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1.
Onderstepoort J Vet Res ; 88(1): e1-e8, 2021 Feb 10.
Article in English | MEDLINE | ID: covidwho-1077469

ABSTRACT

Human coronaviruses are known respiratory pathogens associated with a range of respiratory illnesses, and there are considerable morbidity and hospitalisation amongst immune-compromised individuals of all age groups. The emergence of a highly pathogenic human coronavirus in China in 2019 has confirmed the long-held opinion that these viruses are important emerging and re-emerging pathogens. In this review article, we trace the discovery and emergence of coronaviruses (CoVs) over time since they were first reported. The review article will enrich our understanding on the host range, diversity and evolution, transmission of human CoVs and the threat posed by these viruses circulating in animal populations but overtime have spilled over to humans because of the increased proximity between humans and animals.


Subject(s)
Communicable Diseases, Emerging/virology , Coronavirus Infections/virology , Coronavirus/classification , Animals , Coronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Disease Outbreaks , Host Specificity , Humans
2.
Ann Clin Microbiol Antimicrob ; 20(1): 8, 2021 Jan 18.
Article in English | MEDLINE | ID: covidwho-1067240

ABSTRACT

The Severe Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has gained research attention worldwide, given the current pandemic. Nevertheless, a previous zoonotic and highly pathogenic coronavirus, the Middle East Respiratory Syndrome coronavirus (MERS-CoV), is still causing concern, especially in Saudi Arabia and neighbour countries. The MERS-CoV has been reported from respiratory samples in more than 27 countries, and around 2500 cases have been reported with an approximate fatality rate of 35%. After its emergence in 2012 intermittent, sporadic cases, nosocomial infections and many community clusters of MERS continued to occur in many countries. Human-to-human transmission resulted in the large outbreaks in Saudi Arabia. The inherent genetic variability among various clads of the MERS-CoV might have probably paved the events of cross-species transmission along with changes in the inter-species and intra-species tropism. The current review is drafted using an extensive review of literature on various databases, selecting of publications irrespective of favouring or opposing, assessing the merit of study, the abstraction of data and analysing data. The genome of MERS-CoV contains around thirty thousand nucleotides having seven predicted open reading frames. Spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins are the four main structural proteins. The surface located spike protein (S) of betacoronaviruses has been established to be one of the significant factors in their zoonotic transmission through virus-receptor recognition mediation and subsequent initiation of viral infection. Three regions in Saudi Arabia (KSA), Eastern Province, Riyadh and Makkah were affected severely. The epidemic progression had been the highest in 2014 in Makkah and Riyadh and Eastern Province in 2013. With a lurking epidemic scare, there is a crucial need for effective therapeutic and immunological remedies constructed on sound molecular investigations.


Subject(s)
Antiviral Agents/therapeutic use , Coronavirus Infections/drug therapy , /genetics , Middle East Respiratory Syndrome Coronavirus/genetics , Spike Glycoprotein, Coronavirus/genetics , /genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Cross Infection/epidemiology , Cross Infection/virology , Disease Outbreaks , Humans , Middle East Respiratory Syndrome Coronavirus/isolation & purification , Phylogeny , RNA, Viral/genetics , Saudi Arabia/epidemiology
3.
Infect Genet Evol ; 88: 104708, 2021 03.
Article in English | MEDLINE | ID: covidwho-1039486

