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Analysis of ovine lentivirus infectivity and replication by using a focal immunoassay and an antigen-capture enzyme-linked immunosorbent assay.

A focal immunoassay and an antigen-capture enzyme-linked immunosorbent assay (antigen-capture ELISA) were developed to quantify infectious ovine lentivirus (OvLV) and OvLV capsid protein (CA) (p27), respectively. The in vitro kinetics of replication and cytopathogenicity of distinct biological clones of OvLV (rapid/high and slow/low phenotypic variants) were assessed. Both viruses were detected by focal immunoassay within 48 h postinfection, 2 days before syncytia were observed in goat synovial membrane cells infected with rapid/high OvLV and 4 days before they appeared in cultures infected with slow/low OvLV. CA was first detected by antigen-capture ELISA in supernatants of cells infected with rapid/high OvLV 4 days postinfection, and it reached a plateau by 10 days, 4 days after peak syncytium formation. In contrast, in cultures infected at the same multiplicity of infection with slow/low OvLV, CA was detected 8 days postinfection, and the titer gradually increased over the following 12 days while the number of syncytia gradually decreased. Peripheral blood mononuclear cells (PBMC) from seropositive sheep treated with phorbol 12-myristate 13-acetate (PMA) generally expressed CA earlier and at higher levels than PBMC treated with either phytohemagglutinin or concanavalin A. Serum CA levels above 3 ng/ml were found in 58% (18 of 31) of seropositive sheep. However, there was no correlation between PMA-induced CA expression and levels of antigenemia. Viral heterogeneity may account for variations both in CA expression in cultures of PBMC and in antigenemia, humoral immune response, and viral pathogenicity in infected animals.

Animals↗

Combined single-clade candidate HIV-1 vaccines induce T cell responses limited by multiple forms of in vivo immune interference.

We assessed in mice whether broad CD8+ T cell responses capable of efficient recognition of multiple HIV-1 clades could be induced using current single-clade vaccine constructs that were or will be used in clinical trials in Europe and Africa. We found that single-clade A, B and C vaccines applied alone induced only limited cross-clade reactivity and that the epitope hierarchy varied according to the immunizing clade. However, combining single-clade HIV-1 vaccines into multi-clade formulations resulted in multiple forms of in vivo immune interference such as original antigenic sin and antagonism, which dampened or even abrogated induction of responses to epitope variants and reduced the breadth of induced T cell responses. Simultaneous administration of individual clade-specific vaccines into anatomically separated sites on the body alleviated antagonism and increased the number of detectable epitope responses. Although cross-reactivity of murine CD8+ T cells does not directly translate to humans, the molecular interactions involved in triggering T cell responses are the same in mouse and man. Thus, these results have important ramifications for the design of both prophylactic and therapeutic vaccines against HIV-1 and other highly variable pathogens.

AIDS Vaccines↗

Mortality Among Patients With Early-Onset Atrial Fibrillation and Rare Variants in Cardiomyopathy and Arrhythmia Genes.

