Optimisation and evaluation of viral genomic sequencing of SARS-CoV-2 rapid diagnostic tests: a laboratory and cohort-based study.

BACKGROUND: Sequencing of SARS-CoV-2 from rapid diagnostic tests (RDTs) can bolster viral genomic surveillance efforts; however, approaches to maximise and standardise pathogen genome recovery from RDTs remain underdeveloped. We aimed to systematically optimise the elution of genetic material from RDT components and to evaluate the efficacy of RDT sequencing for outbreak investigation. METHODS: In this laboratory and cohort-based study we seeded RDTs with inactivated SARS-CoV-2 to optimise the elution of genomic material from RDT lateral flow strips. We measured the effect of changes in buffer type, time in buffer, and rotation on PCR cycle threshold (Ct) value. We recruited individuals older than 18 years residing in the greater Boston area, MA, USA, from July 18 to Nov 5, 2022, via email advertising to students and staff at Harvard University, MA, USA, and via broad social media advertising. All individuals recruited were within 5 days of a positive diagnostic test for SARS-CoV-2; no other relevant exclusion criteria were applied. Each individual completed two RDTs and one PCR swab. On Dec 29, 2022, we also collected RDTs from a convenience sample of individuals who were positive for SARS-CoV-2 and associated with an outbreak at a senior housing facility in MA, USA. We extracted all returned PCR swabs and RDT components (ie, swab, strip, or buffer); samples with a Ct of less than 40 were subject to amplicon sequencing. We compared the efficacy of elution and sequencing across RDT brands and components and used RDT-derived sequences to infer transmission links within the outbreak at the senior housing facility. We conducted metagenomic sequencing of negative RDTs from symptomatic individuals living in the senior housing facility. FINDINGS: Neither elution duration of greater than 10 min nor rotation during elution impacted viral titres. Elution in Buffer AVL (Ct=31·4) and Tris-EDTA Buffer (Ct=30·8) were equivalent (p=0·34); AVL outperformed elution in lysis buffer and 50% lysis buffer (Ct=40·0, p=0·0029 for both) as well as Universal Viral Transport Medium (Ct=36·7, p=0·079). Performance of RDT strips was poorer than that of matched PCR swabs (mean Ct difference 10·2 [SD 4·3], p<0·0001); however, RDT swabs performed similarly to PCR swabs (mean Ct difference 4·1 [5·2], p=0·055). No RDT brand significantly outperformed another. Across sample types, viral load predicted the viral genome assembly length. We assembled greater than 80% complete genomes from 12 of 17 RDT-derived swabs, three of 18 strips, and four of 11 residual buffers. We generated outbreak-associated SARS-CoV-2 genomes using both amplicon and metagenomic sequencing and identified multiple introductions of the virus that resulted in downstream transmission. INTERPRETATION: RDT-derived swabs are a reasonable alternative to PCR swabs for viral genomic surveillance and outbreak investigation. RDT-derived lateral flow strips yield accurate, but significantly fewer, viral reads than matched PCR swabs. Metagenomic sequencing of negative RDTs can identify viruses that might underlie patient symptoms. FUNDING: The National Science Foundation, the Hertz Foundation, the National Institute of General Medical Sciences, Harvard Medical School, the Howard Hughes Medical Institute, the US Centers for Disease Control and Prevention, the Broad Institute and the National Institute of Allergy and Infectious Diseases.

Association between viral infections and glioma risk: a two-sample bidirectional Mendelian randomization analysis.

