Machine learning uncovers blood test patterns subphenotypes at hospital admission discerning increased 30-day ICU mortality rates in COVID-19 elderly patients

Introduction: Since March 2020, a number of SARS-CoV-2 patients have frequently required intensive care unit (ICU) admission, associated with moderate survival outcomes and an increasing economic burden. Elderly patients are among the most numerous, due to previous comorbidities and complications they develop during hospitalization [1]. For this reason, a reliable early risk stratification tool could help estimate an early prognosis and allow for an appropriate resources allocation in favour of the most vulnerable and critically ill patients. Method(s): This retrospective study includes data from two Spanish hospitals, HU12O (Madrid) and HCUV (Valencia), from 193 patients aged > 64 with COVID-19 between February and November 2020 who were admitted to the ICU. Variables include demographics, full-blood-count (FBC) tests and clinical outcomes. Machine learning applied a non-linear dimensionality reduction by t-distributed stochastic neighbor embedding (t-SNE) [2];then hierarchical clustering on the t-SNE output was performed. The number of clinically relevant subphenotypes was chosen by combining silhouette and elbow coefficients, and validated through exploratory analysis. Result(s): We identified five subphenotypes with heterogeneous interclustering age and FBC patterns (Fig. 1). Cluster 1 was the 'healthiest' phenotype, with 2% 30-day mortality and characterized by moderate leukocytes and eosinophils. Cluster 5, the severe phenotype, showed 44% 30-day mortality and was characterized by the highest leukocyte, neutrophil and platelet count and minimal monocytes and lymphocyte count. Clusters 2-4 displayed intermediate mortality rates (20-28%). Conclusion(s): The findings of this preliminary report of Eld-ICUCOV19 patients suggest the patient's FBC and age can display discriminative patterns associated with disparate 30-day ICU mortality rates.

Study of the Relationships between COVID-19, Associated Diseases, and Vitamins

Background: Some vitamins play a beneficial role in the immune system and certain diseases may be associated with an increase in the number of COVID-19 cases and mortality. Objective(s): In this work, we aim to verify a possible relationship between vitamin A, vitamin D, sunlight, and COVID-19 cases and mortality. We also aim to study the relationship between chronic diseases and COVID-19 in the world. Method(s): We consulted online databases (Johns Hopkins, World Life Expectancy, NASA, and World Health Organization) and used SPSS (v23) for statistical analysis. Result(s): We found that countries with the highest number of cases and deaths by COVID-19 are the countries with the highest death rates from different types of cancer and multiple sclerosis. Besides, the relationship between cancer death rate and COVID-19 is not biased by the life expectancy. We also found that the low solar incidence and low vitamins A and D levels can be related to the number of cases and deaths by COVID-19. Conclusion(s): Our findings suggest a relationship between different cancer types and multiple sclerosis death rates and COVID-19. We also recommend that vitamins D and A may play a protective role in COVID-19 infection.Copyright © 2021 Bentham Science Publishers.

Predicting the potential for zoonotic transmission and host associations for novel viruses.

Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host-range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as hosts for 513 newly discovered viruses detected by large-scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.

Detecting Polarized Topics Using Partisanship-aware Contextualized Topic Embeddings

Growing polarization of the news media has been blamed for fanning disagreement, controversy and even violence. Early identification of polarized topics is thus an urgent matter that can help mitigate conflict. However, accurate measurement of topic-wise polarization is still an open research challenge. To address this gap, we propose Partisanship-aware Contextualized Topic Embeddings (PaCTE), a method to automatically detect polarized topics from partisan news sources. Specifically, utilizing a language model that has been finetuned on recognizing partisanship of the news articles, we represent the ideology of a news corpus on a topic by corpus-contextualized topic embedding and measure the polarization using cosine distance. We apply our method to a dataset of news articles about the COVID19 pandemic. Extensive experiments on different news sources and topics demonstrate the efficacy of our method to capture topical polarization, as indicated by its effectiveness of retrieving the most polarized topics. © 2021 Association for Computational Linguistics.

Early effects of the COVID-19 outbreak on the African dairy industry: cases of Burkina Faso, Kenya, Madagascar, and Senegal. (Agriculture et syst..mes alimentaires face .. la Covid-19.)

