Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance.

The COVID-19 pandemic has necessitated the rapid development and implementation of whole-genome sequencing (WGS) and bioinformatic methods for managing the pandemic. However, variability in methods and capabilities between laboratories has posed challenges in ensuring data accuracy. A national working group comprising 18 laboratory scientists and bioinformaticians from Australia and New Zealand was formed to improve data concordance across public health laboratories (PHLs). One effort, presented in this study, sought to understand the impact of the methodology on consensus genome concordance and interpretation. SARS-CoV-2 WGS proficiency testing programme (PTP) data were retrospectively obtained from the 2021 Royal College of Pathologists of Australasia Quality Assurance Programmes (RCPAQAP), which included 11 participating Australian laboratories. The submitted consensus genomes and reads from eight contrived specimens were investigated, focusing on discordant sequence data and findings were presented to the working group to inform best practices. Despite using a variety of laboratory and bioinformatic methods for SARS-CoV-2 WGS, participants largely produced concordant genomes. Two participants returned five discordant sites in a high-Cτ replicate, which could be resolved with reasonable bioinformatic quality thresholds. We noted ten discrepancies in genome assessment that arose from nucleotide heterogeneity at three different sites in three cell-culture-derived control specimens. While these sites were ultimately accurate after considering the participants' bioinformatic parameters, it presented an interesting challenge for developing standards to account for intrahost single nucleotide variation (iSNV). Observed differences had little to no impact on key surveillance metrics, lineage assignment and phylogenetic clustering, while genome coverage <90 % affected both. We recommend PHLs bioinformatically generate two consensus genomes with and without ambiguity thresholds for quality control and downstream analysis, respectively, and adhere to a minimum 90 % genome coverage threshold for inclusion in surveillance interpretations. We also suggest additional PTP assessment criteria, including primer efficiency, detection of iSNVs and minimum genome coverage of 90 %. This study underscores the importance of multidisciplinary national working groups in informing guidelines in real time for bioinformatic quality acceptance criteria. It demonstrates the potential for enhancing public health responses through improved data concordance and quality control in SARS-CoV-2 genomic analysis during pandemic surveillance.

Lab-in-a-van: Rapid SARS-CoV-2 testing response with a mobile laboratory.

BACKGROUND: High testing rates and rapid contact tracing have been key interventions to control COVID-19 in Victoria, Australia. A mobile laboratory (LabVan), for rapid SARS-CoV-2 diagnostics, was deployed at sites deemed critical by the Victorian State Department of Health as part of the response. We describe the process of design, implementation, and performance benchmarked against a central reference laboratory. METHODS: A BSL2 compliant laboratory, complete with a class II biological safety cabinet, was built within a Mercedes-Benz Sprinter Panel Van. Swabs were collected by on-site collection teams, registered using mobile internet-enabled tablets and tested using the Xpert® Xpress SARS-CoV-2 assay. Results were reported remotely via HL7 messaging to Public Health Units. Patients with negative results were automatically notified by mobile telephone text messaging (SMS). FINDINGS: A pilot trial of the LabVan identified a median turnaround time (TAT) from collection to reporting of 1:19 h:mm (IQR 0:18, Range 1:03-18:32) compared to 9:40 h:mm (IQR 8:46, Range 6:51-19:30) for standard processing within the central laboratory. During deployment in nine rural and urban COVID-19 outbreaks the median TAT was 2:18 h:mm (IQR 1:18, Range 0:50-16:52) compared to 19:08 h:mm (IQR 5:49, Range 1:36-58:52) for samples submitted to the central laboratory. No quality control issues were identified in the LabVan. INTERPRETATION: The LabVan is an ISO15189 compliant testing facility fully operationalized for mobile point-of-care testing that significantly reduces TAT for result reporting, facilitating rapid public health actions. FUNDING: This work was supported by the Department of Health, Victoria State Government, Australia.

Experiences of and attitudes to lifestyle modification for the management of multiple sclerosis: A qualitative analysis of free-text survey data.

BACKGROUND: Growing evidence suggests a role of lifestyle modification in improved health outcomes for people with multiple sclerosis (pwMS); however, perspectives of pwMS who engage in lifestyle modification are lacking. OBJECTIVE: We explored perspectives of pwMS regarding the modification of lifestyle-related risk factors in multiple sclerosis (MS) for disease management to understand attitudes to and experiences of lifestyle modification as part of self-management from a patient perspective. DESIGN: Participants were ≥18 years and English speaking who responded to a free-text open-ended question in the Health Outcomes and Lifestyle In a Sample of pwMS (HOLISM), an international online survey. Responses were analysed utilizing inductive thematic analysis. RESULTS: Under the exploration of lifestyle modification, themes describing the experiences and attitudes of participants included practical challenges and physical and psychological barriers, enablers of change and experienced outcomes. Although participants reported some practical and psychological challenges to adoption and maintenance of lifestyle behaviours, many expressed an ability to gain control of MS through engagement with lifestyle behaviours and the development of hope and optimism that accompanied this sense of control, at times leading to a sense of personal transformation. CONCLUSION: Findings highlight the challenges experienced by pwMS in adopting lifestyle modifications for disease management as well as the positive benefits from following healthy lifestyle behaviours. Our findings may form the basis of more focussed qualitative explorations of the experiences and outcomes of lifestyle modification in MS in the future. PATIENT CONTRIBUTION: Consenting pwMS completed a survey capturing data on demographics, clinical course, lifestyle behaviours and health outcomes.

The Effect of an Anti-Inflammatory Botanical Cleanser/Night Mask Combination on Facial Redness Reduction.

Facial redness is a common difficult to control cosmetic problem representing various phases of rosacea. Using anti-inflammatory/antioxidant botanicals in moisturizer formulations is a possible approach to minimizing the erythema. This research utilized a common facial cleanser, but only applied the botanically based moisturizer to one half face to properly assess efficacy. 30 female subjects Fitzpatrick skin types I-IV 30-55 years of age with mild to moderate chronic facial redness, defined as a redness score of 3-6 on a 10-point scale, were enrolled. By the end of week 4, statistically significant improvement was seen on the cleanser/mask treated side in scaling (P less than 0.001), flaking (P less than 0.001), tactile smoothness (P less than 0.001), textural smoothness (P less than 0.001), firmness (P less than 0.001), radiance (P less than 0.001), luminosity (P less than 0.001), and overall appearance (P less than 0.001). Thus, cosmetic moisturizers may be useful in reducing facial redness. J Drugs Dermatol. 2018;17(6):671-676.

The Use of an Over-the-Counter Hand Cream With Sweet Almond Oil for the Treatment of Hand Dermatitis.

Hand dermatitis is estimated to affect greater than 15% of the general population. Childhood eczema, frequent hand washing, and occupational exposure to chemicals are predisposing factors. Hand dermatitis treatment involves both prevention of outbreaks and treatment of active disease. Moisturizers are essential to protect the skin from the environment, enhance hydration, and repair the skin barrier. They have been shown in large studies to prevent occupational related breakouts. Natural oils are commonly used in moisturizers for their moisturizing and emollient properties. Sweet almond oil is an oil that contains high levels of fatty acids and has been used for centuries to treat skin diseases such as eczema and psoriasis. In this study, a moisturizer with 7% sweet almond oil and 2% colloidal oatmeal was found to be both safe and effective in treating patients with moderate to severe hand dermatitis.

J Drugs Dermatol. 2018;17(1):78-82.