Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Pathogenic variant”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27Linked to original sources

Highly pathogenic simian immunodeficiency virus mne variants that emerge during the course of infection evolve enhanced infectivity and the ability to downregulate CD4 but not class I major histocompatibility complex antigens.

The replicative, cytopathic, and antigenic properties of simian immunodeficiency virus (SIV) variants influence its replication efficiency in vivo. To further define the viral properties and determinants that may be important for high-level replication in vivo and progression to AIDS, we compared a minimally pathogenic SIVmne molecular clone with two highly pathogenic variants cloned from late stages of infection. Both variants had evolved greater infectivity than the parental clone due to mutations in nef. Interestingly, a pol determinant in one of the highly pathogenic variants also contributed to its increased infectivity. Furthermore, because replication in vivo may also be influenced by the ability of a virus to evade the cellular immune response of the host, we examined whether the variants were more capable of downregulating surface expression of class I major histocompatibility complex (MHC). Decreased MHC class I expression was not observed in cells infected with any of the viruses. Furthermore, the Nef proteins of the highly pathogenic variants only slightly reduced surface MHC class I expression in transfected cells, although they efficiently downregulated CD4. Together, these data demonstrate that mutations which can enhance viral infectivity, as well as CD4 downregulation, may be important for efficient replication of SIV in the host. However, Nef-mediated reduction of MHC class I expression does not appear to be critical for the increased in vivo replicative ability of highly pathogenic late variants.

Amino Acid Sequence↗

A simple procedure to differentiate ailA and ailNA gene variants among human pathogenic Yersinia enterocolitica strains.

The identification and differentiation of the two variants of the ail gene, ailA from the more virulent American serotypes (08, 013a, 13b, 018, 020, 021) and ailNA from the less virulent non-American serotypes (03, 04, 05, 06, 09, 027 and 07, 8) was studied in a panel of 32 Yersinia enterocolitica human pathogenic isolates. A 444 bp fragment corresponding to the ail gene was amplified using a PCR procedure in all tested strains. Subsequent digestion of the PCR product by Rsal and by HaeIII endonucleases, provide electrophoretic patterns that clearly discriminate ailA and ailNA variants. This non-radioactive and reliable procedure allows large clinical and epidemiological studies, and could be proposed to survey the spread of virulent clones.

Base Sequence↗

Evaluation of the molecular basis of pathogenicity of the variant Newcastle disease viruses termed "pigeon PMV-1 viruses".

The amino acid sequence at the F2/F1 cleavage site was determined for 15 strains of the so-called pigeon PMV-1 (PPMV-1) variant of Newcastle disease virus (NDV) which showed close antigenic identity, determined by their reactions with a panel of 28 monoclonal antibodies, but considerable variation in their pathogenicity for chickens. Thirteen of the isolates possessed the motif 112G-R-Q-K-R-F117. This motif was seen for one virus which had initially low pathogenicity and remained unaltered when virulence of the virus for chickens was increased by bird to bird passage. The two other viruses had the sequence 112R-R-Q-K-R-F117 at the cleavage site which is more typical of virulent viruses, however, pathogenicity index tests indicated that these isolates were of moderate and low pathogenicity. The nucleotide sequence coding for the HN/HN0 extension region was determined for two of the PPMV-1 isolates. In both cases a stop codon was present indicating that the product for these viruses would be HN571. We conclude that the wide variation in pathogenicity of the variant PPMV-1 for chickens is not related to variation in the amino acid motif at the F2/F1 cleavage site nor due to production of HN0 which may also influence pathogenicity. The high virulence of some of the viruses examined confirms that a double pair of basic amino acids in the region of the F2/F1 cleavage site is not necessary for the full expression of virulence.

Amino Acid Sequence↗

Pathogenicity of antigenic variants of Newcastle disease virus Italian strain selected with monoclonal antibodies.

Antigenic variants of the Italian strain of NDV were selected using monoclonal antibodies directed against the HN and F proteins of Italian virus. Antigenic mapping of the HN and F proteins using variant viruses in cross neutralization tests revealed the presence of at least two different epitopes on HN and four epitopes on F protein. Immunoselected variant viruses were demonstrated to have different intravenous pathogenicity index than the parental Italian virus.