IMPORTANCE: Patients with early-onset atrial fibrillation (AF) are enriched for rare variants in cardiomyopathy and arrhythmia genes. The clinical significance of these rare variants in patients with early-onset AF is unknown. OBJECTIVE: To assess the association between rare variants in cardiomyopathy and arrhythmia genes detected in patients with early-onset AF and time to death. DESIGN, SETTING, AND PARTICIPANTS: This prospective cohort study included participants with AF diagnosed before 66 years of age who underwent whole-genome sequencing through the National Heart, Lung and Blood Institute's Trans-Omics for Precision Medicine program. Participants were enrolled from November 23, 1999, to June 2, 2015. Data were analyzed from February 26 to September 19, 2021. EXPOSURES: Rare variants identified in a panel of 145 genes that are included in cardiomyopathy and arrhythmia panels used by commercial clinical genetic testing laboratories. MAIN OUTCOMES AND MEASURES: The primary study outcome was time to death and was adjudicated from medical records and the National Death Index. Multivariable Cox proportional hazards regression was used to evaluate the association of disease-associated variants with risk of death after adjustment for age at AF diagnosis, sex, race, body mass index, left ventricular ejection fraction, and an interaction term of age at AF diagnosis and disease-associated variant status. RESULTS: Among 1293 participants (934 [72%] male; median age at enrollment, 56.0 years; IQR, 48.0-61.0 years), disease-associated (pathogenic or likely pathogenic) rare variants were found in 131 (10%). During a median follow-up of 9.9 years (IQR, 6.9-13.2 years), 219 participants (17%) died. In univariable analysis, disease-associated variants were associated with an increased risk of mortality (hazard ratio, [HR], 1.5; 95% CI, 1.0-2.1; P&#x2009;=&#x2009;.05); the association remained significant in multivariable modeling when adjusted for age at AF diagnosis, sex, race, body mass index, left ventricular ejection fraction, and an interaction term between disease-associated variant status and age at AF diagnosis. The interaction demonstrated that disease-associated variants were associated with a significantly higher risk of mortality compared with no disease-associated variant when AF was diagnosed at a younger age (P&#x2009;=&#x2009;.008 for interaction). Higher body mass index (per IQR: HR, 1.4; 95% CI, 1.2-1.6; P&#x2009;<&#x2009;.001) and lower left ventricular ejection fraction (per IQR: HR, 0.8; 95% CI, 0.7-0.8; P&#x2009;<&#x2009;.001) were associated with higher mortality risk. There were 73 cardiomyopathy-related deaths, 40 sudden deaths, and 10 stroke-related deaths. Mortality among patients with the most prevalent genes with disease-associated variants was 26% (10 of 38 patients) for TTN, 33% (6 of 18) for MYH7, 22% (2 of 9) for LMNA, 0% (0 of 10) for MYH6, and 0% (0 of 8) for KCNQ1. CONCLUSIONS AND RELEVANCE: The findings suggest that rare variants in cardiomyopathy and arrhythmia genes may be associated with increased risk of mortality among patients with early-onset AF, especially those diagnosed at a younger age. Genetic testing may provide important prognostic information for patients with early-onset AF.

Atrial Fibrillation↗

Detection and localization of PrPSc in the skeletal muscle of patients with variant, iatrogenic, and sporadic forms of Creutzfeldt-Jakob disease.

Variant Creutzfeldt-Jakob disease (vCJD) differs from other human prion diseases in that the pathogenic prion protein PrP(Sc) can be detected to a greater extent at extraneuronal sites throughout the body, principally within lymphoid tissues. However, a recent study using a high-sensitivity Western blotting technique revealed low levels of PrP(Sc) in skeletal muscle from a quarter of Swiss patients with sporadic CJD (sCJD). This posed the question of whether PrP(Sc) in muscle could also be detected in vCJD, sCJD, and iatrogenic (iCJD) patients from other populations. Therefore, we have used the same high-sensitivity Western blotting technique, in combination with paraffin-embedded tissue blotting, to screen for PrP(Sc) in muscle tissue specimens taken at autopsy from 49 CJD patients in the United Kingdom. These techniques identified muscle PrP(Sc) in 8 of 17 vCJD, 7 of 26 sCJD, and 2 of 5 iCJD patients. Paraffin-embedded tissue blotting analysis showed PrP(Sc) in skeletal muscle in localized anatomical structures that had the morphological and immunohistochemical characteristics of nerve fibers. The detection of PrP(Sc) in muscle tissue from all forms of CJD indicates the possible presence of infectivity in these tissues, suggesting important implications for assessing the potential risk of iatrogenic spread via contaminated surgical instruments.

Animals↗

Rapidly advancing necrotizing fasciitis caused by Photobacterium (Vibrio) damsela: a hyperaggressive variant.

OBJECTIVE: To describe the first case of Vibrio damsela necrotizing fasciitis in New England, emphasizing the importance of very early operative intervention to achieve source control in this extremely aggressive infection. DESIGN: Case report. SETTING: Surgical intensive care unit at Tufts-New England Medical Center in Boston, MA. PATIENT: A 69-yr-old retired fisherman with rapidly progressive necrotizing fasciitis from Photobacterium (Vibrio) damsela infection and ensuing multiple-system organ failure. INTERVENTIONS: Surgical debridement, ventilator support, vasopressors, continuous veno-venous hemofiltration, and blood product transfusions. MEASUREMENTS AND MAIN RESULTS: Death. CONCLUSIONS: A high index of suspicion is necessary for the diagnosis of this specific pathogen and concordant infection. The willingness to surgically debride and amputate without hesitation at a very early point may be the only intervention capable of saving the lives of patients affected by Photobacterium (Vibrio) damsela.

Aged↗

Can presence or absence of periodontal pathogens distinguish between subjects with chronic and aggressive periodontitis? A systematic review.

