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1.
J Virol Methods ; 290: 114093, 2021 Feb 04.
Artículo en Inglés | MEDLINE | ID: mdl-33549574

RESUMEN

BACKGROUND: In immunocompromised patients, BK Virus (BKV) reactivation may cause serious disease with high morbidity. Particularly for patient management after solid organ transplantation, monitoring of viral load in different clinical specimens is crucial to ensure early diagnosis and response to reactivation. In this study, we evaluated the clinical performance of a custom designed primer /probe set for detection of BKV on the cobas® 6800, a high-throughput platform, employing the open channel of the system for integration of a lab-developed test (LDT). MATERIALS/METHODS: A primer/probe set was optimized for the use on a high-throughput platform. Clinical performance was assessed in EDTA-plasma, serum and urine samples. Limit-of-detection (LOD) was determined by using a dilution series of BKV WHO standard. A CE-labeled PCR test (Altona Diagnostics) was used as a comparison to the assay. RESULTS: The LOD for the LDT BKV assay was 6.7 IU/mL. Inter-and intra-run variability (at 5 x LOD) was low (<1.5 Ct in all specimens). All quality control panel specimens (Instand Germany n = 19) were correctly identified. Of 290 clinical samples tested, results were concordant for 280 samples. Sensitivity and specificity of the assay were 96 % and 98 % respectively. The quantitative analysis revealed a strong correlation (linear regression) between the CE-labelled comparator assay and the new BKV LDT assay with r2 = 0.96 for n = 123 urine samples and r2 = 0.98 for n = 167 plasma/serum samples. CONCLUSION: Compared to a CE-IVD assay, the adapted LDT showed good analytical and clinical sensitivity and specificity for the detection and quantification of BKV in different clinical specimens. It represents a convenient solution to automate the LDT workflow with low hands-on time and thus facilitates high-throughput screening for BKV reactivation in immunocompromised patients.

2.
Fertil Steril ; 2021 Jan 16.
Artículo en Inglés | MEDLINE | ID: mdl-33468312

RESUMEN

OBJECTIVES: To investigate the personal, ethical, and financial perspectives of individuals with Mayer-Rokitansky-Küster-Hauser syndrome (MRKH), a congenital uterine factor infertility condition, regarding uterine transplantation (UTx). DESIGN: Cross-sectional, quantitative survey. SETTING: A 60-item anonymous electronic questionnaire was disseminated via social media sites. PATIENTS: International members of the Beautiful You MRKH Foundation. INTERVENTIONS: None. MAIN OUTCOME MEASURES: The survey contained UTx educational materials followed by questions assessing participants' baseline knowledge, global perceptions, financial concerns, and ethical considerations regarding UTx. RESULTS: We received 281 responses, with a mean participant age of 28.2 ± 9.8 years. After reviewing the education material, most participants considered receiving a UTx (73%), believed that it should be an option for all women with uterine factor infertility (86%), and believed that it should be covered by health insurance (78%). Respondents perceived the benefits of the procedure to outweigh the risks (67%) and considered it to be an ethical procedure (82%). Almost one-half (49%) were willing to spend more than $10,000 out of pocket to receive the procedure. When asked to rank the risk of UTx to self, donor, and fetus in order of personal importance, 21% ranked their own safety last. CONCLUSION: There is a profound desire in the MRKH community for UTx to become more widely available and affordable. MRKH patients may represent a vulnerable population requiring special considerations for informed consent and rigorous evaluation for UTx. Providers caring for MRKH patients should be prepared to provide education about UTx and to thoughtfully engage with news and media outlets to communicate evidence-supported information.

