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Results for “Variant pathogenicity assessment”

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PubMed1997

Identification of Abiotrophia adiacens and Abiotrophia defectiva by 16S rRNA gene PCR and restriction fragment length polymorphism analysis.

Abiotrophia adiacens and Abiotrophia defectiva, previously referred to as nutritionally variant streptococci, Streptococcus adjacens and Streptococcus defectivus, respectively, are causes of infective endocarditis. We describe a method of identifying these two species and also of distinguishing them from 15 other major etiological pathogens of infective endocarditis by means of 16S rRNA gene PCR amplification followed by restriction fragment length polymorphism analysis (PCR-RFLP). The 16S rRNA genes were successfully amplified with a set of universal primers from all 17 species of bacteria examined, including viridans group streptococci. The RFLP patterns of A. adiacens and A. defectiva obtained by HaeIII or MspI digestion were readily distinguished from each other and from those of other bacteria. When PCR analysis was performed with the supernatant of a suspension of a boiled colony, the 16S rRNA genes of 80 of 82 isolates (97%) of A. adiacens and all isolates (11 of 11) of A. defectiva were amplified. The HaeIII RFLP patterns of the isolates were the same as those of the corresponding type strains, although 28% of A. adiacens isolates revealed intraspecies polymorphism. The detection limit of this method was 0.1 pg of genomic DNA, as assessed by using the digoxigenin-labeling DNA detection system. Thus, the PCR-RFLP analysis that we developed is applicable for the routine detection of Abiotrophia from clinical specimens.

DNA, Ribosomal↗

PubMedDate not supplied

Current concepts in autoimmune hepatitis.

Autoimmune hepatitis has a global occurrence, diverse clinical phenotype, and evolving treatment options. The goals of this report are to review the codified diagnostic criteria, spectrum of clinical presentations, proposed pathogenic mechanisms, conventional treatment strategies, and promising interventions. The literature published in English from 1980-2005 was reviewed and an updated current perspective provided. Autoimmune hepatitis affects all ages, may be asymptomatic, frequently has an acute onset, and can present as fulminant hepatitis. Perivenular (zone 3) necrosis is within the histological spectrum. Autoimmune hepatitis can recur or develop de novo after liver transplantation. CD4+ T-helper cells and natural killer T cells have been implicated in the pathogenesis, and molecular mimicry may break self-tolerance. DRB1*0301 and DRB1*0401 are the susceptibility alleles among white North Americans and northern Europeans, whereas diverse alleles of HLA DR4 have been associated with the disease in Japan, mainland China, and Mexico. DRB1*1301 is associated with autoimmune hepatitis in South American children, and it may predispose to an indigenous etiologic agent. Antibodies to soluble liver antigen/liver pancreas may have prognostic importance, and cyclosporine and mycophenolate mofetil must be assessed by clinical trial before incorporation into management algorithms. Site-specific interventions are feasible, and they require a confident experimental animal model for evaluation. Variant syndromes lack diagnostic and therapeutic guidelines. In conclusion, autoimmune hepatitis must be considered in all patients with acute and chronic liver disease and those with allograft dysfunction after transplantation. New immunosuppressive agents and site-specific interventions promise to improve care.

Anti-Inflammatory Agents↗

PubMed2025

CREMSA: compressed indexing of (ultra) large multiple sequence alignments.

MOTIVATION: Recent viral outbreaks motivate the systematic collection of pathogenic genomes in order to accelerate their study and monitor the apparition/spread of variants. Due to their limited length and temporal proximity of their sequencing, viral genomes are usually organized, and analyzed as oversized Multiple Sequence Alignments (MSAs). Such MSAs are largely ungapped, and mostly homogeneous on a column-wise level but not at a sequential level due to local variations, hindering the performances of sequential compression algorithms. RESULTS: In order to enable an efficient handling of MSAs, including subsequent statistical analyses, we introduce CREMSA (Column-wise Run-length Encoding for MSAs), a new index that builds on sparse bitvector representations to compress an existing or streamed MSA, all the while allowing for an expressive set of accelerated requests to query the alignment without prior decompression. Using CREMSA, a 65 GB MSA consisting of 1.9M SARS-CoV 2 genomes could be compressed into 22 MB using less than half a gigabyte of main memory, while executing access requests in the order of 100 ns. Such a speed up enables a comprehensive analysis of covariation over this very large MSA. We further assess the impact of the sequence ordering on the compressibility of MSAs and propose a resorting strategy that, despite the proven NP-hardness of an optimal sort, induces greatly increased compression ratios at a marginal computational cost. AVAILABILITY AND IMPLEMENTATION: CREMSA is freely accessible at https://gitlab.univ-lille.fr/cremsa/cremsa. The Snakemake workflow for the benchmarks is available at: https://gitlab.univ-lille.fr/cremsa/bench. The data used in the paper is on Zenodo at https://zenodo.org/records/14698859 and https://zenodo.org/records/15100011.