OBJECTIVES: The purpose of this study was to determine to what extent the presence or absence of periodontal pathogens can distinguish between subjects with chronic and aggressive periodontitis. MATERIAL AND METHODS: A systematic review of cross sectional and longitudinal studies providing microbiological data both from patients with chronic periodontitis (ChP) and aggressive periodontitis (AgP) at a subject level. Strict inclusion criteria were applied. The presence or absence of five microorganisms was selected as primary study parameters: Actinobacillus actinomycetemcomitans (AA), Porphyromonas gingivalis (PG), Prevotella intermedia (PI), Bacteroides forsythus (BF), and Campylobacter rectus (CR). RESULTS: The presence or absence of AA could be evaluated in 11 papers. In seven papers the presence or absence of PG could be analysed. Subject specific data on PI were available from six studies. Two studies could be used regarding the presence or absence of BF, and two regarding CR. Sensitivity and specificity of every microbiological test were individually calculated for each selected study, assuming that the clinical diagnosis of AgP or ChP was the true status the tests attempted to detect. AgP was considered to be the condition of interest and ChP was considered equivalent to 'non-AgP'. Receiver Operator Characteristic (ROC) diagrams were constructed using these data. ROC diagrams indicated the limited discriminatory ability of all of the test parameters to identify subjects with AgP. An additional assessment showed that the highly leukotoxic variant of AA was uniquely associated with patients suffering from aggressive periodontitis. However, in a high proportion of patients diagnosed with AgP the presence of this variant could not be detected. CONCLUSION: The presence or absence of AA, PG, PI, BF or CR could not discriminate between subjects with AgP from those with ChP.

Acute Disease↗

The role of lysosomal alterations in the damage to the pancreas and liver in acute experimental pancreatitis in dogs.

The role of lysosomal hydrolases in the pathogenesis of acute pancreatitis and secondary liver injury, as an important aspect of multisystem organ failure, remains unclear. The purpose of this study was to assess the lysosomal fragility in both organs in acute experimental pancreatitis (AEP) of graded severity in dogs. In 7 dogs, the moderate (M) and in 13 dogs severe (S) variant of bile--trypsin AEP--was induced; 6 dogs were in control group (C). The 24 h survival time was 6/7 and 6/13, respectively. After that time, the dogs were sacrificed and the lysosomal enriched subfraction (L) from both organs was isolated by ultracentrifugation. The total (T) and free (F) activities of beta-glucuronidase (beta G), cathepsins (Cs) and acid phosphatase (AcP) according to Gianetto and de Duve were assayed. The fractional free activity (% F/T) was adapted as and index of lysosomal stability. The %F/T of BG in the homogenate of the pancreas in AEP(S) was higher than that in AEP(M) (92% vs. 71%, p < 0.05, and vs. 37% in C, p < 0.005). The %F/T of Cs and AcP showed a similar pattern. The %F/T of beta G in L of the liver in AEP(S) was 38% vs. 29% in AEP(M), (p < 0.05), and vs. 20% in C (p < 0.05). In AEP in dogs the %F/T activities of lysosomal hydrolases in the pancreas and liver were increased, suggesting the labilization of lysosomal membranes in severe form of this disease. Our results support the pathogenic role of lysosomal hydrolases in the damage to the pancreas and liver in acute pancreatitis.

Acute Disease↗

In vitro evaluation of the anti-prionic activity of newly synthesized congo red derivatives.

