A Multiallelic Molecular Beacon-Based Real-Time RT-PCR Assay for the Detection of SARS-CoV-2.

Funder: European Regional Development Fund and the Republic of Cyprus through the Cyprus Research and Innovation Foundation and the Structural Funds 2021-2027; Grant(s): Project: CONCEPT-COVID_0420_0024Emerging infectious viruses have led to global advances in the development of specific and sensitive detection techniques. Viruses have an inherent potential to easily mutate, presenting major hurdles for diagnostics and requiring methods capable of detecting genetically diverse viral strains. One such infectious agent is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in December 2019 and has resulted in the global coronavirus disease 2019 (COVID-19) pandemic. This study presents a real-time reverse transcription PCR (RT-PCR) detection assay for SARS-CoV-2, taking into account its intrinsic polymorphic nature that arises due to genetic drift and recombination, as well as the possibility of continuous and multiple introductions of genetically nonidentical strains into the human population. This advance was achieved by using mismatch-tolerant molecular beacons designed to specifically detect the SARS-CoV-2 S, E, M, and N genes. These were applied to create a simple and reproducible real-time RT-PCR assay, which was validated using external quality control panels (QCMD: CVOP20, WHO: SARS-CoV-2-EQAP-01) and clinical samples. This assay was designed for high target detection accuracy and specificity and can also be readily adapted for the detection of other emerging and rapidly mutating pathogens

5-Carboxylcytosine levels are elevated in human breast cancers and gliomas

BACKGROUND: DNA methylation (5-methylcytosine (5mC)) patterns are often altered in cancers. Ten-eleven translocation (Tet) proteins oxidise 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). In addition to their presumptive specific biological roles, these oxidised forms of 5mC may serve as intermediates in demethylation process. According to several reports, 5hmC levels are strongly decreased in cancers; however, the distribution of 5fC and 5caC in malignant tissue has not been studied. FINDINGS: Here, we examine the levels of 5hmC and 5caC in 28 samples of normal breast tissue, 59 samples of invasive human breast cancer and 74 samples of gliomas using immunochemistry. In agreement with previous reports, we show that 71 % of normal breast samples exhibit strong 5hmC signal, compared with only 18 % of breast cancer samples with equivalent levels of 5hmC staining. Unexpectedly, although 5caC is not detectable in normal breast tissue, 27 % of breast cancer samples exhibit significant staining for this modification (p < 0.001). Surprisingly, the presence of immunochemically detectable 5caC is not associated with the intensity of 5hmC signal in breast cancer tissue. In gliomas, we show that 5caC is detectable in 45 % of tumours. CONCLUSIONS: We demonstrate that, unlike 5hmC, the levels of 5caC are elevated in a proportion of breast cancers and gliomas. Our results reveal another level of complexity to the cancer epigenome, suggesting that active demethylation and/or 5caC-dependent transcriptional regulation are pre-activated in some tumours and may contribute to their pathogenesis. Larger studies to evaluate the clinicopathological significance of 5caC in cancers are warranted

COVID-19 in children and adolescents in Europe: a multinational, multicentre cohort study

