Global characteristics and outcomes of SARS-CoV-2 infection in children and adolescents with cancer (GRCCC): a cohort study

BACKGROUND: Previous studies have shown that children and adolescents with COVID-19 generally have mild disease. Children and adolescents with cancer, however, can have severe disease when infected with respiratory viruses. In this study, we aimed to understand the clinical course and outcomes of SARS-CoV-2 infection in children and adolescents with cancer. METHODS: We did a cohort study with data from 131 institutions in 45 countries. We created the Global Registry of COVID-19 in Childhood Cancer to capture de-identified data pertaining to laboratory-confirmed SARS-CoV-2 infections in children and adolescents (<19 years) with cancer or having received a haematopoietic stem-cell transplantation. There were no centre-specific exclusion criteria. The registry was disseminated through professional networks through email and conferences and health-care providers were invited to submit all qualifying cases. Data for demographics, oncological diagnosis, clinical course, and cancer therapy details were collected. Primary outcomes were disease severity and modification to cancer-directed therapy. The registry remains open to data collection. FINDINGS: Of 1520 submitted episodes, 1500 patients were included in the study between April 15, 2020, and Feb 1, 2021. 1319 patients had complete 30-day follow-up. 259 (19·9%) of 1301 patients had a severe or critical infection, and 50 (3·8%) of 1319 died with the cause attributed to COVID-19 infection. Modifications to cancer-directed therapy occurred in 609 (55·8%) of 1092 patients receiving active oncological treatment. Multivariable analysis revealed several factors associated with severe or critical illness, including World Bank low-income or lower-middle-income (odds ratio [OR] 5·8 [95% CI 3·8-8·8]; p<0·0001) and upper-middle-income (1·6 [1·2-2·2]; p=0·0024) country status; age 15-18 years (1·6 [1·1-2·2]; p=0·013); absolute lymphocyte count of 300 or less cells per mm3 (2·5 [1·8-3·4]; p<0·0001), absolute neutrophil count of 500 or less cells per mm3 (1·8 [1·3-2·4]; p=0·0001), and intensive treatment (1·8 [1·3-2·3]; p=0·0005). Factors associated with treatment modification included upper-middle-income country status (OR 0·5 [95% CI 0·3-0·7]; p=0·0004), primary diagnosis of other haematological malignancies (0·5 [0·3-0·8]; p=0·0088), the presence of one of more COVID-19 symptoms at the time of presentation (1·8 [1·3-2·4]; p=0·0002), and the presence of one or more comorbidities (1·6 [1·1-2·3]; p=0·020). INTERPRETATION: In this global cohort of children and adolescents with cancer and COVID-19, severe and critical illness occurred in one fifth of patients and deaths occurred in a higher proportion than is reported in the literature in the general paediatric population. Additionally, we found that variables associated with treatment modification were not the same as those associated with greater disease severity. These data could inform clinical practice guidelines and raise awareness globally that children and adolescents with cancer are at high-risk of developing severe COVID-19 illness. FUNDING: American Lebanese Syrian Associated Charities and the National Cancer Institute

How do we know that research ethics committees are really working? The neglected role of outcomes assessment in research ethics review

<p>Abstract</p> <p>Background</p> <p>Countries are increasingly devoting significant resources to creating or strengthening research ethics committees, but there has been insufficient attention to assessing whether these committees are actually improving the protection of human research participants.</p> <p>Discussion</p> <p>Research ethics committees face numerous obstacles to achieving their goal of improving research participant protection. These include the inherently amorphous nature of ethics review, the tendency of regulatory systems to encourage a focus on form over substance, financial and resource constraints, and conflicts of interest. Auditing and accreditation programs can improve the quality of ethics review by encouraging the development of standardized policies and procedures, promoting a common base of knowledge, and enhancing the status of research ethics committees within their own institutions. However, these mechanisms focus largely on questions of structure and process and are therefore incapable of answering many critical questions about ethics committees' actual impact on research practices.</p> <p>The first step in determining whether research ethics committees are achieving their intended function is to identify what prospective research participants and their communities hope to get out of the ethics review process. Answers to this question can help guide the development of effective outcomes assessment measures. It is also important to determine whether research ethics committees' guidance to investigators is actually being followed. Finally, the information developed through outcomes assessment must be disseminated to key decision-makers and incorporated into practice. This article offers concrete suggestions for achieving these goals.</p> <p>Conclusion</p> <p>Outcomes assessment of research ethics committees should address the following questions: First, does research ethics committee review improve participants' understanding of the risks and potential benefits of studies? Second, does the process affect prospective participants' decisions about whether to participate in research? Third, does it change participants' subjective experiences in studies or their attitudes about research? Fourth, does it reduce the riskiness of research? Fifth, does it result in more research responsive to the local community's self-identified needs? Sixth, is research ethics committees' guidance to researchers actually being followed?</p

GOssTo : a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology

Summary: We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine. Availability: GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines. \ua9 The Author 2014

Mapping SARS-CoV-2 antigenic relationships and serological responses

During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, multiple variants escaping preexisting immunity emerged, causing reinfections of previously exposed individuals. Here, we used antigenic cartography to analyze patterns of cross-reactivity among 21 variants and 15 groups of human sera obtained after primary infection with 10 different variants or after messenger RNA (mRNA)–1273 or mRNA-1273.351 vaccination. We found antigenic differences among pre-Omicron variants caused by substitutions at spike-protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and &gt;3 months after a second dose. We found changes in immunodominance of different spike regions, depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine-strain selection.</p