This paper provides an early assessment of the effects of the COVID-19 outbreak and of subsequent response measures on milk production, collection, processing, marketing and consumption in Africa. The researchers focus on the period surrounding the first wave of the outbreak (from February to June 2020), during which the number of cases surged and many steps were taken to curb the epidemic. The paper is based on reports from four countries covered by the Africa-Milk Research Project: Burkina Faso, Kenya, Madagascar and Senegal. Data was collected primarily from nine dairy processors located in those countries. Major conclusions of the study are: (1) Dairy farmers were negatively affected by COVID-19 measures when the health crisis coincided with the peak of the milk production season, and when governments did not take steps to support milk production. (2) Small and informal milk collectors were also affected by traffic restrictions as they could not obtain traffic permits. (3) Milk powder importation remained unaffected during the outbreak. (4) Dairy processors (particularly small ones) faced many challenges restricting their operation. Travel restrictions led to temporary interruptions of milk supply, and because of employee protection and safety measures, processing costs increased. (5) Many small retailers were affected by bans on public transport and reduced their purchases of artisanal dairy products;meanwhile, spoilage of dairy products increased during long curfews coupled with poor storage conditions. Supermarkets were able to increase their market share during the pandemic thanks to their connections with industrial dairy processors and wholesalers. (6) A majority of consumers decreased their consumption of dairy products due to a decrease of purchasing power. In some cases, an increase in consumption occurred (due to Ramadan month and dry season high temperatures) and consumption shifted towards long-life dairy products. (7) Overall, the consequences of the health crisis affected more small and informal dairy supply chains than the larger ones, which are more formal, better organised and finally more resilient to face this kind of global crisis.

Cardiopulmonary exercise test in patients with persistent dyspnea after COVID-19 disease

Introduction: Persistent dyspnea in patients who have suffered from COVID-19 disease has become a constant in cardiology in recent months. Healther workers have been one of the population groups mainly affected during the pandemic. Chronic involvement by COVID-19 infection, such as dyspnea, is frequent, and so far, of unknown mechanism. CardioPulmonary Exercise Test (CPET) is currently the gold standard technique in the differential diagnosis of dyspnea. Therefore, CPET could be useful in the evaluation of patients after infection by the SARS-COV2 virus;a role still unknown in this context. Objective: Evaluate the parameters obtained in CPET in patients who had suffered from COVID-19 disease and who presented persistent dyspnea. Methods: We conducted a single-center and prospective study that included healthcare workers who suffered from COVID-19 disease with mildmoderate intensity symptoms, without the need for hospitalization, between March-December 2020 and who presented dyspnea on exertion at least 3 months after infection, in the absence of structural heart disease. An echo was performed, and a baseline spirometry followed by a CPET. Some of the variables collected such as VO2, OUES and PulseO2 have been quantified as a percentage (%) of the predicted according to predicted equations. Results: 64 healthy patients with an active baseline life (without exertional dyspnea prior to infection) were included. 7 patients were excluded for presenting previously unknown structural heart disease. Of the 57 patients (Figure 1), more than half had a functional capacity lower than predicted (50th percentile), highlighting, among the cardiovascular response variables, a peak VO2 of 79% (SD: 14.0%) of the predicted, denoting slightly depressed functional capacity. In addition, in this subgroup, a VO2 at the level of the first ventilatory threshold (VT1) of 51.1% (SD: 4.2%) is observed over the predicted value -value that is considered in the lower limits of normality-;and a PulseO2 (systolic volume reflex) and an OUES in normal ranges with respect to those predicted. In the total of the 57 patients, no alterations were observed in the ventilatory efficiency parameters with effort, nor in the baseline spirometry, nor in the breathing reserve (BR), nor in final oxygen saturation (SatO2). Conclusion: CPET has made it possible to identify that more than half of the patients show a deterioration -at least slight- in functional capacity (the majority of which are women) reaffirming the value of this test. The combination of this pattern that we observed in our serie is usually seen in patients with physical deconditioning and/or obesity, and is secondary to alterations in the peripheral use of oxygen, mainly at the muscular level. Based on this, a direct or indirect potential myopathic effect of the virus cannot be ruled out as responsible for the deterioration of the functional class of patients after COVID-19 disease. (Figure Presented).

Psychosocial impacts of COVID-19 in the Guinean population. An online cross-sectional survey