3.
Artículo en Inglés | MEDLINE | ID: mdl-33455856

RESUMEN

BACKGROUND: The pathological hallmarks of Parkinson's disease include intraneuronal Lewy bodies, neuronal loss, and gliosis. We aim to correlate Parkinson's disease neuropsychiatric symptoms, (e.g., depression, psychosis, and anxiety) with the severity of neuropathology in the substantia nigra and locus coeruleus. METHODS: The brains of 175 participants with a primary pathologic diagnosis of Parkinson's disease were analyzed semi-quantitatively to ascertain the burden of neuronal loss and gliosis and Lewy body pathology within the locus coeruleus and substantia nigra. Participants' history of anxiety, depression, and psychosis were determined using a chart-extracted medical history or record of formal psychiatric evaluation. RESULTS: Of the sample, 56% (n = 98), 50% (n = 88), and 31.25% (n = 55) of subjects had a diagnosis of psychosis, depression, and anxiety, respectively. Psychosis (χ2 = 7.1, p = 0.008, df = 1) and depression (χ2 = 7.2, p = 0.007, df = 1) were associated with severe neuronal loss and gliosis in the substantia nigra but not in the locus coeruleus. No association was observed between anxiety and neuronal loss and gliosis in either region. No neuropsychiatric symptoms were associated with Lewy body score. After controlling for disease duration and dementia, psychosis (odds ratio [OR]: 3.1, 95% confidence interval [CI]: 1.5-6.4, χ2 = 9.4, p = 0.012, df = 1) and depression (OR: 2.6, 95% CI: 1.3-5.0, χ2 = 7.9, p = 0.005, df = 1) remained associated with severe neuronal loss and gliosis in the substantia nigra. CONCLUSION: These results suggest that psychosis and depression in Parkinson's disease are associated with the underlying neurodegenerative process and demonstrate that cell loss and gliosis may be a better marker of neuropsychiatric symptoms than Lewy body pathology.

5.
J Clin Virol ; 134: 104691, 2020 Nov 18.
Artículo en Inglés | MEDLINE | ID: mdl-33278791

RESUMEN

Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.

6.
mBio ; 11(6)2020 12 15.
Artículo en Inglés | MEDLINE | ID: mdl-33323517

RESUMEN

Viral noncoding RNAs have acquired increasing prominence as important regulators of infection and mediators of pathogenesis. Circular RNAs (circRNAs) generated by backsplicing events have been identified in several oncogenic human DNA viruses. Here, we show that Merkel cell polyomavirus (MCV), the etiologic cause of ∼80% of Merkel cell carcinomas (MCCs), also expresses circular RNAs. By RNase R-resistant RNA sequencing, four putative circRNA backsplice junctions (BSJs) were identified from the MCV early region (ER). The most abundantly expressed MCV circRNA, designated circMCV-T, is generated through backsplicing of all of ER exon II to form a 762-nucleotide (nt) circular RNA molecule. Curiously, circMCV-T, as well as two other less abundantly expressed putative MCV circRNAs, overlaps in a complementary fashion with the MCV microRNA (miRNA) locus that encodes MCV-miR-M1. circMCV-T is consistently detected in concert with linear T antigen transcripts throughout infection, suggesting a crucial role for this RNA molecule in the regulatory functions of the early region, known to be vital for viral replication. Knocking out the hairpin structure of MCV-miR-M1 in genomic early region expression constructs and using a new high-efficiency, recombinase-mediated, recircularized MCV molecular clone demonstrates that circMCV-T levels decrease in the presence of MCV-miR-M1, underscoring the interplay between MCV circRNA and miRNA. Furthermore, circMCV-T partially reverses the known inhibitory effect of MCV-miR-M1 on early gene expression. RNase R-resistant RNA sequencing of lytic rat polyomavirus 2 (RatPyV2) identified an analogously located circRNA, stipulating a crucial, conserved regulatory function of this class of RNA molecules in the family of polyomaviruses.IMPORTANCE Covalently closed circular RNAs were recently described in the human DNA tumor viruses Epstein-Barr virus (EBV), Kaposi's sarcoma-associated herpesvirus (KSHV), and human papillomavirus (HPV). Here, we show that MCV, another DNA tumor virus, generates circRNAs from its early regulatory region in concert with T antigen linear transcripts. MCV circMCV-T interacts with another MCV noncoding RNA, miR-M1, to functionally modulate early region transcript expression important for viral replication and long-term episomal persistence. This work describes a dynamic regulatory network integrating circRNA/miRNA/mRNA biomolecules and underscores the intricate functional modulation between several classes of polyomavirus-encoded RNAs in the control of viral replication.