Background To date, few data on paediatric COVID-19 have been published, and most reports originate from China. This study aimed to capture key data on children and adolescents with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection across Europe to inform physicians and health-care service planning during the ongoing pandemic. Methods This multicentre cohort study involved 82 participating health-care institutions across 25 European countries, using a well established research network—the Paediatric Tuberculosis Network European Trials Group (ptbnet)—that mainly comprises paediatric infectious diseases specialists and paediatric pulmonologists. We included all individuals aged 18 years or younger with confirmed SARS-CoV-2 infection, detected at any anatomical site by RT-PCR, between April 1 and April 24, 2020, during the initial peak of the European COVID-19 pandemic. We explored factors associated with need for intensive care unit (ICU) admission and initiation of drug treatment for COVID-19 using univariable analysis, and applied multivariable logistic regression with backwards stepwise analysis to further explore those factors significantly associated with ICU admission. Findings 582 individuals with PCR-confirmed SARS-CoV-2 infection were included, with a median age of 5·0 years (IQR 0·5–12·0) and a sex ratio of 1·15 males per female. 145 (25%) had pre-existing medical conditions. 363 (62%) individuals were admitted to hospital. 48 (8%) individuals required ICU admission, 25 (4%) mechanical ventilation (median duration 7 days, IQR 2–11, range 1–34), 19 (3%) inotropic support, and one (<1%) extracorporeal membrane oxygenation. Significant risk factors for requiring ICU admission in multivariable analyses were being younger than 1 month (odds ratio 5·06, 95% CI 1·72–14·87; p=0·0035), male sex (2·12, 1·06–4·21; p=0·033), pre-existing medical conditions (3·27, 1·67–6·42; p=0·0015), and presence of lower respiratory tract infection signs or symptoms at presentation (10·46, 5·16–21·23; p<0·0001). The most frequently used drug with antiviral activity was hydroxychloroquine (40 [7%] patients), followed by remdesivir (17 [3%] patients), lopinavir–ritonavir (six [1%] patients), and oseltamivir (three [1%] patients). Immunomodulatory medication used included corticosteroids (22 [4%] patients), intravenous immunoglobulin (seven [1%] patients), tocilizumab (four [1%] patients), anakinra (three [1%] patients), and siltuximab (one [<1%] patient). Four children died (case-fatality rate 0·69%, 95% CI 0·20–1·82); at study end, the remaining 578 were alive and only 25 (4%) were still symptomatic or requiring respiratory support. Interpretation COVID-19 is generally a mild disease in children, including infants. However, a small proportion develop severe disease requiring ICU admission and prolonged ventilation, although fatal outcome is overall rare. The data also reflect the current uncertainties regarding specific treatment options, highlighting that additional data on antiviral and immunomodulatory drugs are urgently needed. Funding ptbnet is supported by Deutsche Gesellschaft für Internationale Zusammenarbeit

Proceedings of the 24th Paediatric Rheumatology European Society Congress: Part three

From Springer Nature via Jisc Publications Router.Publication status: PublishedHistory: collection 2017-09, epub 2017-09-0

A Giant Intrathoracic Malignant Schwannoma Causing Respiratory Failure in a Patient without von Recklinghausen’s Disease

We report an unusual case of a thoracic opacity due to a huge mediastinal malignant schwannoma which compressed the whole left lung and the mediastinum causing respiratory failure in a 73-year-old woman without von Recklinghausen’s disease. Although the tumor was resected, the patient failed to wean from mechanical ventilation and died one month later because of multiple organ dysfunction syndrome

Indoor air quality, ventilation and respiratory health in elderly residents living in nursing homes in Europe

Few data exist on respiratory effects of indoor air quality and comfort parameters in the elderly. In the context of the GERIE study, we investigated for the first time the relationships of these factors to respiratory morbidity among elderly people permanently living in nursing homes in seven European countries. 600 elderly people from 50 nursing homes underwent a medical examination and completed a standardised questionnaire. Air quality and comfort parameters were objectively assessed in situ in the nursing home. Mean concentrations of air pollutants did not exceed the existing standards. Forced expiratory volume in 1 s/forced vital capacity ratio was highly significantly related to elevated levels of particles with a 50% cut-off aerodynamic diameter of <0.1 µm (PM0.1) (adjusted OR 8.16, 95% CI 2.24-29.3) and nitrogen dioxide (aOR 3.74, 95% CI 1.06-13.1). Excess risks for usual breathlessness and cough were found with elevated PM10 (aOR 1.53 (95% CI 1.15-2.07) and aOR 1.73 (95% CI 1.17-10.3), respectively) and nitrogen dioxide (aOR 1.58 (95% CI 1.15-2.20) and aOR 1.56 (95% CI 1.03-2.41), respectively). Excess risks for wheeze in the past year were found with PM0.1 (aOR 2.82, 95% CI 1.15-7.02) and for chronic obstructive pulmonary disease and exhaled carbon monoxide with formaldehyde (aOR 3.49 (95% CI 1.17-10.3) and aOR 1.25 (95% CI 1.02-1.55), respectively). Breathlessness and cough were associated with higher carbon dioxide. Relative humidity was inversely related to wheeze in the past year and usual cough. Elderly subjects aged ≥80 years were at higher risk. Pollutant effects were more pronounced in the case of poor ventilation. Even at low levels, indoor air quality affected respiratory health in elderly people permanently living in nursing homes, with frailty increasing with age. The effects were modulated by ventilation