8,904 results match your criteria epidemic evolution

Positive Selection as a Key Player for SARS-CoV-2 Pathogenicity: Insights into ORF1ab, S and E genes.

Virus Res 2021 Jun 9:198472. Epub 2021 Jun 9.

Center for Informatics Sciences (CIS), Nile University, Giza, Egypt.

The human β-coronavirus SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China. It causes Covid-19 disease which has become pandemic. Each of the five-known human β-coronaviruses has four major structural proteins (E, M, N and S) and 16 non-structural proteins encoded by ORF1a and ORF1b together (ORF1ab) that are involved in virus pathogenicity and infectivity. Read More

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Social, economic, and environmental factors influencing the basic reproduction number of COVID-19 across countries.

PLoS One 2021 9;16(6):e0252373. Epub 2021 Jun 9.

Smithsonian Environmental Research Center, Edgewater, MD, United States of America.

Objective: To assess whether the basic reproduction number (R0) of COVID-19 is different across countries and what national-level demographic, social, and environmental factors other than interventions characterize initial vulnerability to the virus.

Methods: We fit logistic growth curves to reported daily case numbers, up to the first epidemic peak, for 58 countries for which 16 explanatory covariates are available. This fitting has been shown to robustly estimate R0 from the specified period. Read More

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Evolution of outcomes for patients hospitalised during the first 9 months of the SARS-CoV-2 pandemic in France: A retrospective national surveillance data analysis.

Lancet Reg Health Eur 2021 Jun 21;5:100087. Epub 2021 Mar 21.

Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.

Background: As SARS-CoV-2 continues to spread, a thorough characterisation of healthcare needs and patient outcomes, and how they have changed over time, is essential to inform planning.

Methods: We developed a probabilistic framework to analyse detailed patient trajectories from 198,846 hospitalisations in France during the first nine months of the pandemic. Our model accounts for the varying age- and sex- distribution of patients, and explore changes in outcome probabilities as well as length of stay. Read More

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SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment.

Microbiome 2021 06 8;9(1):132. Epub 2021 Jun 8.

Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.

Background: SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. Read More

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Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen.

J R Soc Interface 2021 Jun 9;18(179):20210041. Epub 2021 Jun 9.

Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.

Indirect (environmental) and direct (host-host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods. Read More

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The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Circulating in Europe.

Front Microbiol 2021 21;12:651124. Epub 2021 May 21.

Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom.

The European epidemic monophasic variant of enterica serovar (. 1,4,[5],12:i:-) characterized by the multi sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this in Europe. Read More

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[Feedback from the establishment of a psychiatric regulation line at SAMU 62 in the context of Covid-19].

Ann Med Psychol (Paris) 2021 May 28. Epub 2021 May 28.

CUMP 62, centre hospitalier d'Arras (62), Arras, France.

The epidemic context of Covid-19 and the containment measures, put in place since 16 March 2020, has significantly increased the number of emergencies calls in call center (SAMU). In the department of Pas-de-Calais, one step of the crisis measures was setting up a psychiatric regulation line, which aims to manage calls with strong emotional valence (in connexion with containment, anxiety related to the epidemic context, or break in psychiatric cares for people suffering of mental disorders). This psychiatric hotline was provided from 20 March 2020 to 15 May 2020 by fifteen psychiatric careers (psychiatrists, psychologists and psychiatric nurses) from the network of the medical-psychological emergency unit (unit of the emergency call center which aims to manage people involved in psychotraumatic events). Read More

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Phylogenetic analysis and evolution of feline bocavirus in Anhui Province, eastern China.

Comp Immunol Microbiol Infect Dis 2021 May 27;77:101676. Epub 2021 May 27.