"Transmissible Spongiform Encephalopathies" (TSE) are a group of degenerative progressive fatal disorders of the CNS, affecting both humans and animals. The main pathogenic event is the conversion of cellular prion protein from the normal, enzyme-sensitive (PrPsen), to the insoluble proteinase K-resistant isoform (PrPres). Since the new juvenile variant of Creutzfeldt-Jakob disease (vCJD) is probably due to the transmission of Bovine Spongiform Encephalopathy (BSE) prion protein to man, therapeutic and preventive compounds for animals and humans are urgently needed. Congo Red (benzidine-diazo-bis-1-naphthylamine-4-sulfonic acid sodium salt, CAS 573-58-0, CR), an azoic dye that inhibits amyloid deposition, and some newly synthesized derivatives, more lipophilic and less toxic, were tested for their anti-prionic activity, in different experimental models. Cell-free experiments using the synthetic peptide PrP 106-126, homologous to amino acid residues 106-126 of the human PrP, were run to determine the anti-amyloidogenic properties of some of the molecules. Peptide solutions containing each compound were incubated at 37 degrees C, for increasing times, to analyse the kinetics of aggregation of PrP 106-126 peptide. After incubation, the amount of non-aggregated peptide was measured by RP-HPLC. While CR enhanced the amyloidogenicity of PrP 106-126, derivatives "1a" and "1b" both showed the opposite behaviour, reducing aggregation by 15-20%. In other experiments using electron microscopy PrP 106-126 was assayed with the same molecules to assess the number and size of fibrils formed. CR showed its typical interaction, producing amyloid aggregates, "1a" did not interfere with fibril formation, while "1b" seemed to partially affect the structure of PrP 106-126 fibrils. Using a different cell-free model, it was investigated whether CR derivatives could reverse the protease-resistant PrPres, extracted from Syrian hamster infected brain, into the normal protease sensitive PrPsen. Samples containing fixed amounts of PrPres were incubated at 37 degrees C for 1 h with all the newly synthesized molecules, at concentrations ranging from 50 micrograms/mL to 750 micrograms/mL. After treatment with proteinase K, half of each sample was incubated with 3 mol/L guanidine thiocyanate in order to exclude over-stabilisation of the PrPres aggregates already observed with CR. The remaining amount of PrPres was assessed by Enhanced Chemoluminescence (ECL) Western blotting analysis. None of the compounds induced the reversion of PrPres to PrPsen; nevertheless, 6 of the 8 molecules interacted with PrPres molecules, over-stabilising the PrPres aggregates, from this aspect being similar to CR in activity. Finally, the inhibition of the generation of PrPres in the S12 clone of a mouse neuroblastoma cell line (N2a S12), persistently infected by the mouse adapted Chandler strain of scrapple, was evaluated. Increasing amounts of CR, "1a" and "1b" were added to the culture medium at each cell passage. After various days of treatment, the cells were collected, lysed, and the amount of PrPres was assayed by ECL Western blotting after PK treatment. As expected, there was a decrease in pathological PrP expression starting from the 4th day of treatment, with 5 and 10 micrograms/mL CR; PrPres completely disappeared after respectively 10 and 14 days of treatment. "1a" was strongly effective after 3 days of treatment at 5 and 10 micrograms/mL, but it was also highly toxic; at the concentration of 1 microgram/mL, it had a mild inhibitory effect after 8 days. The reduction of PrPres was also evaluated by intracytoplasmic flow-cytometry immunofluorescence on CR- and "1a"-treated N2a S12 cells. CR induced a dose-related decrease of PrP expression from day 3 to 13 of treatment. At the concentrations of 2 and 1.5 micrograms/mL "1a" also strongly affected the expression of PrP starting from the 3rd day of treatment until the end of the experiment (day 13). These results confirm the importance of using an integrated system, based on different experimental models, to obtain useful information on the mechanism of action of anti-prionic compounds.

Amino Acid Sequence↗

Identification of mycoplasma membrane proteins by systematic Tn phoA mutagenesis of a recombinant library.

Wall-less prokaryotes in the genus Mycoplasma include over 90 species of infectious agents whose pathogenicity for humans and other animals is currently being assessed. Molecular characterization of surface proteins is critical in this regard but is hampered by the lack of genetic systems in these organisms. We used TnphoA transposition to systematically mutagenize, in Escherichia coli, a genomic plasmid library constructed from Mycoplasma fermentans, a potential human pathogen. The strategy circumvented problems of expressing mycoplasma genes containing UGA (Trp) codons and relied on the construction of the vector pG7ZCW, designed to reduce TnphoA transposition into vector sequences. Functional phoA gene fusions directly identified genes encoding 19 putative membrane-associated proteins of M. fermentans. Sequences of fusion constructs defined three types of export sequence: (1) non-cleavable, membrane-spanning sequences, (2) signal peptides with signal peptidase (SPase) I-like cleavage sites, and (3) signal peptides with SPase II-like lipoprotein-cleavage sites which, like most other mycoplasmal lipoprotein signals analysed to date, differed from those in several Gram-negative and Gram-positive eubacteria in their lack of a Leu residue at the -3 position. Antibodies to synthetic peptides that were deduced from two fusions to predicted lipoproteins, identified corresponding amphiphilic membrane proteins of 57 kDa and 78 kDa expressed in the mycoplasma. The P57 sequence contained a proline-rich N-terminal region analogous to an adhesin of Mycoplasma gallisepticum. The P78 protein was identical to a serologically defined phase-variant surface lipoprotein. TnphoA mutagenesis provides an efficient means of systematically characterizing functionally diverse lipoproteins and other exported proteins in mycoplasmas.

Alkaline Phosphatase↗

Molecular and biological characterization of simian immunodeficiency virus macaque strain 32H proviral clones containing nef size variants.