BACKGROUND: Glioma is one of the leading types of brain tumor, but few etiologic factors of primary glioma have been identified. Previous observational research has shown an association between viral infection and glioma risk. In this study, we used Mendelian randomization (MR) analysis to explore the direction and magnitude of the causal relationship between viral infection and glioma. METHODS: We conducted a two-sample bidirectional MR analysis using genome-wide association study (GWAS) data. Summary statistics data of glioma were collected from the largest meta-analysis GWAS, involving 12,488 cases and 18,169 controls. Single-nucleotide polymorphisms (SNPs) associated with exposures were used as instrumental variables to estimate the causal relationship between glioma and twelve types of viral infections from corresponding GWAS data. In addition, sensitivity analyses were performed. RESULTS: After correcting for multiple tests and sensitivity analysis, we detected that genetically predicted herpes zoster (caused by Varicella zoster virus (VZV) infection) significantly decreased risk of low-grade glioma (LGG) development (OR = 0.85, 95% CI: 0.76-0.96, P = 0.01, FDR = 0.04). No causal effects of the other eleven viral infections on glioma and reverse causality were detected. CONCLUSIONS: This is one of the first and largest studies in this field. We show robust evidence supporting that genetically predicted herpes zoster caused by VZV infection reduces risk of LGG. The findings of our research advance understanding of the etiology of glioma.

Evaluating hematologic parameters in newly diagnosed and recurrent glioblastoma: Prognostic utility and clinical trial implications of myelosuppression.

Background: Glioblastoma (GBM) patients are treated with radiation therapy, chemotherapy, and corticosteroids, which can cause myelosuppression. To understand the relative prognostic utility of blood-based biomarkers in GBM and its implications for clinical trial design, we examined the incidence, predictors, and prognostic value of lymphopenia, neutrophil-to-lymphocyte ratio (NLR), and platelet count during chemoradiation (CRT) and recurrence. Methods: This cohort study included 764 newly diagnosed glioblastoma patients treated from 2005 to 2019 with blood counts prior to surgery, within 6 weeks of CRT, and at first recurrence available for automatic extraction from the medical record. Logistic regression was used to evaluate exposures and Kaplan-Meier was used to evaluate outcomes. Results: Among the cohort, median age was 60.3 years; 87% had Karnofsky performance status ≥ 70, 37.5% had gross total resection, and 90% received temozolomide (TMZ). During CRT, 37.8% (248/656) of patients developed grade 3 or higher lymphopenia. On multivariable analysis (MVA), high NLR during CRT remained an independent predictor for inferior survival (Adjusted Hazard Ratio [AHR] = 1.57, 95% CI = 1.14-2.15) and shorter progression-free survival (AHR = 1.42, 95% CI = 1.05-1.90). Steroid use was associated with lymphopenia (OR = 2.66,1.20-6.00) and high NLR (OR = 3.54,2.08-6.11). Female sex was associated with lymphopenia (OR = 2.33,1.03-5.33). At first recurrence, 28% of patients exhibited grade 3 or higher lymphopenia. High NLR at recurrence was associated with worse subsequent survival on MVA (AHR = 1.69, 95% CI = 1.25-2.27). Conclusions: High NLR is associated with worse outcomes in newly diagnosed and recurrent glioblastoma. Appropriate eligibility criteria and accounting and reporting of blood-based biomarkers are important in the design and interpretation of newly diagnosed and recurrent glioblastoma trials.

The Role of Moderators in Facilitating and Encouraging Peer-to-Peer Support in an Online Mental Health Community: A Qualitative Exploratory Study.