Antibodies, Monoclonal↗

Expert consensus on the reporting and clinical follow up of individuals with incidentally discovered germline RET variants in the UK.

Incidentally discovered pathogenic germline genetic variants refer to the finding of a pathogenic variant in a gene that is unrelated to the reason for the initial test and is not actively sought. Our clinical understanding of the risk of developing a particular medical condition and the required clinical action for a specific pathogenic gene variant is predominantly based on knowledge and information acquired from cases ascertained through a 'phenotype-first approach' rather than in clinically unselected individuals. Therefore, a modified approach is required for incidentally discovered gene variants. Data from large UK and US population-based cohorts have demonstrated that RET variants classified as moderate-risk RET variants as per the American Thyroid Association (ATA) classification have a low penetrance for medullary thyroid cancer and other RET-related conditions (e.g. phaeochromocytoma) and are not associated with excess mortality when identified incidentally in clinically unselected adult individuals. Here, we provide guidance based on multidisciplinary expert consensus opinion for the reporting and subsequent clinical surveillance and management of patients with incidentally discovered RET gene variants in the UK.

Humans↗

Properties of cell wall antigens of virulent Brucella canis and a less mucoid variant of reduced pathogenicity.

Properties of cell wall antigenic extracts of 2 Brucella canis strains (wild type, M+; and a less mucoid variant, M-) were compared. Cell wall antigens of each strain were extracted by 2 different methods and compared with respect to their serologic, chromatographic, and surface properties. In addition, selected enzymes were used to compare antigen sensitivity to degradation. Analysis of extracted antigens was done by gel immunodiffusion and immunoelectrophoresis. Two cell wall antigens (2-R and 3-R) were present in extracts of wild type (M+) B canis that had been treated with hot (65 C) phosphate-buffered saline solution (PBSS). Three cell wall antigens (2-S, 3A-S, 3B-S) were revealed in saline extracts of the M- variant. Hot (100 C) 1% sodium deoxycholate extracted an additional antigen (1-R or 1-S) from cells (M+ or M-, respectively) which had previously been treated with hot PBSS. Certain properties of the B canis antigen extracts were examined by ion exchange chromatography, agarose gel chromatography, affinity chromatography, and enzyme degradation. Hydrophobic properties of the cell wall antigens were examined by their behavior in divalent cation, polyethylene glycol, and acid solutions. The antigens of B canis (M+) cells extracted with hot PBSS were smaller in size, had a lower net negative charge, and were more hydrophobic than those of the M- cells.

Animals↗

Mitochondrial tRNA sequences as unusual replication origins: pathogenic implications for Homo sapiens.

The heavy strand of vertebrate mitochondrial genomes accumulates deaminations proportionally to the time it spends single-stranded during replication. A previous study showed that the strength of genome-wide deamination gradients originating from tRNA gene's locations increases with their capacities to form secondary structures resembling mitochondrial origins of light strand replication (OL), suggesting an alternative function for tRNA sequences. We hypothesize that this function is frequently pathogenic for those tRNA genes that normally do not form OL-like structures, because this could cause excess mutations in genome regions unadapted to tolerate them. In human mitochondrial genomes, pathogenic tRNA variants usually form less OL-like structures than non-pathogenic ones in cases where the normal non-pathogenic tRNA variant can function as OL, as evolutionary analyses reveal. For tRNAs lacking the putative OL-like functioning capacity, pathogenic variants form more OL-like secondary structures, particularly structures that might invoke bi-directional replication (true for 14 among 21 tRNA species, p<0.05, sign test; significantly at p<0.05 (1 tailed test) for 7 tRNA species), but not more unidirectional replication invoking structures. Accounting for the functional cloverleaf-like structure-forming capacities of tRNAs yields similar results. Rare, non-pathogenic tRNA mutants tend to form more OL-like structures than the common, non-pathogenic ones, suggesting weak directional selection also among non-pathogenic variants. The duration spent single stranded by a region of the heavy strand (D(ssH)) during replication, estimated by integrating over all regions that can function as OL in Homo sapiens mitochondrial genomes, increases with distance of that region from the Dloop. This suggests convergence of single-strandedness during replication and transcription, and explains conserved locations of tRNA species in mitochondrial genomes and bacterial operons. These locations minimize deamination costs only in anticodons and not in other tRNA regions, during replication and transcription. Therefore, putative functioning as OLs by tRNA sequences is normal at some locations and pathogenic at others.

