific RT-qPCR, and whole-genome amplification followed by sequencing on Illumina platforms. Despite the protocol being optimized for individual mosquitoes, it results in high-quality RNA suitable for both entomological surveillance and genomic analysis. As this protocol allows recovery of complete CHIKV genomes from mosquito specimens, it can serve as a basis for genomic epidemiology studies, enabling monitoring of viral diversity and lineage dynamics, and facilitating early detection of emerging variants to support timely and targeted public health interventions in endemic and at-risk regions.

Animals↗
PubMed2026

Detection of lymphocytic choriomeningitis virus (LCMV) in the common house mice (Mus musculus) in Italy: an underrecognized threat to human health.

Lymphocytic choriomeningitis virus (LCMV) is a neglected zoonotic pathogen primarily transmitted by the house mouse (Mus musculus). Despite being an underestimated zoonotic threat in Europe, LCMV lacks comprehensive surveillance. In this study, we report the first molecular detection and full genomic characterization of LCMV in Italy. Between May and November 2021, 107 rodents were captured on livestock farms in the Piedmont Region and screened for arenaviruses using a pan-arenavirus RT-PCR assay. LCMV RNA was detected in three Mus musculus specimens (3.5%), all originating from two neighboring farms. Viral presence was confirmed by LCMV-specific qRT-PCR. Complete S and L genome segments were successfully obtained from one sample using a combination of RT-PCR and nanopore sequencing. Phylogenetic analyses placed the Italian strain within LCMV lineage I, clustering with strains previously detected in Europe. Host genetic analysis confirmed that infected mice belonged to the subspecies Mus musculus domesticus.IMPORTANCEThis study provides the first molecular evidence and complete genomic characterization of Lymphocytic choriomeningitis virus (LCMV) in Italy in its primary reservoir, Mus musculus. The identification of LCMV at the livestock-wildlife interface suggests a significant anthropozoonotic risk, particularly for farm workers. These findings emphasize the urgent necessity for integrated molecular surveillance and increased clinical awareness to better define the public health impact of LCMV in Italy.

Animals↗
PubMed2024

Development of methodology to support molecular endotype discovery from synovial fluid of individuals with knee osteoarthritis: The STEpUP OA consortium.

OBJECTIVES: To develop a protocol for largescale analysis of synovial fluid proteins, for the identification of biological networks associated with subtypes of osteoarthritis. METHODS: Synovial Fluid To detect molecular Endotypes by Unbiased Proteomics in Osteoarthritis (STEpUP OA) is an international consortium utilising clinical data (capturing pain, radiographic severity and demographic features) and knee synovial fluid from 17 participating cohorts. 1746 samples from 1650 individuals comprising OA, joint injury, healthy and inflammatory arthritis controls, divided into discovery (n = 1045) and replication (n = 701) datasets, were analysed by SomaScan Discovery Plex V4.1 (>7000 SOMAmers/proteins). An optimised approach to standardisation was developed. Technical confounders and batch-effects were identified and adjusted for. Poorly performing SOMAmers and samples were excluded. Variance in the data was determined by principal component (PC) analysis. RESULTS: A synovial fluid standardised protocol was optimised that had good reliability (<20% co-efficient of variation for >80% of SOMAmers in pooled samples) and overall good correlation with immunoassay. 1720 samples and >6290 SOMAmers met inclusion criteria. 48% of data variance (PC1) was strongly correlated with individual SOMAmer signal intensities, particularly with low abundance proteins (median correlation coefficient 0.70), and was enriched for nuclear and non-secreted proteins. We concluded that this component was predominantly intracellular proteins, and could be adjusted for using an 'intracellular protein score' (IPS). PC2 (7% variance) was attributable to processing batch and was batch-corrected by ComBat. Lesser effects were attributed to other technical confounders. Data visualisation revealed clustering of injury and OA cases in overlapping but distinguishable areas of high-dimensional proteomic space. CONCLUSIONS: We have developed a robust method for analysing synovial fluid protein, creating a molecular and clinical dataset of unprecedented scale to explore potential patient subtypes and the molecular pathogenesis of OA. Such methodology underpins the development of new approaches to tackle this disease which remains a huge societal challenge.

Humans↗
PubMed1975

The molecular basis of self-association of IgG-Rheumatoid factors.

The intermediate complexes, sedimenting between 19S and 6.6S components of normal serum on analytical ultracentrifugation, were purified from plasma of three patients with rheumatoid arthritis. Sequential gel filtration and removal of contaminants by agarose-antibody immunoadsorbents were employed for purification of these complexes. The isolated complexes from the three patients consisted of IgG with k and lambda light chains. Sedimentation equilibrium ultracentrifugation experiments showed that the isolated complexes underwent concentration-dependent self-association, whereby the smallest detectable molecular species had a molecular weight of 292,000. These IgG dimers were formed by self-association of IgG-rheumatoid factors, since nearly all F(ab) fragments, prepared from the isolated complexes by pepsin digestion, bound to normal IgG. The association constants for the interaction between normal IgG and one binding site of the F(ab) fragments were about 10-5 liters/mole. Since a cyclic structure with two antigen-antibody bonds was thought to form in the self-association of two IgG-rheumatoid factors, the association constant for dimer formation was calculated to be 10-10 liters/mole. The preferential self-association of IgG-rheumatoid factor was supported by the observation that monomeric normal human IgG did not replace the IgG-rheumatoid factor when the complexes were dissociated and reformed in the presence of excess normal IgG. The self-association of IgG-rheumatoid factors may be a general phenomenon in rheumatoid arthritis, as suggested by the observations of other investigators.

Antibody Specificity↗