Online peer support platforms have gained popularity as a potential way for people struggling with mental health problems to share information and provide support to each other. While these platforms can offer an open space to discuss emotionally difficult issues, unsafe or unmoderated communities can allow potential harm to users by spreading triggering content, misinformation or hostile interactions. The purpose of this study was to explore the role of moderators in these online communities, and how moderators can facilitate peer-to-peer support, while minimizing harms to users and amplifying potential benefits. Moderators of the Togetherall peer support platform were recruited to participate in qualitative interviews. The moderators, referred to as 'Wall Guides', were asked about their day-to-day responsibilities, positive and negative experiences they have witnessed on the platform and the strategies they employ when encountering problems such as lack of engagement or posting of inappropriate content. The data were then analyzed qualitatively using thematic content analysis and consensus codes were deduced and reviewed to reach final results and representative themes. In total, 20 moderators participated in this study, and described their experiences and efforts to follow a consistent and shared protocol for responding to common scenarios in the online community. Many reported the deep connections formed by the online community, the helpful and thoughtful responses that members give each other and the satisfaction of seeing progress in members' recovery. They also reported occasional aggressive, sensitive or inconsiderate comments and posts on the platform. They respond by removing or revising the hurtful post or reaching out to the affected member to maintain the 'house rules'. Lastly, many discussed strategies they elicit to promote engagement from members within the community and ensure each member is supported through their use of the platform. This study sheds light on the critical role of moderators of online peer support communities, and their ability to contribute to the potential benefits of digital peer support while minimizing risks to users. The findings reported here accentuate the importance of having well-trained moderators on online peer support platforms and can guide future efforts to effectively train and supervise prospective peer support moderators. Moderators can become an active 'shaping force' and bring a cohesive culture of expressed empathy, sensitivity and care. The delivery of a healthy and safe community contrasts starkly with non-moderated online forums, which can become unhealthy and unsafe as a result.

Predicting glioblastoma molecular subtypes and prognosis with a multimodal model integrating convolutional neural network, radiomics, and semantics.

OBJECTIVE: The aim of this study was to build a convolutional neural network (CNN)-based prediction model of glioblastoma (GBM) molecular subtype diagnosis and prognosis with multimodal features. METHODS: In total, 222 GBM patients were included in the training set from Sun Yat-sen University Cancer Center (SYSUCC) and 107 GBM patients were included in the validation set from SYSUCC, Xuanwu Hospital Capital Medical University, and the First Hospital of Jilin University. The multimodal model was trained with MR images (pre- and postcontrast T1-weighted images and T2-weighted images), corresponding MRI impression, and clinical patient information. First, the original images were segmented using the Multimodal Brain Tumor Image Segmentation Benchmark toolkit. Convolutional features were extracted using 3D residual deep neural network (ResNet50) and convolutional 3D (C3D). Radiomic features were extracted using pyradiomics. Report texts were converted to word embedding using word2vec. These three types of features were then integrated to train neural networks. Accuracy, precision, recall, and F1-score were used to evaluate the model performance. RESULTS: The C3D-based model yielded the highest accuracy of 91.11% in the prediction of IDH1 mutation status. Importantly, the addition of semantics improved precision by 11.21% and recall in MGMT promoter methylation status prediction by 14.28%. The areas under the receiver operating characteristic curves of the C3D-based model in the IDH1, ATRX, MGMT, and 1-year prognosis groups were 0.976, 0.953, 0.955, and 0.976, respectively. In external validation, the C3D-based model showed significant improvement in accuracy in the IDH1, ATRX, MGMT, and 1-year prognosis groups, which were 88.30%, 76.67%, 85.71%, and 85.71%, respectively (compared with 3D ResNet50: 83.51%, 66.67%, 82.14%, and 70.79%, respectively). CONCLUSIONS: The authors propose a novel multimodal model integrating C3D, radiomics, and semantics, which had a great performance in predicting IDH1, ATRX, and MGMT molecular subtypes and the 1-year prognosis of GBM.

Tangent normalization for somatic copy-number inference in cancer genome analysis.