7.
Kidney Int ; 2020 Dec 22.
Artículo en Inglés | MEDLINE | ID: mdl-33359499

RESUMEN

BK polyomavirus-associated nephropathy is a common complication after kidney transplantation leading to reduced graft function or loss. The molecular pathogenesis of BK polyomavirus-induced nephropathy is not well understood. A recent study had described a protective effect of the activating natural killer cell receptor KIR3DS1 in BK polyomavirus-associated nephropathy, suggesting a role of NK cells in modulating disease progression. Using an in vitro cell culture model of human BK polyomavirus infection and kidney biopsy samples from patients with BK polyomavirus-associated nephropathy, we observed significantly increased surface expression of the ligand for KIR3DS1, HLA-F, on BK polyomavirus-infected kidney tubular cells. Upregulation of HLA-F expression resulted in significantly increased binding of KIR3DS1 to BK polyomavirus-infected cells and activation of primary KIR3DS-positive natural killer cells. Thus, our data provide a mechanism by which KIR3DS-positive natural killer cells can control BK polyomavirus infection of the kidney, and rationale for exploring HLA-F/KIR3DS1 interactions for immunotherapeutic approaches in BK polyomavirus-associated nephropathy.

8.
Artículo en Inglés | MEDLINE | ID: mdl-33007476

RESUMEN

OBJECTIVES: Investigation whether in depth characterization of virus variant patterns can be used for epidemiological analysis of the first SARS-CoV-2 infection clusters in Hamburg, Germany. METHODS: Metagenomic RNA- and amplicon-sequencing and subsequent variant calling in 25 respiratory samples from SARS-CoV-2 infected patients involved in the earliest infection clusters in Hamburg. RESULTS: Amplikon sequencing and cluster analyses of these SARS-CoV-2 sequences allowed the identification of the first infection cluster and five non-related infection clusters occurring at the beginning of the viral entry of SARS-CoV-2 in the Hamburg metropolitan region. Viral genomics together with epidemiological analyses revealed that the index patient acquired the infection in Northern Italy and transmitted it to two out of 134 contacts. Single nucleotide polymorphisms clearly distinguished the virus variants of the index and other clusters and allowed to track in which sequences worldwide these mutations were first described. Minor variant analyses identified the transmission of intra-host variants in the index cluster and household clusters. CONCLUSIONS: SARS-CoV-2 variant tracing allows the identification of infection clusters and the follow up of infection chains occurring in the population. Furthermore, the follow up of minor viral variants in infection cluster can provide further resolution on transmission events indistinguishable on consensus sequence level.

9.
J Clin Virol ; 132: 104650, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-33011643

RESUMEN

BACKGROUND: The ongoing SARS-CoV-2 pandemic presents a unique challenge to diagnostic laboratories. There are preliminary studies correlating qRT-PCR results from different materials to clinical outcomes, yet, comparability is limited due to the plethora of different assays used for diagnostics. In this study we evaluate clinical performance and linear range for the SARS-CoV-2 IVD (cobas6800/8800 system, a fully automated sample-to-result platform) in different clinically relevant matrix materials outside official specifications. METHODS: Assay performance was assessed in human plasma, BAL/BL and transport medium following chemical inactivation. For analytical evaluation, respective matrix materials were spiked with SARS-CoV-2 RNA in ten-fold dilution series. The efficacy of chemical inactivation by guanidine hydrochloride solution was confirmed in cell culture infectivity experiments. For correlation, a total of 289 predetermined clinical samples including respiratory swabs, plasma and lower respiratory tract specimens were subjected to the SARS-CoV-2 IVD test and results were compared. RESULTS: The SARS-CoV-2 IVD showed excellent linearity over four to six log steps depending on matrix material. Chemical inactivation resulted in a reduction in plaque forming units of at least 3.5 log steps, while having no significant impact on assay performance. Inter-run consistency from three different testing sites demonstrated excellent comparability of RT-PCR results (maximum deviation was 1.53 CT). Clinical evaluation for respiratory swabs showed very good agreement with the comparator assay (Positive agreement 95.7 %, negative agreement 98.9 %). CONCLUSION: The SARS-CoV-2 IVD test for the cobas6800/8800 systems offers excellent linear range and inter-run consistency for quantification of SARS-CoV-2 RNA in different matrices outside official specifications.