SARS-CoV-2↗

PubMed2004

Distribution of fimA genotypes of Porphyromonas gingivalis in subjects with various periodontal conditions.

Fimbria encoded by the gene fimA is considered one of the main factors in the colonization of the oral cavity by Porphyromonas gingivalis. Allelic variation in fimA led to the classification of strains of P. gingivalis into six genotypes. The occurrence of P. gingivalis was determined by polymerase chain reaction using 16S rRNA primers in 302 subgingival samples obtained from 102 Brazilian subjects exhibiting different periodontal conditions. Distribution of fimA genotypes was assessed in 146 P. gingivalis positive samples by polymerase chain reaction using primers pairs homologous to the different fimA genes. P. gingivalis was detected in 51 of 57 (89.4%) patients with periodontal attachment loss, in six of 20 gingivitis patients (30.0%) and in two of 25 (8.0%) subjects with a healthy periodontium. Variant type II was the only type detected in 53 sites (39.3%), distributed among 19 periodontitis patients (37.3%) and in one patient with no periodontal destruction. Type Ib was the second most prevalent genotype in periodontitis patients (19.6%). Genotype V was not detected in the studied population. Type IV was the most commonly type found among gingivitis patients, either alone or in combination with other genotypes. Multiple genotypes were detected in nine sites (6.1%). A fimA genotype was not identified in 26 sites (17.8%) of 146 sites positive for P. gingivalis, suggesting that other alleles of fimA not yet sequenced may be prevalent in this population. These data demonstrated that P. gingivalis type II strains followed by type Ib are more prevalent in periodontitis patients from a multiracial population in Brazil, suggesting an increased pathogenic potential of these types.

Adolescent↗

PubMed2025

Fe-S cluster deficiency drives small colony variant formation in persistent infections.

INTRODUCTION: Small colony variants (SCVs) of Staphylococcus aureus (S. aureus) are associated with persistent infections and poor clinical outcomes. The mechanisms driving stable SCV formation remain poorly understood, particularly concerning metabolic adaptations. This study explores the in-host evolutionary dynamics of S. aureus and identifies a novel genetic determinant linked to SCV formation. OBJECTIVES: To investigate the genetic mutations and phenotypic adaptations underlying SCV formation, with a focus on the role of a novel mutation in the sufB gene, which is critical for Fe-S cluster biosynthesis. METHODS: Sequential isolates from a patient with recurrent infections were analyzed using whole-genome sequencing, antimicrobial susceptibility testing, and functional assays. The phylogenetic relationship of the isolates was determined, and specific mutations were identified. Functional assays included aconitase and glutamate synthase activity measurements, ATP level quantification, reactive oxygen species (ROS) production, and biofilm formation assays. In vivo pathogenesis was assessed using a murine catheter infection model. RESULTS: A novel frameshift mutation in sufB was identified, disrupting Fe-S cluster biosynthesis and impairing the TCA cycle and electron transport chain, leading to reduced ATP and ROS production. This metabolic reprogramming promoted stable SCV formation, characterized by slow growth, enhanced tolerance to antibiotics and neutrophil-mediated killing, and persistent inflammation in vivo. Restoration of sufB reversed these phenotypes, confirming its pivotal role in SCV-associated persistence. CONCLUSION: sufB is a novel genetic determinant of stable SCV formation through Fe-S cluster deficiency, driving metabolic shifts that enhance immune evasion and chronic infection. Our findings highlight antibiotic stewardship and suggest potential therapeutic strategies for managing persistent SCV-associated infections.