New Ruipeng Tianhong Pet Hospital, Hefei 230036, PR China. Electronic address:

To understand the epidemic status of feline bocavirus (FBoV) in Anhui Province, eastern China, FBoV was successfully extracted from fecal samples of domestic cats, and five complete genomes were amplified in this study. Phylogenetic analysis showed that these five strains belong to three different FBoV genotypes. Recombination analysis showed that inter- and intra-genotype recombination events occurred. Read More

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Mental health and stress among ICU healthcare professionals in France according to intensity of the COVID-19 epidemic.

Ann Intensive Care 2021 Jun 4;11(1):90. Epub 2021 Jun 4.

Service de Médecine Intensive Réanimation-Unité de Sevrage Ventilatoire et Réhabilitation, CH de Bethune, Bethune, France.

Background: We investigated the impact of the COVID-19 crisis on mental health of professionals working in the intensive care unit (ICU) according to the intensity of the epidemic in France.

Methods: This cross-sectional survey was conducted in 77 French hospitals from April 22 to May 13 2020. All ICU frontline healthcare workers were eligible. Read More

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Lockdown as a last resort option in case of COVID-19 epidemic rebound: a modelling study.

Euro Surveill 2021 06;26(22)

Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.

BackgroundGiven its high economic and societal cost, policymakers might be reluctant to implement a large-scale lockdown in case of coronavirus disease (COVID-19) epidemic rebound. They may consider it as a last resort option if alternative control measures fail to reduce transmission.AimWe developed a modelling framework to ascertain the use of lockdown to ensure intensive care unit (ICU) capacity does not exceed a peak target defined by policymakers. Read More

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Exploring the role of non-pharmaceutical interventions (NPIs) in flattening the Greek COVID-19 epidemic curve.

Sci Rep 2021 06 3;11(1):11741. Epub 2021 Jun 3.

Department of Management Science and Technology, University of Patras, Patras, Greece.

Due to the COVID-19 pandemic originating in China in December 2019, apart from the grave concerns on the exponentially increasing casualties, the affected countries are called to deal with severe repercussions in all aspects of everyday life, from economic recession to national and international movement restrictions. Several regions managed to handle the pandemic more successfully than others in terms of life loss, while ongoing heated debates as to the right course of action for battling COVID-19 have divided the academic community as well as public opinion. To this direction, in this paper, an autoregressive COVID-19 prediction model with heterogeneous explanatory variables for Greece is proposed, taking past COVID-19 data, non-pharmaceutical interventions (NPIs), and Google query data as independent variables, from the day of the first confirmed case-February 26th-to the day before the announcement for the quarantine measures' softening-April 24th. Read More

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Prostate Cancer Diagnosis and Management During One Year of the COVID-19 Pandemic.

Anticancer Res 2021 Jun;41(6):3127-3130

Pathology Unit, Cannizzaro Hospital, Catania, Italy.

Background/aim: To evaluate the diagnosis and treatment of prostate cancer (PCa) during 1 year of the COVID-19 pandemic.

Patients And Methods: The management of men with PCa during COVID-19 pandemic (March 2020-2021) was compared with the clinical activity of the 12 months before the COVID-19 pandemic (March 2019-2020).

Results: The number of clinical visits, prostate biopsy, and men enrolled in active surveillance was significantly lower during the COVID-19 pandemic (p<0. Read More

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Transient disease dynamics across ecological scales.

Theor Ecol 2021 May 27:1-16. Epub 2021 May 27.

Department of Biology Center for Infectious Disease Dynamics, Penn State University, University Park, PA 16802 USA.

Analyses of transient dynamics are critical to understanding infectious disease transmission and persistence. Identifying and predicting transients across scales, from within-host to community-level patterns, plays an important role in combating ongoing epidemics and mitigating the risk of future outbreaks. Moreover, greater emphases on non-asymptotic processes will enable timely evaluations of wildlife and human diseases and lead to improved surveillance efforts, preventive responses, and intervention strategies. Read More

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Predicting of the Coronavirus Disease 2019 (COVID-19) Epidemic Using Estimation of Parameters in the Logistic Growth Model.

Infect Dis Rep 2021 May 24;13(2):465-485. Epub 2021 May 24.