10.
EMBO Mol Med ; 12(12): e13296, 2020 12 07.
Artículo en Inglés | MEDLINE | ID: mdl-33012091

RESUMEN

We describe a multifactorial investigation of a SARS-CoV-2 outbreak in a large meat processing complex in Germany. Infection event timing, spatial, climate and ventilation conditions in the processing plant, sharing of living quarters and transport, and viral genome sequences were analyzed. Our results suggest that a single index case transmitted SARS-CoV-2 to co-workers over distances of more than 8 m, within a confined work area in which air is constantly recirculated and cooled. Viral genome sequencing shows that all cases share a set of mutations representing a novel sub-branch in the SARS-CoV-2 C20 clade. We identified the same set of mutations in samples collected in the time period between this initial infection cluster and a subsequent outbreak within the same factory, with the largest number of confirmed SARS-CoV-2 cases in a German meat processing facility reported so far. Our results indicate climate conditions, fresh air exchange rates, and airflow as factors that can promote efficient spread of SARS-CoV-2 via long distances and provide insights into possible requirements for pandemic mitigation strategies in industrial workplace settings.

11.
Artículo en Inglés | MEDLINE | ID: mdl-33035320

RESUMEN

CONTEXT: In-vitro and in-vivo evidence has supported the role of angiotensin II blockade in reducing leiomyoma cell proliferation and growth. However, no population-based study to date has investigated this potential association. OBJECTIVE: To determine if prior Angiotensin-Converting Enzyme inhibitor (ACEi) use is associated with reduced odds of leiomyoma development. DESIGN: A nested case-control study. SETTING: The population was assembled from the Truven Health Marketscan® Research Database, which includes private health insurance claims from January 1 st, 2012 to December 31 st, 2017. PATIENTS OR OTHER PARTICIPANTS: We included (n=353,917) women aged 18-65 with hypertension. Cases (n=13,108) with a leiomyoma diagnosis were matched to controls (n=340,808) with no such diagnosis at a 1:26 ratio by age and region of origin within the United States. INTERVENTION(S): Prior use of ACEi was determined from outpatient drug claims. MAIN OUTCOME MEASURE(S): Leiomyoma development was indicated by a first time diagnosis code. RESULTS: Women on an ACEi experienced a 31.8% reduced odds of developing clinically recognized leiomyoma compared to non-users (OR 0.68, 95% CI 0.65-0.72). This association was significant for each age group: 30-39 (OR 0.86, 95% CI 0.74-0.99), 40-49 (OR 0.71, 95% CI 0.66-0.76), 50-59 (OR 0.63, 95% CI 0.58-0.69) and 60-65 years old (OR 0.58, 95% CI 0.50-0.69). Of the ACEi's, Lisinopril (OR 0.67, 95% CI 0.64-0.71), Quinapril (OR 0.62, 95% CI 0.41-0.92) and Ramipril (OR 0.35, 95% CI 0.23-0.50) demonstrated a significant association with reduced leiomyoma incidence. CONCLUSIONS: ACEi use is associated with reduced odds of developing clinically recognized leiomyoma in adult hypertensive women.