Staphylococcus aureus↗

PubMed2026

GenProb-PCSM: A Simplified Weighted Germline Score for Prostate Cancer-Specific Mortality.

BACKGROUND: We previously developed a tier-based germline classification using the National Comprehensive Cancer Network (NCCN)-recommended DNA damage repair (DDR) genes and KLK3 I179T to predict prostate cancer (PCa)-specific mortality (PCSM). To provide an easier-to-use single inherited risk score while preserving gene-specific effects, we developed GenProb-PCSM. METHODS: We analyzed 14,644 men with incident PCa from the UK Biobank. The cohort was randomly divided into training (60%) and independent testing (40%) datasets. GenProb-PCSM was developed in the training cohort by integrating pathogenic variants in ten NCCN-recommended DDR genes and the KLK3 I179T variant using gene-specific weights derived from Fine-Gray competing-risk models. Performance was evaluated in the independent testing cohort by discrimination, calibration, and risk stratification. Secondary analyzes evaluated metastatic progression and the composite endpoint of metastatic progression and/or PCSM. RESULTS: Among 14,644 men with incident PCa, 1,581 died from PCa. GenProb-PCSM remained significantly associated with PCSM in the independent testing cohort (HR per SD, 1.18; 95% CI, 1.12-1.24; p < 0.001). Using predefined risk thresholds derived from the training cohort, patients in the intermediate- and high-risk groups had significantly increased risks of PCSM compared with the low-risk group (HR 1.49, 95% CI 1.22-1.84; and HR 4.04, 95% CI 2.58-6.33, respectively). GenProb-PCSM also predicted independent metastatic progression and the composite endpoint of metastatic progression and/or PCSM. CONCLUSIONS: GenProb-PCSM transforms complex germline findings into a single inherited risk score for PCSM and metastatic progression. Its simplicity and preservation of gene-specific effects may facilitate clinical implementation of germline prognostic assessment in PCa.

DNA damage repair genes↗

PubMed1999

The welfare problems associated with using transgenic mice to bioassay for bovine spongiform encephalopathy.

Prion diseases are fatal neurodegenerative disorders, epitomized by the the recent bovine spongiform encephalopathy (BSE) epidemic in cattle and the emergence of a novel variant of Creutzfeldt-Jacob disease (vCJD) in humans. In prion disease, the agent of infection is believed to be composed of proteinaceous particles, termed prions, which are converted from a normal isoform into a pathogenic isoform during pathogenesis. A bioassay to detect pathogenic prions of BSE in bovine products consumed by humans was unattainable until the development of transgenic mice, due to the significantly lower susceptibility of wild-type mice to BSE. Transgenic mice have now been generated which express the bovine prion protein and are susceptible to BSE. Following an intracerebral injection with brain homogenate of BSE-infected cattle, transgenic mice develop numerous clinical signs of prion disease, including truncal ataxia (inability to coordinate the torso's muscular activity), increased tone of the tail, generalized tremor, and lack of a forelimb extensor response. In this study, the ethical score system devised by Porter (1992) was applied to the BSE bioassay as a tool for identifying welfare issues affecting animals used in the bioassay. We acknowledge that there are limitations to the use of the information arising from the application of the Porter scoring scheme for assessing the justification to proceed with any animal experiment; notwithstanding these problems, however, our application of the Porter model to the BSE bioassay enabled us to identify potential targets for refinement: pain involved, duration of distress and the duration of the experiment. This was despite lenient scoring for the duration of distress and pain experienced by the mice, and optimal scoring for the quality of animal care. The targets identified for refinement are discussed in relation to the method of inoculation, the duration of the bioassay, and the duration of the clinical phase, with the objective of exploring ways of reducing the severity of the bioassay.

Animal Experimentation↗

PubMed2006

Proinflammatory and immunomodulatory cytokine mRNA time course profiles in hamsters infected with a virulent variant of Leptospira interrogans.