The proviral genome of the 32H reisolate of simian immunodeficiency of macaques (SIVmac32H) has been cloned and sequenced. Including both long terminal repeats, it is 10277 base pairs in length and contains open reading frames for all known SIV genes (gag, pol, vif, vpx, vpr, tat, rev, env and nef). This is the first report of an infectious SIVmac molecular clone which contains no premature termination codons. Three molecular clones of SIVmac32H have been constructed differing in sequence only within their last 1.2 kb. Two of the molecular clones, SIVmac32H(pJ5) and SIVmac32H (pC8), differ in the nef coding region by an in-frame deletion of four amino acids in pC8 and two conservative amino acid changes; other nucleotide changes in the 3' LTR were not associated with known functionally critical motifs. The third clone, SIVmac32H(pB1), contains the last 1.2 kb of the SIVmac251 clone pBK28. The biological properties of virus produced after electroporation of these clones into C8166 cells has been assessed by infection of rhesus and cynomolgus macaques, time to seroconversion and by induction of cytopathic effects upon co-cultivation of infected rhesus peripheral blood lymphocytes with C8166 cells. The viruses obtained from these clones have identical growth kinetics in vitro but differ in their ability to persist in macaques. Macaques infected with pJ5 derived virus remain viraemic longer than macaques infected with pC8-derived virus. PCR analysis of circulating provirus indicates that the nef gene evolved over time in pJ5 virus-infected macaques, whereas late in infection in pC8 virus-infected macaques the nef gene remained invariant in sequence. These results support the observation that a nef deletion mutant of SIVmac239 lost its pathogenic potential and resulted in low-level viraemia when rhesus macaques were infected. Virus challenge pools for vaccine studies have been prepared for pJ5 using both human and monkey cell substrates and these stocks have been titrated both in vitro and in vivo. Virus has also been prepared from pC8 and titrated in vitro. This virus pool is being assessed as an attenuated live-virus vaccine in macaques. Since only virus originating from the SIVmac239 molecular clone is known to cause AIDS-like symptoms in rhesus macaques consistently, the SIVmac32H molecular clones should tell us more about which viral sequence features are important for the pathogenesis of AIDS.

Amino Acid Sequence↗

Unique pattern of convergent envelope evolution in simian immunodeficiency virus-infected rapid progressor macaques: association with CD4-independent usage of CCR5.

The rate of disease development in simian immunodeficiency virus (SIV) infection of macaques varies considerably among individual macaques. While the majority of macaques inoculated with pathogenic SIV develop AIDS within a period of 1 to 2 years, a minority exhibit a rapid disease course characterized by absence or transience of humoral and cellular immune responses and high levels of virus replication with widespread dissemination of SIV in macrophages and multinucleated giant cells. The goal of this study was to examine viral evolution in three SIVsmE543-3-inoculated rapid progressors to determine the contribution of viral evolution to the development of rapid disease and the effect of the absence of immune pressure upon viral evolution. PCR was used to amplify and clone the entire SIV genome from tissues collected at necropsy, and the course of viral evolution was assessed by env sequences cloned from sequential plasma samples of one rapid progressor (RP) macaque. The majority of sequence changes in RP macaques occurred in the envelope gene. Substitutions were observed in all three animals at specific conserved residues in envelope, including loss of a glycosylation site in V1/V2, a D-to-N/V substitution in a highly conserved GDPE motif, and a P-to-V/H/T substitution in the V3 loop analog. A cell-cell fusion assay revealed that representative env clones utilized CCR5 as a coreceptor, independent of CD4. The selection of specific substitutions in envelope in RP macaques suggests novel selection pressures on virus in such animals and suggests that viral variants that evolve in these animals may play a role in disease progression.

Amino Acid Sequence↗

Human Variation-Informed Prioritization of MPHOSPH6 in Lung Adenocarcinoma: A Source-Aware Multiomics Evidence Framework.