Aging↗

Bayesian approach to discovering pathogenic SNPs in conserved protein domains.

The success rate of association studies can be improved by selecting better genetic markers for genotyping or by providing better leads for identifying pathogenic single nucleotide polymorphisms (SNPs) in the regions of linkage disequilibrium with positive disease associations. We have developed a novel algorithm to predict pathogenic single amino acid changes, either nonsynonymous SNPs (nsSNPs) or missense mutations, in conserved protein domains. Using a Bayesian framework, we found that the probability of a microbial missense mutation causing a significant change in phenotype depended on how much difference it made in several phylogenetic, biochemical, and structural features related to the single amino acid substitution. We tested our model on pathogenic allelic variants (missense mutations or nsSNPs) included in OMIM, and on the other nsSNPs in the same genes (from dbSNP) as the nonpathogenic variants. As a result, our model predicted pathogenic variants with a 10% false-positive rate. The high specificity of our prediction algorithm should make it valuable in genetic association studies aimed at identifying pathogenic SNPs.

Algorithms↗

Selection of resistant variants of respiratory pathogens by quinolones.

Quinolones are widely used in the treatment of respiratory tract infections. However, some disquiet has been expressed over using quinolones for community-acquired pneumonia since their activity is generally rather poor against Streptococcus pneumoniae. In addition, it is known that resistant variants emerge at a fairly high frequency during exposure of Enterobacteriaceae to quinolones; if this also occurred during quinolone treatment of community-acquired pneumonia it could lead to an increased risk of clinical failure. We therefore determined the selection rate of quinolone-resistant variants for six strains of S. pneumoniae, Haemophilus influenzae and Moraxella catarrhalis with nalidixic acid (except for S. pneumoniae), ciprofloxacin, ofloxacin and levofloxacin. We were only able to select resistant variants at low frequency from two of the six strains of S. pneumoniae with ciprofloxacin: no resistant variants were selected by either ofloxacin or levofloxacin. Variants of H. influenzae and M. catarrhalis with decreased susceptibility to quinolones were produced both with more strains and with a greater frequency; however, these variants still remained susceptible according to the NCCLS guidelines. Our study suggests that resistant variants of S. pneumoniae are relatively unlikely to occur in individuals treated with fluoroquinolones especially if they are given quinolones with enhanced anti-gram-positive activity compared to ciprofloxacin.

Anti-Infective Agents↗

Development of RS1-specific ACMG/AMP variant classification criteria with pilot variant curation.

Gene-based therapies are being developed for retinal diseases, including RS1-related X-linked retinoschisis. Therefore it is essential to determine which variants are pathogenic and which are benign when enrolling patients. The Clinical Genome Resource (ClinGen) X-Linked Inherited Retinal Diseases (XLRD) Variant Curation Expert Panel (VCEP) brings together clinician scientists, molecular biologists, and geneticists to apply their expertise and review the clinical, genetic, population, and functional evidence for variants. American College of Medical Genetics (ACMG) guidelines have been modified for RS1 to develop a highly systematic and conservative framework for evaluating variants. The curation process involves applying 28 different codes, each with 4 strength levels (very strong, strong, moderate, supporting) across different domains of phenotype, population data, computational assessment, functional impact, and segregation. With RS1-specific rules, a total of 54 pilot variants were tested. These included 47 variants in ClinVar. Of these 21 variants were re-classified: 2 likely pathogenic variants and one likely benign were changed to variants of uncertain significance and 4 previously unclassified variants were changed to pathogenic, likely pathogenic and likely benign. Other changes resolved conflicts or multiple classifications.

Humans↗

Early-Onset Atrial Fibrillation and the Prevalence of Rare Variants in Cardiomyopathy and Arrhythmia Genes.