12.
PLoS Pathog ; 16(8): e1008562, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32833988

RESUMEN

Merkel Cell Polyomavirus (MCPyV) is the etiological agent of the majority of Merkel Cell Carcinomas (MCC). MCPyV positive MCCs harbor integrated, defective viral genomes that constitutively express viral oncogenes. Which molecular mechanisms promote viral integration, if distinct integration patterns exist, and if integration occurs preferentially at loci with specific chromatin states is unknown. We here combined short and long-read (nanopore) next-generation sequencing and present the first high-resolution analysis of integration site structure in MCC cell lines as well as primary tumor material. We find two main types of integration site structure: Linear patterns with chromosomal breakpoints that map closely together, and complex integration loci that exhibit local amplification of genomic sequences flanking the viral DNA. Sequence analysis suggests that linear patterns are produced during viral replication by integration of defective/linear genomes into host DNA double strand breaks via non-homologous end joining, NHEJ. In contrast, our data strongly suggest that complex integration patterns are mediated by microhomology-mediated break-induced replication, MMBIR. Furthermore, we show by ChIP-Seq and RNA-Seq analysis that MCPyV preferably integrates in open chromatin and provide evidence that viral oncogene expression is driven by the viral promoter region, rather than transcription from juxtaposed host promoters. Taken together, our data explain the characteristics of MCPyV integration and may also provide a model for integration of other oncogenic DNA viruses such as papillomaviruses.


Asunto(s)
Carcinoma de Células de Merkel/patología , Reparación del ADN por Unión de Extremidades , Poliomavirus de Células de Merkel/genética , Infecciones por Polyomavirus/complicaciones , Infecciones Tumorales por Virus/complicaciones , Integración Viral , Replicación Viral , Antígenos Virales de Tumores , Neoplasias Óseas/genética , Neoplasias Óseas/secundario , Neoplasias Óseas/virología , Carcinoma de Células de Merkel/genética , Carcinoma de Células de Merkel/virología , Humanos , Infecciones por Polyomavirus/genética , Infecciones por Polyomavirus/virología , Recombinación Genética , Neoplasias Cutáneas/genética , Neoplasias Cutáneas/patología , Neoplasias Cutáneas/virología , Infecciones Tumorales por Virus/genética , Infecciones Tumorales por Virus/virología , Proteínas Virales/genética
13.
Eur J Haematol ; 105(6): 722-730, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32658347

RESUMEN

OBJECTIVES: Major complications affecting the central nervous system (CNS) present a challenge after allogeneic stem cell transplantation (allo-SCT). METHODS: Incidence, risk factors, and outcome were retrospectively analyzed in 888 patients in a monocentric study. RESULTS: Cumulative incidence (CI) of major CNS complications at 1 year was 14.8% (95%CI 12.3%-17.2%). Median follow-up is 11 months. CNS complications were documented in 132 patients: in 36 cases, classified metabolic; 26, drug-related neurotoxicity (14 attributed to cyclosporine A, 4 to antilymphocyte globulin); 11, cerebrovascular (ischemic n = 8, bleeding n = 3); 9, infections; 9, psychiatric; and 9, malignant. The cause of CNS symptoms remained unclear for 37 patients (28%). Multivariate analysis demonstrated an association of CNS complication with patient age (P < .001). The estimated OS of patients with any CNS complication was significantly lower than in patients without neurological complications (P < .001), and the CI of non-relapse mortality (NRM) was higher for patients with CNS complication (P < .001). A significant negative impact on survival can only be demonstrated for metabolic CNS complications and CNS infections (NRM, P < .0001 and P = .0003, respectively), and relapse (P < .0001). CONCLUSION: CNS complications after allo-SCT are frequent events with a major contribution to morbidity and mortality. In particular, the situations of unclear neurological complications need to be clarified by intensive research.