Guinea, like many other African countries, has been facing an unprecedented COVID-19 outbreak, since March 2020. In April 2020, Guinean National agency for health security recorded 1351 confirmed cases of COVID-19, including 313 recoveries and 07 deaths. To address this health crisis, some drastic measures were implemented to prevent the spread of COVID-19. Those measures might potentially cause some psychological problems among Guineans. Thus, we conducted this study to assess the psychosocial impacts of COVID-19 in the Guinean population. We carried out an online cross-sectional survey among internet users in Guinea. A free e-survey platform was used, and questionnaires were sent to internet users. The study ran from May 1 through May 10 2020. Participation in the study was voluntary. Data collection was based on sociodemographic information and self-reported questionnaires: Impact of Event Scale-Revised (IES-R) for stress evaluation, Penn state worry questionnaire (PSWQ), and an adapted Social Psychological Measurements of COVID-19. A total of 280 participants took part in the study;responses from 5 participants were deleted because of incompleteness. The average age of participants was 28.9 [95% CI: 28.1;29.6]. Most of participants were male 65.5% [95% CI: 59.5%;71.1%]. Unemployed participants stood for 48.7% [95% CI: 42.7%;54.8%]. IES-R scale for stress evaluation yielded the following findings: 19.6% (mild), 5.23% (moderate) and 9.15% (severe);82.8% and 17.2% of participants had respectively reported low and moderate worry. No significant statistical association was found between sociodemographic variables and traumatic events (IES-R and PSWQ). However, 82% of our participants had to cope with the negative impacts of COVID-19. Although there were few cases of traumatic events, negative impacts of COVID-19 on study participants deserve to be underlined. So, further investigations are necessary to identify and disentangle specific psychosocial problems in different Guinean socio-cultural contexts.

Prédiction de la gravité de la COVID-19 à l’admission à l’aide du Score NEWS2 : étude transversale au Maroc

Introduction Certains patients atteints de la COVID-19 sont plus susceptibles de développer une forme grave ou des complications de la maladie. Leur identification à l’admission faciliterait la prise en charge immédiate. Le « National Early Warning Score 2 » (NEWS2) est un score de stratification des risques chez les patients atteints de septicémie et de pneumonie. L’OMS et le Royal College of Physicians of London (RCP) recommandent l’utilisation du score NEWS2 dans le cadre de la COVID-19 pour la stratification du risque chez les patients. L’objectif de cette étude était d’identifier les patients ayant une forme grave à l’admission aux urgences à l’aide du score NEWS2 au Maroc. Méthodes Il s’agit d’une étude transversale réalisée à l’Hôpital universitaire Cheikh Khalifa de Casablanca, Maroc du 15 avril au 15 juin 2020. Seuls les patients âgés de 18 ans ou plus, avec COVID-19 confirmé par RT-PCR ont été inclus dans cette étude. Les données sociodémographiques et les manifestations cliniques à l’admission ont été collectées et le score NEWS2 a été calculé pour chaque patient. Les patients ayant une forme grave ont été définis comme étant ceux qui sont admis à l’unité de soins intensifs. La régression logistique a été utilisée pour explorer la prédiction de la gravité de la COVID-19 par le Score NEWS2. Résultats Au total, 134 patients ont été retenus dans notre étude avec une moyenne d’âge de 50,8±17,9 dont 54,5 % étaient des hommes, 30,8 % présentaient un état grave. La moyenne d’âge dans le groupe des patients graves était significativement plus élevée que celle dans le groupe non grave (64,20±12,13 versus 44,03±16,66 ans ;p<0,001). La comorbidité était significative chez le groupe des patients graves (75,6 % versus 28,1 % ;p<0,001). La moyenne du score NEWS2 était élevée chez les patients graves comparativement aux non graves (5,9±2,4 versus 1,2±1,5 ;p<0,001). Après ajustement sur les facteurs de confusion, OR ajusté=3,03 (1,85-4,94), p<0,001. Conclusion Nos résultats montrent que le score NEWS2 réalisé à l’admission permet d’identifier les patients présentant des états graves. Il pourrait fournir aux équipes d’urgence un outil complémentaire efficace de stratification des risques pour les patients gravement atteints de la COVID-19. D’autres études avec un grand échantillon seraient intéressantes pour confirmer les résultats de cette étude. Figure : http://extranet.insight-outside.fr/upload/compte1352/Base/inscriptions_projets/image/100131-image.pdf

[Impact of the COVID-19 pandemic on the activities of the cardiology department of the Ignace Deen National Hospital at the Conakry University Hospital]. / Impact de la pandémie de COVID-19 sur les activités du service de cardiologie de l'hôpital national Ignace Deen du CHU de Conakry.

The new coronavirus pandemic (COVID-19) is the main global health crisis of our time and the greatest threat we have faced in this century. According to the National Health Security Agency (ANSS), which is the national body responsible for managing epidemics and pandemics, 1927 cases of COVID-19 were confirmed, 11 deaths with more than 4000 contact subjects. The objective of this study was to assess the impact of the COVID-19 pandemic on the activities of the cardiology department of the Ignace Deen National Hospital at the Conakry University Hospital. This was a descriptive retrospective study from January 2020 to April 2020, focusing on consultation and hospitalisation activities in the cardiology department of Ignace Deen National Hospital at Conakry University Hospital. The study consisted of assessing the impact of the pandemic on patient use of the service during the first weeks of the pandemic. We recorded the frequency of consultations and hospitalisations from March to April 2020, which we compared to the frequency of consultations and hospitalisations in January and February 2020. During this study from March to April 2020, we identified 130 patients in consultation against 450 patients for the two months preceding the official declaration of the pandemic in Guinea, a drop of 71.1% (320 patients). The same remark was made in hospitalisation with a drop of 75% (35 patients against 140 for the two months preceding the pandemic). At the start of the COVID-19 pandemic in Guinea, it is clear that there has been a rapid and significant drop in the effective use of the cardiology service.