Moving from an association signal to a clinically credible biomarker requires several links that are often conflated: verified variant identity, aligned allelic effects, reproducible gene-level association, relevant cellular expression, and a plausible functional consequence. We developed a source-aware multiomics framework to assess MPHOSPH6 in lung adenocarcinoma (LUAD) while keeping those evidence classes separate. Six prespecified rsIDs were recovered from the harmonized TRICL LUAD dataset, of which five reached p < 5 &#xd7; 10 - 8. Only rs112333466 and rs76474922 were available with alignable alleles in FinnGen R10, and both showed concordant directions. Fixed-effect estimates were OR = 1.592 for rs112333466-T (95% CI, 1.401-1.809; p = 9.91 &#xd7; 10 - 13) and OR = 0.819 for rs76474922-C (95% CI, 0.773-0.867; p = 1.03 &#xd7; 10 - 11). In a prespecified two-variant GTEx v8 lung model, genetically predicted MPHOSPH6 expression was positively associated with LUAD in TRICL (Z = 3.341, p = 8.35 &#xd7; 10 - 4) and FinnGen (Z = 2.697, p = 0.0070). This gene-level result did not establish colocalization or connect MPHOSPH6 to the six susceptibility rsIDs. Patient-level analysis of 89,241 immune cells from six paired tumor and normal-adjacent lung samples found no significant difference in MPHOSPH6 pseudobulk abundance (exact paired Wilcoxon p = 0.3125). None of 688 lung-lineage pharmacogenomic tests remained significant after false-discovery-rate correction. Ten recorded MPHOSPH6 missense alleles, including five ClinVar variants of uncertain significance, were curated; structural analysis identified I58 at an experimental RNA-exosome interface and defined a focused perturbation series. MPHOSPH6 is therefore supported as a human-variation-informed candidate for functional evaluation, not as a validated LUAD biomarker, pathogenic gene, drug-response predictor, or therapeutic target.

Humans↗

Histopathologic, Genomic, and Clinical Characteristics of Primary Cutaneous Melanocytic Tumors With Concomitant NRAS Q61 and IDH1 R132C Mutations.

Cutaneous melanocytic tumors with concomitant NRAS Q61 and IDH1 R132C mutations have been described as intermediate-grade melanocytomas with characteristic biphasic morphology, but the malignant end of this genotype-defined spectrum remains poorly characterized. We assessed histopathologic, immunohistochemical, molecular, and clinical features of 16 primary cutaneous melanocytic tumors harboring both mutations. Following integrated review, 7 tumors were classified as melanocytoma and 9 as melanoma. Melanocytomas showed reproducible biphasic architecture with congenital nevus-like features, a biphasic HMB-45 pattern, low Ki-67, PRAME negativity, retained p16, and minimal copy number variations (CNVs). Melanomas retained partial morphologic overlap in a subset but were distinguished by higher-grade cytology, immunohistochemical features supportive of malignancy, and progression-associated genomic alterations, including TERT promoter mutation (9/9), 9p21/CDKN2A loss (4/7), and higher CNV burden. NRAS and IDH1 variant allele frequencies were strongly concordant (r = 0.83, P < 0.001), supporting their presence in the same dominant clone. Clinically, two patients presented with stage IIIB disease, but no distant metastasis or melanoma-related death occurred during a median melanoma follow-up of 3.9 years (IQR, 2.5-5.1). In exploratory analyses, moderate-to-severe atypia (RR, 6.2; 95% CI, 1.0-38.8; P = .009), Ki-67 &#x2265;10% (RR, 4.4; 95% CI, 1.1-18.4; P = .003), lymphocytic infiltrate (RR, 2.4; 95% CI, 1.1-5.3; P = .03), absence of the typical biphasic pattern (RR, 2.4; 95% CI, 1.1-5.3; P = .03), and complete p16 loss (RR, 2.4; 95% CI, 1.1-5.3; P = .03) were associated with molecular or clinical progression to melanoma, defined as the presence of at least one of the following: TERT promoter mutation, pathogenic CDKN2A mutation, 9p21/CDKN2A loss, &#x2265;3 genome-wide segmental CNVs, or any metastasis. These findings support the existence of NRAS/IDH1 co-mutated melanoma as the malignant counterpart of NRAS/IDH1-mutated melanocytoma within a single genotype-defined spectrum.

IDH1 mutations↗

Expanded detection of canine enteric viruses in UK dogs with diarrhoea.

Canine enteric viruses are an important cause of gastrointestinal disease in pet dogs worldwide. Routine diagnosis often relies on pathogen-specific PCR assays, which may fail to detect some viruses, particularly neglected pathogens or genetically divergent variants of established threats. This limits both clinical characterization of affected patients and broader understanding of disease ecology. To address these limitations, we applied metagenomics and a viral discovery bioinformatics pipeline to faecal samples from diarrhoeic dogs in the UK that had been submitted routinely for PCR-based diagnostic testing. Across 80 dogs, we identified 12 viruses known to infect canids, 9 of which have not previously been reported in UK dogs. Among these, several taxa with prior associations to gastrointestinal disease were identified, including canine sapovirus and canine minute virus. By contrast, for other viruses newly detected in the UK, including bufavirus and rotavirus C, clinical relevance in dogs remains unclear. Notably, an identified protoparvovirus fell within the same species as human-canine-associated parvovirus 1, a recently described lineage detected in both canine and human oropharyngeal samples. We also identified a canine parvovirus 2 strain that clustered with a predominantly wildlife-associated lineage, consistent with occasional exposure at the domestic-wildlife interface rather than established circulation in dogs. These two detections illustrate how genome-level surveillance can help prioritize viruses for targeted investigation of host range and transmission context. Overall, these data broaden the catalogue of viruses associated with diarrhoeic dogs in the UK and support periodic review of diagnostic targets informed by viral metagenomic surveillance, while highlighting the need for controlled studies to assess causality and clinical relevance.