In order to quantify in vivo the mRNAs of cytokines which play important roles in leptospirosis, we have developed quantitative real-time PCR assays for interleukin-2 (IL-2), IL-4, IL-10, IL-12p40, tumor necrosis factor alpha (TNF-alpha), gamma interferon (IFN-gamma), transforming growth factor beta, and two housekeeping genes (encoding beta-actin and hypoxanthine phosphoribosyltransferase). We used a lethal hamster model reflecting severe leptospirosis in humans. The LightCycler system was used to quantify the gene expression levels with the SYBR green I detection format using external standard curves for each target. We compared the expression levels of cytokine mRNA in the peripheral blood mononuclear cells of both control (uninfected) hamsters and Leptospira interrogans-inoculated hamsters from 1 to 24 h and then 1 to 4 days postinfection. In this kinetic study, there was pronounced expression of Th1 cytokine mRNA (TNF-alpha, IFN-gamma, and IL-12), with transcripts being detected as early as 1 h postinfection. Expression of anti-inflammatory cytokines, such as IL-4 and IL-10, was prominent in delayed samples from 1 to 4 days postinfection in response to infection with Leptospira interrogans. Our data are the first to establish that pathogenic leptospires can stimulate in vivo the production of type 1 cytokines involved in cellular immunity by using this informative animal model. Measuring and assessing cytokine profiles may provide a useful method for accurate study of the mechanisms of anti-Leptospira immunity, indications of prognosis factors, and prospective evaluation of leptospirosis vaccine efficacy in humans.

Animals↗

PubMed2025

Hidden diversity in Enterococcus faecalis revealed by CRISPR2 screening: eco-evolutionary insights into a novel subspecies.

Enterococcus faecalis is a commensal bacterium that colonizes the gut of humans and animals and is a major opportunistic pathogen, known for causing multidrug-resistant healthcare-associated infections (HAIs). Its ability to thrive in diverse environments and disseminate antimicrobial resistance genes (ARGs) across ecological niches highlights the importance of understanding its ecological, evolutionary, and epidemiological dynamics. The CRISPR2 locus has been used as a valuable marker for assessing clonality and phylogenetic relationships in E. faecalis. In this study, we identified a group of E. faecalis strains lacking CRISPR2, forming a distinct, well-supported clade. We demonstrate that this clade meets the genomic criteria for classification as a novel subspecies, here referred to as "subspecies B." Through a comprehensive pangenome analysis and comparative genomics, we explored the adaptive ecological traits underlying this diversification process, identifying clade-specific features and their predicted functional roles. Our findings suggest that the frequent isolation of subspecies B from meat products and processing facilities may reflect dissemination routes involving environmental contamination (e.g., water, plants, soil) from avian species. The absence of key virulence traits required for pathogenicity in mammals, particularly humans, and the lack of clinically relevant resistance determinants indicate that subspecies B currently poses minimal threat to public health compared with the broadly disseminated "subspecies A." Nevertheless, the unclear potential for genetic exchange between these subspecies and the frequent association of subspecies B with food sources calls for continued genomic surveillance of E. faecalis from a One Health perspective to detect and mitigate the emergence of high-risk variants in advance.IMPORTANCEExploring intraspecific genetic variability in generalist bacteria with pathogenic potential, such as Enterococcus faecalis, is a key to uncovering stable evolutionary trends. By screening the CRISPR2 locus across a representative set of genomes from diverse sources, this study reveals a previously unrecognized lineage within the population structure of E. faecalis, associated with underexplored nonhuman and nonhospital reservoirs. These findings broaden our knowledge of the species' genetic landscape and shed light on its adaptive strategies and patterns of ecological dissemination. By bridging phylogenetic patterns with variation in genetic defense systems and accessory traits, the study generates testable hypotheses about the genomic determinants and corresponding selective pressures that shape the species' behavior and long-term dissemination. This work offers new perspectives on the eco-evolutionary dynamics of E. faecalis and highlights the value of genomic surveillance beyond clinical settings, in alignment with One Health principles.

Enterococcus faecalis↗

PubMed1996

What went wrong in BSE? From prion disease to public disaster.