MOTIVATION: Somatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of The Cancer Genome Atlas, the Broad Institute Genome Characterization Center developed the Tangent normalization method to generate copy-number profiles using data from single-nucleotide polymorphism (SNP) arrays and whole-exome sequencing (WES) technologies for over 10 000 pairs of tumors and matched normal samples. Here, we describe the Tangent method, which uses a unique linear combination of normal samples as a reference for each tumor sample, to subtract systematic errors that vary across samples. We also describe a modification of Tangent, called Pseudo-Tangent, which enables denoising through comparisons between tumor profiles when few normal samples are available. RESULTS: Tangent normalization substantially increases signal-to-noise ratios (SNRs) compared to conventional normalization methods in both SNP array and WES analyses. Tangent and Pseudo-Tangent normalizations improve the SNR by reducing noise with minimal effect on signal and exceed the contribution of other steps in the analysis such as choice of segmentation algorithm. Tangent and Pseudo-Tangent are broadly applicable and enable more accurate inference of SCNAs from DNA sequencing and array data. AVAILABILITY AND IMPLEMENTATION: Tangent is available at https://github.com/broadinstitute/tangent and as a Docker image (https://hub.docker.com/r/broadinstitute/tangent). Tangent is also the normalization method for the copy-number pipeline in Genome Analysis Toolkit 4 (GATK4). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Structural variants shape driver combinations and outcomes in pediatric high-grade glioma.

We analyzed the contributions of structural variants (SVs) to gliomagenesis across 179 pediatric high-grade gliomas (pHGGs). The most recurrent SVs targeted MYC isoforms and receptor tyrosine kinases (RTKs), including an SV amplifying a MYC enhancer in 12% of diffuse midline gliomas (DMG), indicating an underappreciated role for MYC in pHGG. SV signature analysis revealed that tumors with simple signatures were TP53 wild type (TP53WT) but showed alterations in TP53 pathway members PPM1D and MDM4. Complex signatures were associated with direct aberrations in TP53, CDKN2A and RB1 early in tumor evolution and with later-occurring extrachromosomal amplicons. All pHGGs exhibited at least one simple-SV signature, but complex-SV signatures were primarily restricted to subsets of H3.3K27M DMGs and hemispheric pHGGs. Importantly, DMGs with complex-SV signatures were associated with shorter overall survival independent of histone mutation and TP53 status. These data provide insight into the impact of SVs on gliomagenesis and the mechanisms that shape them.

Sequence and vector shapes vaccine induced antibody effector functions in HIV vaccine trials.

Despite the advent of long-acting anti-retroviral therapy able to control and prevent infection, a preventative vaccine remains a global priority for the elimination of HIV. The moderately protective RV144 vaccine trial suggested functional IgG1 and IgG3 antibodies were a potential correlate of protection, but the RV144-inspired HVTN702 validation trial failed to demonstrate efficacy despite inducing targeted levels of IgG1/IgG3. Alterations in inserts, and antigens, adjuvant, and regimen also resulted in vaccine induced target quantitative levels of the immune correlates, but drove qualitative changes to the humoral immune response, pointing to the urgent need to define the influence of vaccine strategies on shaping antibody quality, not just quantity. Thus, defining how distinct prime/boost approaches tune long-lived functional antibodies represents an important goal in vaccine development. Here, we compared vaccine responses in Phase I and II studies in humans utilizing various combinations of DNA/vector, vector/vector and DNA/protein HIV vaccines. We found that adenoviral vector immunization, compared to pox-viral vectors, resulted in the most potent IgG1 and IgG3 responses, linked to highly functional antibody activity, including assisting NK cell related functions. Minimal differences were observed in the durability of the functional humoral immune response across vaccine regimens, except for antibody dependent phagocytic function, which persisted for longer periods in the DNA/rAd5 and rAd35/rAd5 regimen, likely driven by higher IgG1 levels. Collectively, these findings suggest adenoviral vectors drive superior antibody quality and durability that could inform future clinical vaccine studies. Trial registration: ClinicalTrials.gov NCT00801697, NCT00961883, NCT02207920, NCT00125970, NCT02852005).

Addressing Mental Health Stigma in Low-Income and Middle-Income Countries: A New Frontier for Digital Mental Health.