14.
Curr Opin Cardiol ; 35(5): 508-516, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32649350

RESUMEN

PURPOSE OF REVIEW: A healthy lifestyle throughout one's lifespan is the core foundation for both primary and secondary prevention of cardiovascular disease (CVD). Risk-based decisions for pharmacological therapy is added on-top of lifestyle management. Thus, understanding lifestyle-based recommendations is central to CVD prevention. RECENT FINDINGS: In 2018 and 2019, the American Heart Association (AHA) and American College of Cardiology (ACC) published new guidelines for lipid management and primary prevention of cardiovascular disease (CVD), respectively. The European Society of Cardiology (ESC) and European Atherosclerosis Society (EAS) published new guidelines on lipids and diabetes management in 2019. These guidelines provide recommendations on diet and lifestyle for reducing cardiovascular risk. Both encourage heart-healthy diets consistent with Mediterranean, DASH, or healthy vegetarian patterns. Both provide guidance for recommended physical activity levels but acknowledge any physical activity, even less than recommended, is better than inactivity. Although both ACC/AHA and ESC/EAS guidelines have similar approaches to achieve the same goal of CVD prevention, there were some differences between them. SUMMARY: In this review, we discussed similarities and differences between the American and European guidelines to familiarize clinicians with both sets of lifestyle recommendations in an effort to provide best practices in individualized patient-care for CVD prevention.

15.
Orthop J Sports Med ; 8(7): 2325967120931399, 2020 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-32704506

RESUMEN

Background: The biomechanical properties of coracoid fixation with a miniplate during the Latarjet procedure have not been described. Purpose: To determine the biomechanical properties of miniplate fixation for the Latarjet procedure compared with various screw fixation configurations. Study Design: Controlled laboratory study. Methods: A total of 8 groups (n = 5 specimens per group) were tested at a screw insertion angle of 0°: (1) 3.75-mm single screw, (2) 3.75-mm double screw, (3) 3.75-mm double screw with washers, (4) 3.75-mm double screw with a miniplate, (5) 4.00-mm single screw, (6) 4.00-mm double screw, (7) 4.00-mm double screw with washers, and (8) 4.00-mm double screw with a miniplate. In addition, similar to groups 1 to 3 and 5 to 7, there were 30 additional specimens (n = 5 per group) tested at a screw insertion angle of 15° (groups 9-14). To maintain specimen uniformity, rigid polyurethane foam blocks were used. Testing parameters included a preload of 214 N for 10 seconds, cyclical loading from 184 to 736 N at 1 Hz for 100 cycles, and failure loading at a rate of 15 mm/min until 10 mm of displacement or specimen failure occurred. Results: All single-screw constructs and 77% of 15° screw constructs failed before the completion of cyclical loading. Across all groups, group 8 (4.00-mm double screw with miniplate) demonstrated the highest maximum failure load (P < .001). There were no differences in failure loads among specimens with single-screw fixation (groups 1, 5, 9, and 12; P > .05). All specimens in groups 9, 10, 11, 12, 13, and 14 (insertion angle of 15°) had significantly lower maximum failure loads compared with specimens in groups 2, 3, 4, 6, 7, and 8 (insertion angle of 0°) (P < .001 for all). Conclusion: These results indicate significantly superior failure loads with the miniplate compared with all other constructs. Across all fixation techniques and screw sizes, constructs with screws inserted at 0° performed better than constructs with screws inserted at 15°. Clinical Relevance: The use of a miniplate for coracoid fixation during the Latarjet procedure may provide a more durable construct for the high-demand contact athlete.

16.
Microbiol Resour Announc ; 9(23)2020 Jun 04.
Artículo en Inglés | MEDLINE | ID: mdl-32499358

RESUMEN

Here, we describe the complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab sample from a female patient with COVID-19 who was infected in Hamburg, northern Germany.