Department of Physics, Faculty of Mathematical and Natural Sciences, IPB University (Bogor Agricultural University), Jalan Meranti, Building Wing S, 2nd Floor, Kampus IPB Dramaga, Bogor 16680, Indonesia.

The COVID-19 pandemic was impacting the health and economy around the world. All countries have taken measures to control the spread of the epidemic. Because it is not known when the epidemic will end in several countries, then the prediction of the COVID-19 pandemic is a very important challenge. Read More

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Epidemic Spread of SARS-CoV-2 Lineage B.1.1.7 in Brazil.

Viruses 2021 05 26;13(6). Epub 2021 May 26.

Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil.

The emergence of diverse lineages harboring mutations with functional significance and potentially enhanced transmissibility imposes an increased difficulty on the containment of the SARS-CoV-2 pandemic [... Read More

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Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China.

Viruses 2021 May 31;13(6). Epub 2021 May 31.

Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Agricultural University, Beijing 100193, China.

Porcine reproductive and respiratory syndrome virus (PRRSV) is economically important and characterized by its extensive variation. The codon usage patterns and their influence on viral evolution and host adaptation among different PRRSV strains remain largely unknown. Here, the codon usage of ORF5 genes from lineages 1, 3, 5, and 8, and MLV strains of type 2 PRRSV in China was analyzed. Read More

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The Impact of COVID 19 on University Staff and Students from Iberoamerica: Online Learning and Teaching Experience.

Int J Environ Res Public Health 2021 May 28;18(11). Epub 2021 May 28.

Deusto Business School Health, University of Deusto, 48014 Bilbao, Spain.

(1) Background: The COVID-19 pandemic has created a great impact on mental health in society. Considering the little attention paid by scientific studies to either students or university staff during lockdown, the current study has two aims: (a) to analyze the evolution of mental health and (b) to identify predictors of educational/professional experience and online learning/teaching experience. (2) Methods: 1084 university students and 554 staff in total from four different countries (Spain, Colombia, Chile and Nicaragua) participated in the study, affiliated with nine different universities, four of them Spanish and one of which was online. Read More

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Health Sufficiency Indicators for Pandemic Monitoring.

Int J Environ Res Public Health 2021 05 18;18(10). Epub 2021 May 18.

Data Science Laboratory, Rey Juan Carlos University, 28933 Móstoles, Spain.

The outbreak of the COVID-19 disease, spreading all around the world and causing a worldwide pandemic, has lead to the collapse of the health systems of the most affected countries. Due to the ease of transmission, early prevention measures are proved to be fundamental to control the pandemic and, hence, the saturation of the health systems. Given the difficulty of obtaining characteristics of these systems of different countries and regions, it is necessary to define indicators based on basic information that enable the assessment of the evolution of the impact of a disease in a health system along with fair comparisons among different ones. Read More

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Natural Ventilation Characterization in a Classroom under Different Scenarios.

Int J Environ Res Public Health 2021 05 19;18(10). Epub 2021 May 19.

Nuclear Engineering and Fluid Mechanics Department, University of the Basque Country, UPV/EHU, Nieves Cano 12, Vitoria-Gasteiz, 01006 Araba, Spain.

The COVID-19 pandemic has pointed to the need to increase our knowledge in fields related to human breathing. In the present study, temperature, relative humidity, carbon dioxide (CO) concentration, and median particle size diameter measurements were taken into account. These parameters were analyzed in a computer classroom with 15 subjects during a normal 90-minute class; all the subjects wore surgical masks. Read More

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Compelling Evidence for the Activity of Antiviral Peptides against SARS-CoV-2.

Viruses 2021 05 14;13(5). Epub 2021 May 14.

Institute for Insect Biotechnology, Justus Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.