The recent report of 10 cases of a new variant of Creutzfeldt-Jakob disease (CJD) which could be related to bovine spongiform encephalopathy (BSE) has precipitated alarm throughout Europe. The beef trade in the UK has collapsed and the European beef market has been seriously damaged. What went wrong? Much of the difficulty of handling the BSE epidemic arose from the 4-5 year incubation period which made it difficult to ascertain whether measures taken to contain the epidemic had been effective. Public consternation and scientific equivocation arose because these prion diseases are unlike any other group of infectious diseases. Rather than being caused by a conventional micro-organism, the primary pathogenic event consists of the transformation of a normal protein (the prion protein) into an abnormal form, which can transmit disease. Prion disease is endemic in humans and sheep where it is associated with polymorphisms or mutations within the prion protein gene. Although the disease in these cases arises spontaneously, it produces an infectious prion protein. Under certain circumstances, abnormal prion protein contaminates other animals or humans resulting in epidemics of acquired prion disease. This review describes the events of the BSE epidemic and considers the difficulties in assessing the current risk to human health.

Animals↗

PubMed2006

Genetic diversity of Borrelia burgdorferi sensu stricto in Peromyscus leucopus, the primary reservoir of Lyme disease in a region of endemicity in southern Maryland.

In the north central and northeastern United States, Borrelia burgdorferi sensu stricto, the etiologic agent of Lyme disease (LD), is maintained in an enzootic cycle between the vector, Ixodes scapularis, and the primary reservoir host, Peromyscus leucopus. Genetic diversity of the pathogen based on sequencing of two plasmid-located genes, those for outer surface protein A (ospA) and outer surface protein C (ospC), has been examined in both tick and human specimens at local, regional, and worldwide population scales. Additionally, previous studies have only been conducted with tick or human specimens at the local population level in areas with high LD transmission rates. This study examined the genetic diversity of circulating borreliae in the reservoir population from a large region of the western coastal plains of southern Maryland, where moderate numbers of human LD cases are reported. Six ospA mobility classes, including two that were not previously described, and eight ospC groups were found among the P. leucopus samples. Twenty-five percent of all specimens were infected with more than one ospA or ospC variant. The frequency distribution of variants was homogeneous, both locally and spatially. The spirochete diversity found in Maryland was not as high as that observed among northern tick populations, yet similar genotypes were observed in both populations. These results also show that mice are important for maintaining Borrelia variants, even rare variants, and that reservoir populations should therefore be considered when assessing the diversity of B. burgdorferi.

Animals↗

PubMed2005

Mechanisms of disease: the genetic epidemiology of gallbladder stones.

Cholelithiasis is one of the most prevalent and most expensive gastroenterologic diseases. It belongs to the group of complex metabolic disorders that affect humans, and its critical pathogenic mechanisms are not well defined. As a result, primary or secondary prevention strategies are sparse, and the only effective treatment is cholecystectomy. Here we provide an update on the molecular pathogenesis of gallbladder stones, evidence supporting the hypothesis that genetic factors are key elements predisposing to gallstones, and progress in human genetic studies of cholesterol stones. Data from recent identical twin, family and linkage studies provide conclusive evidence for a strong genetic component to gallstone disease. Furthermore, epidemiologic studies in at-risk populations indicate that gallstone formation is caused by multiple environmental influences and common genetic factors and their interactions. By contrast, monogenic subtypes of cholelithiasis, such as ATP-binding-cassette transporter deficiencies, appear to be rare. The summary of human association studies illustrates that distinct common gene variants might contribute to gallstone formation in different ethnic groups. The characterization of lithogenic genes in knockout and transgenic mice and the identification of many gallstone-susceptibility loci in inbred mice provide the basis for studies of the corresponding genes in patients with gallstones. The transfer of findings from mouse genetics to the bedside might lead to new strategies for individual risk assessment and reveal novel molecular targets for prevention and medical therapies.

Animals↗

PubMed2006

Occurrence of extended spectrum beta-lactamases among isolates of Enterobacteriaceae from urinary tract infections in southern Italy.

The present investigation was undertaken to assess the prevalence of extended-spectrum beta-lactamases (ESbetaLs) among urinary tract infection (UTI) isolates. During 4 months in 2004, a total of 650 Enterobacteriaceae strains from UTIs was collected by five clinical microbiology laboratories located in southern Italy and the beta-lactamase production was investigated. A total of 50 of the 650 isolates were double-disk positive and suspected of producing an ESbetaL; Escherichia coli (36.0%) and Klebsiella pneumoniae (32.0%) were the most common species among all ESbetaL producers. Characterization of ESbetaL determinants was carried out by the colony blot hybridization method, and polymerase chain reaction (PCR) and DNA sequencing in order to identify the presence of bla (TEM), bla (SHV), bla (PER), and bla (CTX-M) determinants. The ESbetaL variants found in this study were the following: TEM-15, TEM-24, TEM-52, TEM-134, SHV-12, CTX-M-1, CTX-M-3, CTX-M-15, and PER-1. As expected, the majority of the isolates were found to be susceptible to imipenem (94%), cefepime (54%) and piperacillin-tazobactam (54%). The results of this survey show the prevalence of ESbetaL enzymes among enterobacterial pathogens causing UTIs in southern Italy.

