Probing Non-Canonical A*C Base Pairs in DNA using SERS

Raman spectroscopy probes the vibrational modes of a molecule. In recent years, surface-enhanced Raman spectra (SERS) of oligonucleotides on gold or silver nanoparticles have yielded significantly stronger signals. Raman spectra of DNA are high throughput, quantitative, and label-free and show distinct features created by vibrational modes such as ring deformation, backbone bending, and hydrogen bond stretching. Here we are using gold nanoparticles to probe various structural changes in a short helical DNA designed to mimic SL1 of coronavirus and SL of U6 snRNA. Phosphate buffers containing 1 M KCl or 10 mM magnesium chloride were utilized at two different pH (5.5 and 7). Differences in peak intensity are being observed between canonically paired helical DNA and DNA of similar composition with modifications containing non-canonical A*C base pair. We are comparing ion binding, pH-related, and temperature-variable conditions to observe changes in DNA structures.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

The Thresholds of Caprini Score Associated With Increased Risk of Venous Thromboembolism Across Different Specialties: A Systematic Review.

OBJECTIVE: Estimation of the specific thresholds of the Caprini risk score (CRS) that are associated with the increased incidence of venous thromboembolism (VTE) across different specialties, including identifying the highest level of risk. BACKGROUND: Accurate risk assessment remains an important but often challenging aspect of VTE prophylaxis. One well-established risk assessment model is CRS, which has been validated in thousands of patients from many different medical and surgical specialties. METHODS: A search of MEDLINE and the Cochrane Library was performed in March 2022. Manuscripts that reported on 1) patients admitted to medical or surgical departments and 2) had their VTE risk assessed by CRS and 3) reported on the correlation between the score and VTE incidence, were included in the analysis. RESULTS: A total of 4562 references were identified, and the full text of 202 papers was assessed for eligibility. The correlation between CRS and VTE incidence was reported in 68 studies that enrolled 4,207,895 patients. In all specialties, a significant increase in VTE incidence was observed in patients with a CRS of ≥5. In most specialties thresholds of ≥7, ≥9, and ≥11-12 were associated with dramatically increased incidences of VTE. In COVID-19, cancer, trauma, vascular, general, head and neck, and thoracic surgery patients with ≥9 and ≥11-12 scores the VTE incidence was extremely high (ranging from 13% to 47%). CONCLUSION: The Caprini score is being used increasingly to predict VTE in many medical and surgical specialties. In most cases the VTE risk for individual patients increases dramatically at a threshold CRS of 7-11.

Detailed analysis of in-hospital transmission of SARS-CoV-2 using whole genome sequencing.

BACKGROUND: Hospital transmission of SARS-CoV-2 has proved difficult to control, with healthcare-associated infections troublesome throughout. AIM: To understand factors contributing to hospital transmission of infections, which is necessary for containing spread. METHODS: An outbreak of 56 staff and patient cases of COVID-19 over a 31-day period in a tertiary referral unit is presented, with at least a further 29 cases identified outside of the unit and the hospital by whole genome sequencing (WGS). FINDINGS: Transmission is documented from staff to staff, staff to patients, and patients to staff, showing disruption of a tertiary referral service, despite implementation of nationally recommended control measures, superior ventilation, and use of personal protective equipment. There was extensive spread from the index case, despite this patient spending only 10 h bed bound on the ward in strict cubicle isolation and with an initial single target low level (CT = 32) polymerase chain reaction test. CONCLUSION: This investigation highlights how effectively and rapidly SARS-CoV-2 can spread in certain circumstances. It raises questions about infection control measures in place at the time and calls into question the premise that transmissibility can be reliably detected by using lower sensitivity rapid antigen lateral flow tests. We also highlight the value of early intervention in reducing impact as well as the value of WGS in understanding outbreaks.

Getting to the Heart of In-hospital Transmission of SARS-CoV-2 with the Help of Whole Genome Sequencing

We present an outbreak of 56 staff and patient cases of COVID-19 over a 31 day period in a tertiary referral unit, with at least a further 29 cases identified outside of the unit and the hospital by whole genome sequencing (WGS). We document transmission from staff-to-staff, staff-to-patients and patients-to-staff and show disruption of a tertiary referral service, despite implementation of nationally recommended control measures, superior ventilation and use of PPE. We demonstrate extensive spread from the index case, despite them spending only 10 hours bed bound on the ward in strict cubicle isolation and with an initial single target low level (CT=32) PCR test. This investigation highlights critical issues including how effectively and explosively SARS-CoV-2 can spread in certain circumstances. It raises questions about infection control measures in place at the time and calls into question the premise that transmissibility can be reliably detected using lower sensitivity rapid antigen lateral flow tests. We also highlight the value of early intervention in reducing impact as well as the value of WGS in understanding outbreaks.

The performance of wearable sensors in the detection of SARS-CoV-2 infection: a systematic review

Containing the COVID-19 pandemic requires rapidly identifying infected individuals. Subtle changes in physiological parameters (such as heart rate, respiratory rate, and skin temperature), discernible by wearable devices, could act as early digital biomarkers of infections. Our primary objective was to assess the performance of statistical and algorithmic models using data from wearable devices to detect deviations compatible with a SARS-CoV-2 infection. We searched MEDLINE, Embase, Web of Science, the Cochrane Central Register of Controlled Trials (known as CENTRAL), International Clinical Trials Registry Platform, and ClinicalTrials.gov on July 27, 2021 for publications, preprints, and study protocols describing the use of wearable devices to identify a SARS-CoV-2 infection. Of 3196 records identified and screened, 12 articles and 12 study protocols were analysed. Most included articles had a moderate risk of bias, as per the National Institute of Health Quality Assessment Tool for Observational and Cross-Sectional Studies. The accuracy of algorithmic models to detect SARS-CoV-2 infection varied greatly (area under the curve 0.52-0.92). An algorithm's ability to detect presymptomatic infection varied greatly (from 20% to 88% of cases), from 14 days to 1 day before symptom onset. Increased heart rate was most frequently associated with SARS-CoV-2 infection, along with increased skin temperature and respiratory rate. All 12 protocols described prospective studies that had yet to be completed or to publish their results, including two randomised controlled trials. The evidence surrounding wearable devices in the early detection of SARS-CoV-2 infection is still in an early stage, with a limited overall number of studies identified. However, these studies show promise for the early detection of SARS-CoV-2 infection. Large prospective, and preferably controlled, studies recruiting and retaining larger and more diverse populations are needed to provide further evidence.