Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

The painful crisis of homozygous sickle cell disease: clinical features

The details of onset, perceived precipitating factors, associated symptoms, and pain distribution in the painful crisis of homozygous sickle cell (SS) disease have been prospectively recorded in 183 painful crises in 118 patients admitted to a day-care centre in Kingston, Jamaica. Painful crises developed most frequently between 3 p.m. and midnight, most commonly affected patients aged 15-29 years, affected the sexes equally, and were not obviously influenced by menstrual cycle. Of the perceived precipitating factors, skin cooling occurred in 34%, emotional stress in 10%, physical exertion in 7%, and pregnancy in 5% of women of child-bearing age. Cold as a precipitant was not less common in patients with more subcutaneous fat. Pain affected the lumbar spine in 49%, abdomen in 32%, femoral shaft in 30%, and knees in 21%. There was a highly significant excess of bilateral involvement in limb and rib pain. Recurrent painful crises occurred in 40 patients but showed no evidence of involving similar sites on successive occasions. Abdominal painful crises were associated with abdominal distention in 18 (31%) and with referred rib pain in a further 15 (26%) of crises. Fever was common even in apparently uncomplicated painful crises, suggesting that fever is characteristic of the painful crisis itself and not necessarily indicative of infection. Following investigation and treatment in a day-care centre, over 90% of patients returned hom

Phenotype/genotype relationships in sickle cell disease: a pilot twin study.

The roles of genetic and non-genetic factors in the haematology, growth and clinical features of sickle cell disease have been studied in nine identical twin pairs (six homozygous sickle cell disease, three sickle cell-haemoglobin C disease). A comparison group of 350 age-gender matched sibling pairs, selected to have an age difference of <5 years, was used for assessing the concordance of numerical data. Attained height, weight at attained height, fetal haemoglobin, total haemoglobin, mean cell volume, mean cell haemoglobin and total bilirubin levels showed significantly greater correlation in identical twins than in siblings. Twins showed similarities in the prevalence and degree of splenomegaly, susceptibility to priapism, and in onset of menarche, but other clinical complications were discordant in prevalence and severity. These findings suggest that physical growth and many haematological characteristics are subject to genetic influences, but that non-genetic factors contribute to the variance in disease manifestations

Incremental – Adaptive – Knowledge Based – Learning for Informative Rules Extraction in Classification Analysis of aGvHD

Part 17: BioinformaticsInternational audienceAcute graft-versus-host disease (aGvHD) is a serious systemic complication of allogeneic hematopoietic stem cell transplantation (HSCT) that occurs when alloreactive donor-derived T cells recognize host-recipient antigens as foreign. The early events leading to GvHD seem to occur very soon, presumably within hours from the graft infusion. Therefore, when the first signs of aGvHD clinically manifest, the disease has been ongoing for several days at the cellular level, and the inflammatory cytokine cascade is fully activated. So, it comes as no surprise that to identify biomarker signatures for approaching this very complex task is a critical issue. In the past, we have already approached it through joint molecular and computational analyses of gene expression data proposing a computational framework for this disease. Notwithstanding this, there aren’t in literature quantitative measurements able to identify patterns or rules from these biomarkers or from aGvHD data, thus this is the first work about the issue. In this paper first we have applied different feature selection techniques, combined with different classifiers to detect the aGvHD at onset of clinical signs, then we have focused on the aGvHD scenario and in the knowledge discovery issue of the classification techniques used in the computational framework

Factors affecting prepubertal growth in homozygous sickle cell disease.

OBJECTIVE: To investigate the role of haematological indices, socioeconomic status, and morbidity in prepubertal growth in homozygous sickle cell (SS) disease. METHOD: Height, weight, and haematology were serially recorded in a cohort study of 315 children with SS disease from birth to 9 years at the sickle cell clinic of the University Hospital of the West Indies, Kingston, Jamaica. RESULTS: Height increment between 3 and 9 years correlated positively with total haemoglobin at age 7 years in boys but not girls. Attained height and weight at age 7 years correlated positively with haemoglobin and fetal haemoglobin in boys but not girls. Only the correlation between haemoglobin and weight showed a significant gender difference. Partial correlation analysis suggested that the effect of haemoglobin was accounted for by the effect of fetal haemolglobin and further analysis indicated that height correlated with F reticulocyte count (a measure of fetal haemoglobin production) in both sexes but not with the ratio of F cells to F reticulocytes (a measure of F cell enrichment). Growth was not significantly related to mean red cell volume, proportional reticulocyte count, alpha thalassaemia, socioeconomic status, or morbidity. CONCLUSION: A high concentration of fetal haemoglobin in boys with SS disease is associated with greater linear growth. It is postulated that in boys, low concentrations of fetal haemoglobin increase haemolysis and hence metabolic requirements for erythropoiesis, putting them at greater risk of poor growth. Differences in the relationship of haematology and growth between boys and girls with SS disease dictate that future analyses of growth take gender into account

Stability of resistance to Phytophthora infestans in potato: an international evaluation

Ten institutions in nine countries joined together to test the stability of resistance of 14 potato genotypes to the oomycete pathogen Phytophthora infestans in three separate trials. Seven of the genotypes were tested in one trial involving seven locations, and all 14 were tested in two subsequent trials, each involving eight locations. Stability of resistance was tested with nonparametric tests and with an additive main effects and multiplicative interaction (AMMI) model. Overall, resistance to P. infestans was robust; resistant genotypes were consistently resistant in all locations and trials. The nonparametric analysis indicated that specific genotypes were basically stable across sites for resistance. In trial 3, the Z statistic for overall stability was significant at 0·05%, indicating a significant level of interaction across the trial, but there were no significant interactions for specific genotypes in this trial. The genotype by environment (G × E) effect of the AMMI model was highly significant in both trials, but the mean square of G × E was less than 10% of the genotype effect in each trial. The first two principal components (PCA1 and PCA2) of the AMMI analyses together explained 75 and 80% of the interaction effects in trials 2 and 3, respectively. Based on both nonparametric and AMMI analyses, Ecuador and Argentina were locations of relatively high interaction effects for both trials 2 and 3, although in Ecuador this interaction was not associated with any particular potato genotype. Other locations also had high interaction effects, but these occurred in only one trial. The genotypes Chata Blanca and, to a lesser extent, Torridon were relatively unstable in trials 2 and 3, but in the case of Torridon, resistant, this did not represent a significant loss of resistanc