17.
BMC Bioinformatics ; 21(1): 233, 2020 Jun 08.
Artículo en Inglés | MEDLINE | ID: mdl-32513098

RESUMEN

BACKGROUND: The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. RESULTS: We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify known and potentially new Papillomaviridae sequences from NGS amplicon sequencing with degenerate PV primers. Here, we describe the features of PVAmpliconFinder and its implementation using biological data obtained from amplicon sequencing of human skin swab specimens and oral rinses from healthy individuals. CONCLUSIONS: PVAmpliconFinder identified putative new HPV sequences, including one that was validated by wet-lab experiments. PVAmpliconFinder can be easily modified and applied to other viral families. PVAmpliconFinder addresses a gap by providing a solution for the analysis of NGS amplicon sequencing, increasingly used in clinical research. The PVAmpliconFinder workflow, along with its source code, is freely available on the GitHub platform: https://github.com/IARCbioinfo/PVAmpliconFinder.


Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Papillomaviridae/aislamiento & purificación , Interfaz Usuario-Computador , ADN Viral/química , ADN Viral/metabolismo , Humanos , Papillomaviridae/genética , Flujo de Trabajo
18.
ArXiv ; 2020 Apr 21.
Artículo en Inglés | MEDLINE | ID: mdl-32550250

RESUMEN

In severe viral pneumonias, including Coronavirus disease 2019 (COVID-19), the viral replication phase is often followed by a hyperinflammatory reaction ('cytokine storm syndrome') that leads to acute respiratory distress syndrome and death, despite maximal supportive care. Preventing hyperinflammation is key to avoiding these outcomes. We previously demonstrated that alpha-1 adrenergic receptor antagonists ($\alpha$-blockers) can prevent cytokine storm syndrome and death in mice. Here, we conduct a retrospective analysis of patients with acute respiratory distress or pneumonia (n = 13,125 and n = 108,956, respectively) from all causes; patients who were incidentally taking $\alpha$-blockers had a reduced risk of requiring ventilation (by 35% and 16%, respectively), and a reduced risk of being ventilated and dying (by 56% and 20%, respectively), compared to non-users. Beta-adrenergic receptor antagonists had no significant effects. These results highlight the urgent need for prospective trials testing whether prophylactic $\alpha$-blockers improve outcomes in diseases with a prominent hyperinflammatory component such as COVID-19.

20.
J Clin Virol ; 128: 104390, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32388471

RESUMEN

BACKGROUND: The ongoing SARS-CoV-2 pandemic presents a unique challenge for diagnostic laboratories around the world. Automation of workflows in molecular diagnostics is instrumental for coping with the large number of tests ordered by clinicians, as well as providing fast-tracked rapid testing for highly urgent cases. In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 system, a fully automated device performing extraction and real-time PCR. METHODS: A publicly available SARS-CoV-2 RT-PCR assay was adapted for the automated system. Analytical performance was evaluated using in-vitro transcribed RNA and clinical performance was compared to the cobas 6800-based reference assay within the lab. RESULTS: The Envelope (E) Gene-LDT displayed good analytical performance with an LoD of 95.55 cp/mL and no false positives during evaluation of cross-reactivity. A total of 176 patient samples were tested with both the E-Gene-LDT and the reference assay. Positive and negative agreement were 100 % and 99.2 % respectively. Invalid-rate was 6.3 %. CONCLUSION: The E-Gene-LDT showed analytical and clinical performance comparable to the cobas6800-based reference assay. Due to its random-access workflow concept and rapid time-to-result of about 80 min, the system is very well suited for providing fast-tracked SARS-CoV-2 diagnostics for urgent clinical samples in the hospital setting.


Asunto(s)
Técnicas de Laboratorio Clínico/métodos , Pandemias , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , Betacoronavirus , Técnicas de Laboratorio Clínico/instrumentación , Infecciones por Coronavirus/diagnóstico , Hospitales , Humanos , Neumonía Viral , Reacción en Cadena en Tiempo Real de la Polimerasa/instrumentación , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/instrumentación , Factores de Tiempo , Flujo de Trabajo
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