Multiple outbreaks of epidemic and pandemic viral diseases have occurred in the last 20 years, including those caused by Ebola virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The emergence or re-emergence of such diseases has revealed the deficiency in our pipeline for the discovery and development of antiviral drugs. One promising solution is the extensive library of antimicrobial peptides (AMPs) produced by all eukaryotic organisms. Read More

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Evolution of the Illegal Substances Market and Substance Users' Social Situation and Health during the COVID-19 Pandemic.

Int J Environ Res Public Health 2021 May 7;18(9). Epub 2021 May 7.

Addiction Suisse, Avenue Louis-Ruchonnet 14, 1003 Lausanne, Switzerland.

The outbreak of the COVID-19 pandemic and the measures taken for tackling it had the potential to lead to deep modifications in the supply of illegal drugs and to impact substance users' health and social situation. To investigate this, we used mixed methods, i.e. Read More

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Avian Influenza in Wild Birds and Poultry: Dissemination Pathways, Monitoring Methods, and Virus Ecology.

Pathogens 2021 May 20;10(5). Epub 2021 May 20.

Life Sciences Research Center, Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.

Avian influenza is one of the largest known threats to domestic poultry. Influenza outbreaks on poultry farms typically lead to the complete slaughter of the entire domestic bird population, causing severe economic losses worldwide. Moreover, there are highly pathogenic avian influenza (HPAI) strains that are able to infect the swine or human population in addition to their primary avian host and, as such, have the potential of being a global zoonotic and pandemic threat. Read More

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Molecular Epidemiological Survey of Canine Parvovirus Circulating in China from 2014 to 2019.

Pathogens 2021 May 11;10(5). Epub 2021 May 11.

Veterinary Pathology Laboratory, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.

The global distribution of canine parvovirus (CPV-2) derived from a closely related carnivore parvovirus poses a considerable threat to the dog population. The virus is continuously undergoing genetic evolution, giving rise to several variants. To investigate the prevalence of Chinese CPV-2 strains in recent years, a total of 30 CPV-2 strains were collected from 2018 to 2021 and the VP2 gene was sequenced and analyzed. Read More

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Disparities in the Evolution of the COVID-19 Pandemic between Spanish Provinces.

Int J Environ Res Public Health 2021 May 11;18(10). Epub 2021 May 11.

Preventive Medicine and Public Health Department, Lozano Blesa University Hospital, 50009 Zaragoza, Spain.

Spain experienced a second wave of the COVID-19 pandemic in autumn 2020, which has been approached with different measures by regional authorities. We analyze the presence of convergence in the cumulative incidence for 14 days (CI) in provinces and self-governing cities. The Phillips-Sul methodology was used to study the grouping of behavior between provinces, and an ordered logit model was estimated to understand the forces that drive creating the different convergence clubs. Read More

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Systemic Treatment Initiation in Classical and Endemic Kaposi's Sarcoma: Risk Factors and Global Multi-State Modelling in a Monocentric Cohort Study.

Cancers (Basel) 2021 May 21;13(11). Epub 2021 May 21.

Université de Paris, AP-HP, Dermatology Department, INSERM U976, Saint Louis Hospital, 75010 Paris, France.

Background: Although several studies described the clinical course of epidemic and post-transplant Kaposi's Sarcoma (KS), the lack of large cohorts of classic/endemic KS, precluded such characterization.

Methods: We used multi-state modelling in a retrospective monocentric study to evaluate global disease evolution and identify risk factors for systemic treatment (ST) initiation. 160 classic/endemic KS patients consecutively diagnosed between 1990 and 2013 were included. Read More

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The Evolution in Anxiety and Depression with the Progression of the Pandemic in Adult Populations from Eight Countries and Four Continents.

Int J Environ Res Public Health 2021 05 1;18(9). Epub 2021 May 1.

Department of Family Medicine & Emergency Medicine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada.