Animals↗

Cancer spectrum in Mexican patients with the CHEK2 p.(Leu236Pro) variant: a retrospective study.

This study aimed to characterize, for the first time, the cancer spectrum associated with the most frequent pathogenic CHEK2 variant-NM_007194.4(CHEK2):c.707T&#x2009;>&#x2009;C p.(Leu236Pro)-in Mexican individuals. Although this variant is frequently detected through multi-gene panel testing, limited data on its associated cancer risks complicates genetic counseling and surveillance strategies. We retrospectively analyzed 5,759 patients who underwent multi-gene panel testing between August 2015 and August 2024 due to suspected hereditary cancer syndromes. Among them, 58 CHEK2 p.(Leu236Pro) carriers with confirmed cancer diagnoses were identified. Geographical clustering was observed, with 81% of patients originating from central Mexico, suggesting a possible founder effect. Ten distinct clinical indications for genetic testing were identified, with hereditary breast and ovarian cancer (HBOC) syndrome being the most common (74.1%). The mean age at first diagnosis among carriers was 43.8&#x2009;&#xb1;&#x2009;12 years, and 61.1% of them reported a family history of cancer in first- or second-degree relatives. A second or third primary cancer occurred in 20.7% of cases. Tumors were identified in 12 anatomical sites. Breast cancer predominated (67.6%, including one male case), followed by ovarian (8.1%), prostate (6.7%), gastric (4.1%), thyroid (2.7%), and endometrial (2.7%) cancers. Lymphoma, lung, sacrococcygeal bone, colorectal, and non-melanoma skin cancers each occurred in a single patient. Significant risk association was identified only for breast, ovarian, and gastric cancers. These results highlight the need for personalized surveillance, especially for breast cancer. Incorporating CHEK2 p.(Leu236Pro) into clinical decision-making tools may enhance risk assessment in the Mexican population, but larger studies are needed to refine risk estimates and to clarify the possible founder effect.

Humans↗

Clinical implications of hypermucoviscosity phenotype in Klebsiella pneumoniae isolates: association with invasive syndrome in patients with community-acquired bacteraemia.

BACKGROUND: Klebsiella pneumoniae, a Gram-negative bacillus usually forming glistening mucoid colonies with viscid consistency on the culture plate, is a common pathogen causing various clinical infection patterns. However, little is known about the clinical implications of this mucoid character. OBJECTIVE: The purposes of this study, therefore, were to investigate the frequency of hypermucoviscosity (HV) in bacteraemic isolates of K. pneumoniae, and determine the significance of any association between HV and various clinical manifestations. DESIGN: Retrospective observational study. PATIENTS: Patients diagnosed with K. pneumoniae bacteraemia at a community-based university hospital between June 1999 and June 2001 were enrolled in this analysis. MEASUREMENTS: Clinical data concerning comorbid diseases and infection patterns was collected. K. pneumoniae bacteraemic isolates were examined for the presence of HV using a modified string test. The clinical impact of HV and risk factors for the invasive syndrome were assessed using statistical analysis. Polymerase chain reaction (PCR) was performed to detect magA, a gene related to HV phenotype. RESULTS: Overall, 200 (64.9%) of the 308 cases of K. pneumoniae bacteraemia were community-acquired infections. Compared with hospital-acquired K. pneumoniae bacteraemia (HA-KpB), community-acquired K. pneumoniae bacteraemia (CA-KpB) was more likely to be monomicrobial in nature (83.5% vs. 64.8%; P < 0.001) and caused by HV strains (41.5% vs. 14.8%; P < 0.001). The prevalence rate of magA among HV phenotypical K. pneumoniae strains was 24.1%. Patients infected with HV-positive strains were more likely to have the distinctive invasive syndrome (i.e. liver abscess, meningitis, pleural empyaema or endophthalmitis) than those infected with HV-negative variants (37.3% vs. 6.8%; P < 0.001). Multivariate logistic regression analysis, adjusted for age, showed that HV phenotype in K. pneumoniae strains (OR 8.86; 95% CI, 3.70-21.25; P < 0.001) was positively associated with the development of the invasive syndrome in CA-KpB cases. CONCLUSIONS: The HV phenotype of K. pneumoniae bacteraemic isolates was associated with the development of a distinctive invasive syndrome. Identification of the HV phenotype should prompt clinicians to initiate aggressive investigations for invasive diseases.