BACKGROUND: Mental health stigma is a major barrier to seeking help, and leads to poor quality of life and social withdrawal for individuals living with mental illness. These concerns are especially severe in low-income and middle-income countries (LMICs) that face a disproportionate share of the global burden of mental illnesses. With growing access to digital technologies in LMICs, there may be new opportunities to address mental health stigma. This review considers the potential for emerging digital technologies to advance efforts to challenge mental health stigma in LMICs. METHODS: Promising digital strategies to reduce mental health stigma were identified through searching the peer-reviewed literature. Drawing from the Mental Illness Stigma Framework, these studies of digital strategies were grouped into three categories: 1) protest; 2) education, and 3) contact. RESULTS: These three categories align with established stigma reduction programs. Digital strategies could expand the reach of or complement existing efforts. There are challenges with digital stigma reduction strategies, including the need for cultural adaptation of these programs to diverse contexts and settings, consideration of reliable measurement of mental health related stigma, and risks that digital media could perpetuate the spread of misinformation and exacerbate concerns pertaining to mental health stigma. CONCLUSION: This review highlights the promise of technology for addressing mental health stigma in LMICs. This is imperative in the face of growing demand for mental health services owing to the economic and social impacts of the COVID-19 pandemic, and the increasing reliance on digital platforms among individuals in most countries.

The emergence of digital mental health in low-income and middle-income countries: A review of recent advances and implications for the treatment and prevention of mental disorders.

In low-income and middle-income countries (LMICs), emerging digital mental health interventions should be accompanied by regular and comprehensive assessment of available scientific evidence. This review aims to support efforts to monitor progress in digital mental health research, ensuring new evidence can guide researchers, clinicians, policymakers and program managers positioned to adopt and implement these digitally-enabled treatments. In accordance with PRISMA guidelines, an electronic database search from 2016 to 2020 yielded 37 digital intervention studies for detection, diagnosis, prevention, treatment, and/or management of a broad range of mental disorders in 13 LMICs. This date range was selected to update previous reviews. Most studies involved online interventions and many reported feasibility and acceptability, reflected by participant satisfaction or program adherence. About half the studies (N = 23) reported clinical benefits based on changes in mental health. For depression and mood disorders, some digital interventions showed improvements in depressive symptoms, quality of life, treatment adherence, and recovery. However, sample sizes were small and studies focused primarily on adults. Further limiting generalizability was the lack of consistency in clinical assessment and measurement tools between studies. No studies reported worsening symptoms, negative acceptability or dissatisfaction with digital interventions, suggesting possible publication bias. While digital interventions show promise, it remains difficult to conclude that digital interventions are effective from these studies, as it is prudent to exercise caution before drawing conclusions about clinical effectiveness. This review reflects continued growth in digital mental health research in LMICs and further highlights the need for rigorous evaluation of effectiveness and cost-effectiveness.

Psychological Impact of COVID-19 Pandemic on Frontline Health Workers in Low- and Middle-Income Countries.

Healthcare systems in many countries have been overwhelmed by the coronavirus disease (COVID-19) pandemic, with increasing demands to contain and respond to the virus. The result has been increased pressure on frontline health workers. As the pandemic unfolds, the impact on health systems in low-income and middle-income countries (LMICs) is becoming apparent. In lower resource settings, the detrimental effects on frontline health workers will likely be significant due to fragmented infrastructure, low compensation, and significant shortages of necessary resources such as personal protective equipment. These high stress conditions, coupled with risk of infection and fears and anxieties among patients, can result in grave psychosocial consequences for frontline health workers, who play a vital role in delivering the bulk of primary care services in LMICs. In this narrative review, we consider the psychological impact of the COVID-19 pandemic on frontline health workers in LMICs. We describe the important role of frontline health workers, summarize existing literature on burnout and risks to mental health in this essential workforce, and consider how public health emergencies exacerbate these concerns to showcase their vulnerability to mental health impacts of COVID-19. We explore emerging research on the detrimental effects of the COVID-19 pandemic on health workers and consider possible approaches to mitigate these consequences. This review draws from existing studies and emerging evidence to highlight the critical need to consider the wellbeing of frontline health workers, and to address these challenges as health systems respond to the pandemic.