IMPORTANCE: Early-onset atrial fibrillation (AF) can be the initial manifestation of a more serious underlying inherited cardiomyopathy or arrhythmia syndrome. OBJECTIVE: To examine the results of genetic testing for early-onset AF. DESIGN, SETTING, AND PARTICIPANTS: This prospective, observational cohort study enrolled participants from an academic medical center who had AF diagnosed before 66 years of age and 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 analysis was performed from October 24, 2020, to March 11, 2021. EXPOSURES: Rare variants identified in a panel of 145 genes that are included on cardiomyopathy and arrhythmia panels used by commercial clinical genetic testing laboratories. MAIN OUTCOMES AND MEASURES: Sequencing data were analyzed using an automated process followed by manual review by a panel of independent, blinded reviewers. The primary outcome was classification of rare variants using American College of Medical Genetics and Genomics criteria: benign, likely benign, variant of undetermined significance, likely pathogenic, or pathogenic. Disease-associated variants were defined as pathogenic/likely pathogenic variants in genes associated with autosomal dominant or X-linked dominant disorders. RESULTS: Among 1293 participants (934 [72.2%] male; median [interquartile range] age at enrollment, 56 [48-61] years; median [interquartile range] age at AF diagnosis, 50 [41-56] years), genetic testing identified 131 participants (10.1%) with a disease-associated variant, 812 (62.8%) with a variant of undetermined significance, 92 (7.1%) as heterozygous carriers for an autosomal recessive disorder, and 258 (20.0%) with no suspicious variant. The likelihood of a disease-associated variant was highest in participants with AF diagnosed before the age of 30 years (20 of 119 [16.8%; 95% CI, 10.0%-23.6%]) and lowest after the age of 60 years (8 of 112 [7.1%; 95% CI, 2.4%-11.9%]). Disease-associated variants were more often associated with inherited cardiomyopathy syndromes compared with inherited arrhythmias. The most common genes were TTN (n&#x2009;=&#x2009;38), MYH7 (n&#x2009;=&#x2009;18), MYH6 (n&#x2009;=&#x2009;10), LMNA (n&#x2009;=&#x2009;9), and KCNQ1 (n&#x2009;=&#x2009;8). CONCLUSIONS AND RELEVANCE: In this cohort study, genetic testing identified a disease-associated variant in 10% of patients with early-onset AF (the percentage was higher if diagnosed before the age of 30 years and lower if diagnosed after the age of 60 years). Most pathogenic/likely pathogenic variants are in genes associated with cardiomyopathy. These results support the use of genetic testing in early-onset AF.

Adult↗

[RNA-polymerase activity of pathogenic and nonpathogenic influenza A virus variants].

The transcriptase activity of original mouse-apathogenic strains of human (A/USSR/05/81) and animal (A/walrus/Massachusetts/1/80) influenza viruses and their pathogenic variants was studied. Also RNA-polymerase was studied in two types of antigenic recombinants produced by hybridization of the parental strains one of which (A/PR8/34) was pathogenic for mice. The nonpathogenic viruses under study were shown to have a low transcriptase activity, while pathogenic variants of these strains had a higher RNA-polymerase activity (1 1/2-3 times higher than in the original virus). All the recombinants tested, irrespective of their pathogenicity, had approximately similar transcriptase activity, 1 1/2-2 times higher than the enzymatic activity of the parental nonpathogenic virus.

Animals↗

The increased replicative capacity of a late-stage simian immunodeficiency virus mne variant is evident in macrophage- or dendritic cell-T-cell cocultures.

Human and simian immunodeficiency virus (HIV and SIV) may co-opt antigen capture and presentation functions of antigen presenting cells (APCs) to facilitate infection of CD4+ T-cells. To address whether the replicative capacity of SIV in the host may be associated with the extent of viral replication in response to APC-T-cell interactions, we compared the replicative phenotypes of cloned early and late-stage SIVmne variants of known pathogenicity. Here, we show that the highly pathogenic late variant SIVmne027 replicates more efficiently in both macrophage- and dendritic cell (DC)-T-cell cocultures than the minimally pathogenic early virus SIVmneCl8. Contact between either macrophages or DC and T-cells increases replication of SIVmne027. Our analysis also demonstrates that mutations in pol and nef contribute to the greater replicative capacity of SIVmne027 in DC- or macrophage-T-cell cocultures. Together, these data suggest that variant viruses that evolve to replicate vigorously in response to APC-T-cell interactions may have increased replicative capacity in vivo.

Animals↗

Mitochondrial DNA mutation detection by electrospray mass spectrometry.