Aged↗

Evaluation of the efficacy of optical genome mapping in prenatal diagnosis: a retrospective cohort study.

BACKGROUND: Optical genome mapping (OGM) is an emerging cytogenetic method for concurrently detecting structural variants (SVs) and copy number variants (CNVs). However, its clinical application in prenatal diagnosis remains underexplored. METHODS: This study retrospectively evaluated the clinical validity of OGM in prenatal diagnosis by comparing with two routine genetic testing methods: karyotyping and chromosomal microarray analysis (CMA). Both positive and negative cases detected by routine genetic methods were enrolled to evaluate the technical concordance of OGM and its capability to improve diagnostic rate in negative cases. The exclusion criteria were balanced centromeric translocations, mosaic cases with cellular fractions&#x2009;<&#x2009;20%, and loss of heterozygosity (LOH)&#x2009;<&#x2009;25&#xa0;Mb. All samples subjected to OGM testing were anonymized and analyzed blindly. The results from OGM were compared with those from routine genetic testing, and statistical analyses were performed to assess technical concordance and diagnostic rate. RESULTS: Of 217 samples (166 positive samples and 51 negative samples for routine genetic testing), all were successfully tested with OGM, including 2 umbilical cord blood samples, 4 chorionic villi samples, and 211 cultured amniotic fluid samples. Of the 207 reportable chromosomal aberrations from 166 positive samples, the blinded concordance between OGM and CMA, karyotyping, and combination of karyotyping plus CMA was 97.81%, 96.36%, and 97.10%, respectively. OGM missed six aberrations initially, including one LOH, two marker chromosomes, and three microdeletions. However, after reanalysis, its concordance improved to 100% with CMA and 99.03% with karyotyping plus CMA. OGM also diagnosed one additional case of a 3-kb deletion in 51 negative samples, improving the diagnostic rate by 1.96%. Moreover, OGM reclassified the pathogenicity of two microdeletions from pathogenic to uncertain significance in 2 positive cases. Furthermore, OGM clarified the diagnosis suspected by routine genetic testing and improved diagnostic accuracy in some cases. CONCLUSION: As far as we know, this is the largest retrospective study on OGM in prenatal diagnosis, and it includes a broad range of sample types. The results showed that OGM exhibits high concordance among the tested methods and increases the diagnostic rate. Thus, OGM has the potential to become a first-line technique for prenatal diagnosis in the future.

Humans↗

Ticks (Ixodidae) from passerine birds in the Carpathian region.

Birds have been found to be a reservoir host of borrelia. In order to assess the situation in Slovakia ticks were collected from a total of 3057 mist-netted, ringed and released passerine birds in two locations at 500 m (in 2001) and 1000 m (in 2003) above sea level in the Bukovské Vrchy Hills, part of the Carpathian region in the north-east of Slovakia. A total of 75 birds of 16 species were infested with subadult ticks of Ixodes ricinus species (prevalence of parasitization 5%). Sixty-two larvae from 31 birds of 9 species and 80 nymphs from 52 birds of 15 species were found. The highest intensity of parasitization was observed on blackbirds Turdus merula, song thrushes T. philomelos and dunnocks Prunella modularis. Six Ixodes ricinus adult ticks were found on humans working with birds, and one I. ricinus female tick on their dog. In ticks, the presence of Rickettsia sp., Coxiella burnetii, Borrelia burgdorferi sensu lato and members of the Anaplasmataceae and Piroplasmidae, were investigated by polymerase chain reaction, followed by sequence analysis. Rickettsia sp. was found in 1 nymph from the European robin Erithacus rubecula, in 3 adult ticks (1 male, 2 females) from humans and in the tick from the dog. The closely related Ehrlichia- like species "Schotti variant" was detected in 1 nymph from the song thrush. Borrelia afzelii was identified in 1 male and B. garinii in 1 female tick collected on humans. Ixodes ricinus was found to be the vector of a wide spectrum of tick-borne pathogens in a mountainous area of the Carpathians. Because of the low yield of ticks and pathogens the importance of birds as reservoir hosts is still poorly understood.

Animals↗