Anti-Bacterial Agents↗

PubMed2003

Phytopthora ramorum in Belgium: 2002 survey results and research efforts.

Phytophthora ramorum is a new and aggressive Phytophthora species that causes leaf blight and dieback symptoms on Viburnum and Rhododendron plants in Europe. A variant of this fungus is responsible for Sudden Oak Death (SOD) in California and Oregon. In Europe, problems so far are mostly restricted to nursery plants of Rhododendron and Viburnum while in the US, the fungus has been isolated from over 20 host species and is responsible for massive killing of oak trees (mostly Quercus agrifolia and Lithocarpus densiflorus) in forest and park settings. The potential for infection of native tree species in Europe and the recent detection of the fungus in nurseries of several European countries has lead to the implementation of EU emergency phytosanitary measures. As a result, most European countries have conducted surveys and are doing research as part of risk assessment efforts. The first part of this paper focuses on the plant diagnoses of the 2002 survey of P. ramorum in Belgian nurseries. The data from the survey indicates P. ramorum is present in Belgium at similar rates as in the neighbouring countries, in an apparent random distribution. The second part of this paper describes research results relating to the in vitro effect of oomycete fungicides on P. ramorum, Rhododendron cultivar susceptibility, the determination of the leaf infection site, and pathogen survival. Some fungicides had excellent in vitro activity against P. ramorum and should be tested further on plants. Use of host resistance as a control strategy may be limited as little difference in cultivar sensitivity was observed. Infection studies showed that wounds and the lower sides of the leaves are most susceptible to infection. Once the pathogen gets inside, it can survive well on detached leaves, especially when they are kept cool and moist. These data can contribute to management decisions of P. ramorum at the level of nurseries as well as the government.

Belgium↗

PubMed2003

Specific phobia is a frequent non-motor feature in stiff man syndrome.

OBJECTIVE: To investigate systematically the rate and type of phobia in stiff man syndrome and its variants, and to compare patients with stiff man syndrome with and without phobia for sociodemographic and neurological characteristics. METHODS: 43 consecutive patients with stiff man syndrome referred to a university department of neurology were assessed using the anxiety disorders interview schedule, revised (ADIS-R), a structured diagnostic interview for anxiety disorders, in addition to a full clinical neurological and psychiatric assessment. RESULTS: 19 patients (44.2%) developed task specific phobia--that is, fear and avoidance of situations difficult to master owing to the motor symptoms of stiff man syndrome (such as crossing streets). Three further patients (7%) had subthreshold phobia--that is, phobic anxiety without avoidance. There were no significant differences between patients with and without phobia in terms of age, illness duration, type of stiff man syndrome, antibody status, or frequency of falls. Patients with phobia were more likely to present with exaggerated startle responses and to have an initial misdiagnosis of psychogenic movement disorder. CONCLUSIONS: Specific phobia is a frequent non-motor symptom of stiff man syndrome. Early recognition is an important aid to correct diagnosis. The aetiology of phobia in stiff man syndrome is unknown. There is no evidence of a direct pathogenic role of autoantibodies directed against glutamic acid decarboxylase in the development of phobia.

Adolescent↗

PubMed2026

Costello Syndrome Associated With Somatic Mosaicism of Rare p.Gly13Asp HRAS Variant: Expanding the Phenotypic Spectrum.