Caractéristiques épidémiologiques et cliniques des patients COVID-19 admis en réanimation à l’hôpital Donka de Conakry, Guinée: étude descriptive des 140 premiers cas hospitalisés

Résumé Objectif Décrire les caractéristiques épidémiologiques et cliniques des patients COVID-19 admis au service de réanimation. Méthodes Il s’agissait d’une étude prospective observationnelle de 4 mois (12 mars au 12 juillet) réalisée au service de réanimation du Centre de Traitement COVID-19 de l’hôpital national Donka. Résultats Durant la période d’étude, 6044 malades ont été testés positifs au SARS-CoV-2,140 parmi eux ont été admis en réanimation soit une prévalence de 2,3 %. L’âge moyen des patients était de 59 ± 14ans. La majorité des patients (79 %) était de sexe masculin. Concernant les comorbidités, 77 % des patients avaient au moins une comorbidité médicale dont l’hypertension artérielle (55 %) et le diabète (38 %). Les signes cliniques les plus fréquents étaient la dyspnée, (81 %), l’asthénie physique (64 %) et la toux (60 %). La majorité de nos patients (91 %) a bénéficié d’une oxygénothérapie classique. Le Syndrome de Détresse Respiratoire Aiguë (SDRA) était la complication la plus représentée (38 %). Le taux de létalité était de 25 % sur l’ensemble des patients admis en réanimation. Conclusion Une faible proportion de patients COVID-19 ont été admis en réanimation. Ces patients étaient principalement des personnes âgées, de sexe masculin ayant au moins une comorbidité. La symptomatologie était dominée par la dyspnée et les complications par le SDRA. La létalité était comparable en Europe et aux États-Unis. Objective To describe the epidemiological and clinical characteristics of COVID-19 patients admitted to the intensive care unit. Methods This was a 4-month (from the 12th of March to the 12th of July) prospective and observational study carried out in the intensive care unit of the COVID-19 Treatment Centre at Donka National Hospital, Conakry, Guinea. Results During the duration of the study, 6044 patients tested positive for SARS-CoV-2, of whom 140 were admitted to intensive care, i.e. 2.31%. The average age of the patients was 59 ± 14 years. The majority of patients were male, 79% (n = 110). Concerning co-morbidities, 77% (n = 108) of the patients had at least 1 medical co-morbidity, mainly hypertension (55% of cases n = 77) and diabetes (38% of cases n = 53). Main clinical signs were dyspnea (81%), physical asthenia (64%) and cough (60%). The majority of our patients (91%) benefited from conventional oxygen therapy. Acute Respiratory Distress Syndrome (ARDS) was the most represented complication (38%). The lethality rate in resuscitation was 25%. Conclusion The rate of admission of COVID-19 patients to intensive care was relatively low, and it concerned mainly elderly, male patients with at least one comorbidity. The symptomatology was dominated by dyspnea and complications by ARDS with significant mortality.

Preparing for the COVID-19 pandemic response in a country emerging from an Ebola Epidemic: assessment of health workers' knowledge, attitudes and practices on coronavirus (COVID-19) in Guinea

On January 30, 2020, the World Health Organization designated the outbreak as a Public Health Emergency of International Scope (USPPI). The purpose of this study was to assess the knowledge, attitudes and practices of medical personnel on the prevention of Covid-2019. A cross-sectional study among front-line health workers in the health facilities in the city of Conakry was carried out. The knowledge and attitude score were performed and categorized in 2: Good if at the average score and bad if < 50%. Logistic regression models were conducted to identify factors associated with knowledge and attitude. Among 548 health workers surveyed, 70.6% had a good knowledge of Covid-19. Among the health personnel interviewed, 57.7% had a good attitude towards a suspected case of Covid-19. Independent factors associated with poor knowledge of Covid-19 prevention were sex, health facility, and staff grade. As for poor attitude, the associated factors were knowledge of Ebola cases reported in the facility and the rank of the health staff. The health personnel have good knowledge of the virus but the attitudes are not related to knowledge. This study could serve as a basis for reorienting interventions involving front-line staff.