BACKGROUND: Mitochondrial DNA (mtDNA) mutations cause a large spectrum of clinically important neurodegenerative, neuromuscular, cardiovascular, and endocrine disorders. We describe the novel application of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) to the rapid and accurate identification of pathogenic mtDNA variants. METHODS: In a blinded study, we used ESI-FTICR MS to analyze 24 unrelated samples of total cellular DNA containing 12 mtDNA variants and compared the results with those obtained by conventional PCR-restriction fragment length polymorphism (PCR-RFLP) analysis and gel electrophoresis. RESULTS: From the 24-sample blinded panel, we correctly identified 12 of the samples as bearing an mtDNA variant and found the remaining 12 samples to have no pathogenic variants. The correlation coefficient between the 2 methods for mtDNA variant detection was 1.0; there were no false positives or false negatives in this sample set. In addition, the ESI-FTICR method identified 4 single-nucleotide polymorphisms (SNP) that had previously been missed by standard PCR-RFLP analysis. CONCLUSIONS: ESI-FTICR MS is a rapid, sensitive, and accurate method for the identification and quantification of mtDNA mutations and SNPs.

DNA, Mitochondrial↗

T cells expressing the gamma delta T-cell receptor potentiate coxsackievirus B3-induced myocarditis.

Initial studies determined whether intraperitoneal (i.p.) injection of BALB/c mice with 0.1, 1.0, and 10 mg of adriamycin (a cardiotoxic anthracycline antibiotic) for times ranging between 1 and 9 weeks prior to i.p. injection of 10(5) PFU of coxsackievirus B3 (CVB3) would alter the severity of virus-induced myocarditis. Prior adriamycin exposure enhanced pathogenicity of a poorly pathogenic CVB3 variant (H310A1) but had no effect on myocarditis produced by the pathogenic variant (H3). Cardiac virus concentrations were equivalent in H3- and H310A1-infected mice irrespective of adriamycin treatment. BALB/c mice treated with either 0.1 ml of complete Freund's adjuvant (CFA), 10 mg of adriamycin, or 10(5) PFU of H3 and H310A1 i.p. developed cytolytic Thy 1.2+ lymphocytes (CTL) to H3-infected myocytes 7 days later. CFA-, adriamycin-, and H3-treated mice developed CTL expressing the gamma delta+ T-cell receptors, while H310A1-infected animals did not. Only H3- and H310A1-infected mice developed alpha beta+ CTL. Treatment of BALB/c mice with 0.1 ml of CFA 5 days prior to H310A1 infection dramatically increased myocarditis. Selective depletion of gamma delta+ T cells abrogated this effect. The ability of gamma delta+ T cells to augment the pathogenicity of H310A1 infection was confirmed by adoptive transfer of CFA-stimulated T cells depleted of either gamma delta- or gamma delta+ cells into H310A1-infected recipients.

Animals↗

Structural basis for segmental gene conversion in generation of Anaplasma marginale outer membrane protein variants.

Bacterial pathogens in the genus Anaplasma generate surface coat variants by gene conversion of chromosomal pseudogenes into single-expression sites. These pseudogenes encode unique surface-exposed hypervariable regions flanked by conserved domains, which are identical to the expression site flanking domains. In addition, Anaplasma marginale generates variants by recombination of oligonucleotide segments derived from the pseudogenes into the existing expression site copy, resulting in a combinatorial increase in variant diversity. Using the A. marginale genome sequence to track the origin of sequences recombined into the msp2 expression site, we demonstrated that the complexity of the expressed msp2 increases during infection, reflecting a shift from recombination of the complete hypervariable region of a given pseudogene to complex mosaics with segments derived from hypervariable regions of different pseudogenes. Examination of the complete set of 1183 variants with segmental changes revealed that 99% could be explained by one of the recombination sites occurring in the conserved flanking domains and the other within the hypervariable region. Consequently, we propose an 'anchoring' model for segmental gene conversion whereby the conserved flanking sequences tightly align and anchor the expression site sequence to the pseudogene. Associated with the recombination sites were deletions, insertions and substitutions; however, these are a relatively minor contribution to variant generation as these occurred in less than 2% of the variants. Importantly, the anchoring model, which can account for more variants than a strict segmental sequence identity mechanism, is consistent with the number of msp2 variants predicted and empirically identified during persistent infection.

Amino Acid Sequence↗