BACKGROUND: Costello syndrome (CS) is a rare RASopathy, mostly caused by de novo heterozygous pathogenic variants in the HRAS gene. Over 80% of cases involve the germline p.Gly12Ser variant, resulting in a fairly uniform phenotype of neuro-cardio-facio-cutaneous involvement with an increased risk of malignancy. Consequences of other rare HRAS variants are less well understood due to the limited number of reported cases. METHODS: An adult, young woman was referred due to sparse, slow-growing scalp hair, Blaschko-linear hyperpigmentation, acanthosis nigricans, palmoplantar hyperkeratosis, and joint hyperlaxity. Molecular, imaging, and detailed laboratory studies were performed. RESULTS: Although initial clinical exome- and whole-exome sequencing (WES) were inconclusive, indicating possible mosaicism, subsequent WES from hair-derived DNA samples revealed somatic mosaicism for the rare HRAS p.Gly13Asp variant. Brain MRIs showed a cerebral cavernoma, while cardiological evaluation, urinalysis, abdominal, and pelvic ultrasound were unremarkable. Nevertheless, she remains under close follow-up. CONCLUSION: Among the ten reported individuals carrying the p.Gly13Asp variant, our patient is only the second with confirmed mosaicism and the fifth mosaic CS case described to date. This case expands the phenotypic spectrum of CS and highlights the need for multi-tissue analysis in attenuated or atypical presentations to ensure a correct diagnosis, oncological risk assessment, and informed genetic and reproductive counseling.

Humans↗

PubMed1993

Characterisation of isolates and strains of citrus tristeza closterovirus using restriction analysis of the coat protein gene amplified by the polymerase chain reaction.

Citrus Tristeza Virus (CTV) exists as a large number of distinct strains differing in biological properties and with different distributions in citrus producing countries. Strategies such as eradication or cross protection, aimed at controlling severe variants of the pathogen, require procedures to identify virus strains accurately and reliably. To fill the need for a rapid, reproducible assay, we have investigated the use of restriction analysis of the CTV coat protein gene amplified using the polymerase chain reaction (PCR). The primers 5' ATG GAC GAC GAA ACA AAG 3' and 5' TCA ACG TGT GTT GAA TTT 3' amplified a DNA copy of the CTV coat protein gene (approx. 670 base pairs) when used in a reverse transcriptase PCR assay. Amplifications were carried out using dsRNA prepared from field and indicator plants, or from single-stranded RNA prepared from crude PEG precipitates of intact virions. All 51 CTV isolates tested produced an amplified product of the same size, regardless of country of origin or biological properties. Digestion of the amplified coat protein genes with the restriction enzymes Hinf1 or Rsa1 revealed sequence variation in the PCR products. Hinf1 provided the best discrimination between strains, defining seven Restriction Fragment Length Polymorphism (RFLP) groups, some of which circumscribed sets of isolates with similar biological properties. Limited analysis of field isolates using this method showed that individual trees could contain mixtures of CTV strains, as assessed by the recovery of several RFLP types from individual reactions. Single aphid transmissions of isolates usually, but not always, generated apparently pure single strains judged by the recovery of single RFLP groups.

Animals↗

PubMed1993

Feline immunodeficiency virus infection of cats as a model to test the effect of certain in vitro selection pressures on the infectivity and virulence of resultant lentivirus variants.

Three groups of specific pathogen-free (SPF) domestic cats, each containing 5 animals, were infected with one of three closely related FIV variants and monitored for 36 weeks. A fourth group of 5 cats was sham-infected and served as uninfected controls. FIV variants included: (1) a fully virulent animal passaged FIV-Petaluma; (2) a Crandell feline kidney (CrFK) cell-adapted FIV-Petaluma (FIV-CrFK); and (3) a variant of FIV-CrFK (FIV-CrFKAZT) that had been selected in vitro for resistance to azidothymidine. Cats infected with fully virulent FIV-Petaluma strongly seroconverted, became persistently viremic, and exhibited lymphadenopathy, neutropenia, and inversion of the CD4+:CD8+ T cell ratio. Cats infected with FIV-CrFK seroconverted but the antibody responses were much weaker and more variable; two of the cats became transiently viremic and no hematologic abnormalities or clinical signs of illness other than a very mild lymphadenopathy were observed. None of the five cats inoculated with FIV-CrFKAZT seroconverted, became viremic, or exhibited any gross or hematologic signs of disease, even though proviral DNA was transiently detected in tissue following inoculation. This study demonstrates that the FIV infection model can be used to assess differences in the virulence of FIV variants, including variants selected for antiretroviral drug resistance.

Animals↗