Nearly a year after the classification of the COVID-19 outbreak as a global pandemic, it is clear that different factors have contributed to an increase in psychological disorders, including public health measures that infringe on personal freedoms, growing financial losses, and conflicting messages. This study examined the evolution of psychosocial impacts with the progression of the pandemic in adult populations from different countries and continents, and identified, among a wide range of individual and country-level factors, which ones are contributing to this evolving psychological response. An online survey was conducted in May/June 2020 and in November 2020, among a sample of 17,833 adults (Phase 1: 8806; Phase 2: 9027) from eight countries/regions (Canada, the United States, England, Switzerland, Belgium, Hong Kong, the Philippines, New Zealand). Read More

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Evolution of VIM-1-Producing Klebsiella pneumoniae Isolates from a Hospital Outbreak Reveals the Genetic Bases of the Loss of the Urease-Positive Identification Character.

mSystems 2021 Jun 1:e0024421. Epub 2021 Jun 1.

EERA Unit "Ecology and Evolution of Antibiotics Resistance," Institut Pasteur-Assistance Publique/Hôpitaux de Paris-Université Paris-Saclay, Paris, France.

Outbreaks of carbapenemase-producing Klebsiella pneumoniae (CP) represent a major threat for hospitals. We molecularly characterized the first outbreak of VIM-1-producing K. pneumoniae in Spain, which raised fears about the spread of this strain or of the plasmid carrying . Read More

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French organization for the pharmacovigilance of COVID-19 vaccines: A major challenge.

Therapie 2021 May 7. Epub 2021 May 7.

Centre régional de pharmacovigilance et d'information sur le médicament, service de pharmacologie clinique et pharmacovigilance, Aix Marseille Université, AP-HM, hôpital Sainte-Marguerite, 270, boulevard Sainte-Marguerite 13009, Marseille, France. Electronic address:

In this special issue, we present the main highlights of the first weeks of pharmacovigilance monitoring of coronavirus disease 2019 (COVID-19) vaccines in this unprecedented situation in France: the deployment of a vaccination during an epidemic period with the aim of vaccinating the entire population and the intense pharmacovigilance and surveillance of these vaccines still under conditional marketing authorizations. In this unprecedented situation, the cross approach and interaction between the French pharmacovigilance network and French National Agency for the Safety of Medicines and Health Products (ANSM) has been optimized to provide a real-time safety related to COVID-19 vaccines. Every week, pair of regional pharmacovigilance centers gathered safety data from the French pharmacovigilance network, to acutely expertise all the adverse drug reactions (ADRs) reported with each COVID-19 vaccine within a direct circuit with ANSM. Read More

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Comprehensive Ecological and Geographic Characterization of Eukaryotic and Prokaryotic Microbiomes in African .

Front Microbiol 2021 12;12:635772. Epub 2021 May 12.

Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States.

Exposure of mosquitoes to numerous eukaryotic and prokaryotic microbes in their associated microbiomes has probably helped drive the evolution of the innate immune system. To our knowledge, a metagenomic catalog of the eukaryotic microbiome has not been reported from any insect. Here we employ a novel approach to preferentially deplete host 18S ribosomal RNA gene amplicons to reveal the composition of the eukaryotic microbial communities of larvae sampled in Kenya, Burkina Faso and Republic of Guinea (Conakry). Read More

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Optimizing time-limited non-pharmaceutical interventions for COVID-19 outbreak control.

Philos Trans R Soc Lond B Biol Sci 2021 07 31;376(1829):20200282. Epub 2021 May 31.

Usher Institute, University of Edinburgh, Edinburgh, UK.

Retrospective analyses of the non-pharmaceutical interventions (NPIs) used to combat the ongoing COVID-19 outbreak have highlighted the potential of optimizing interventions. These optimal interventions allow policymakers to manage NPIs to minimize the epidemiological and human health impacts of both COVID-19 and the intervention itself. Here, we use a susceptible-infectious-recovered (SIR) mathematical model to explore the feasibility of optimizing the duration, magnitude and trigger point of five different NPI scenarios to minimize the peak prevalence or the attack rate of a simulated UK COVID-19 outbreak. Read More

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