ABSTRACT

The pandemic due to novel coronavirus, SARS-CoV-2 is a serious global concern now. More than thousand new COVID-19 infections are getting reported daily for this virus across the globe. Thus, the medical research communities are trying to find the remedy to restrict the spreading of this virus, while the vaccine development work is still under research in parallel. In such critical situation, not only the medical research community, but also the scientists in different fields like microbiology, pharmacy, bioinformatics and data science are also sharing effort to accelerate the process of vaccine development, virus prediction, forecasting the transmissible probability and reproduction cases of virus for social awareness. With the similar context, in this article, we have studied sequence variability of the virus primarily focusing on three aspects: (a) sequence variability among SARS-CoV-1, MERS-CoV and SARS-CoV-2 in human host, which are in the same coronavirus family, (b) sequence variability of SARS-CoV-2 in human host for 54 different countries and (c) sequence variability between coronavirus family and country specific SARS-CoV-2 sequences in human host. For this purpose, as a case study, we have performed topological analysis of 2391 global genomic sequences of SARS-CoV-2 in association with SARS-CoV-1 and MERS-CoV using an integrated semi-alignment based computational technique. The results of the semi-alignment based technique are experimentally and statistically found similar to alignment based technique and computationally faster. Moreover, the outcome of this analysis can help to identify the nations with homogeneous SARS-CoV-2 sequences, so that same vaccine can be applied to their heterogeneous human population.


Subject(s)
/epidemiology , Coronavirus Infections/epidemiology , Genetic Variation , Genome, Viral , Pandemics , Severe Acute Respiratory Syndrome/epidemiology , Africa/epidemiology , Americas/epidemiology , Asia/epidemiology , Australia/epidemiology , Base Sequence , /virology , Computational Biology/methods , Coronavirus Infections/transmission , Coronavirus Infections/virology , Europe/epidemiology , Host-Pathogen Interactions/genetics , Humans , Middle East Respiratory Syndrome Coronavirus/genetics , Middle East Respiratory Syndrome Coronavirus/pathogenicity , SARS Virus/genetics , SARS Virus/pathogenicity , Sequence Alignment , Severe Acute Respiratory Syndrome/transmission , Severe Acute Respiratory Syndrome/virology
8.
Health Place ; 64: 102404, 2020 07.
Article in English | MEDLINE | ID: covidwho-1023586

ABSTRACT

The role of geospatial disparities in the dynamics of the COVID-19 pandemic is poorly understood. We developed a spatially-explicit mathematical model to simulate transmission dynamics of COVID-19 disease infection in relation with the uneven distribution of the healthcare capacity in Ohio, U.S. The results showed substantial spatial variation in the spread of the disease, with localized areas showing marked differences in disease attack rates. Higher COVID-19 attack rates experienced in some highly connected and urbanized areas (274 cases per 100,000 people) could substantially impact the critical health care response of these areas regardless of their potentially high healthcare capacity compared to more rural and less connected counterparts (85 cases per 100,000). Accounting for the spatially uneven disease diffusion linked to the geographical distribution of the critical care resources is essential in designing effective prevention and control programmes aimed at reducing the impact of COVID-19 pandemic.


Subject(s)
Coronavirus Infections , Health Services Accessibility , Hospital Bed Capacity , Intensive Care Units , Pandemics/statistics & numerical data , Pneumonia, Viral , Spatial Analysis , Betacoronavirus/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Humans , Incidence , Models, Theoretical , Ohio/epidemiology , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Rural Population
9.
Ann Thorac Surg ; 110(4): e333-e334, 2020 10.
Article in English | MEDLINE | ID: covidwho-1023473

ABSTRACT

The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic pointed out that the need to ensure emergent surgery in patients positive for infection is no longer hypothetical. Among emergency procedures, thoracic surgical operations are frequent. A standardized surgical pathway is mandatory to achieve effective and safe management of this subset of patients. We briefly present the protocol adopted by our thoracic surgery division.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Disease Transmission, Infectious/prevention & control , Guidelines as Topic , Health Facilities/standards , Pandemics , Pneumonia, Viral/epidemiology , Thoracic Surgical Procedures/standards , Coronavirus Infections/transmission , Humans , Italy/epidemiology , Pneumonia, Viral/transmission
11.
PLoS One ; 15(9): e0239113, 2020.
Article in English | MEDLINE | ID: covidwho-798750

ABSTRACT

Social distancing interventions can be effective against epidemics but are potentially detrimental for the economy. Businesses that rely heavily on face-to-face communication or close physical proximity when producing a product or providing a service are particularly vulnerable. There is, however, no systematic evidence about the role of human interactions across different lines of business and about which will be the most limited by social distancing. Here we provide theory-based measures of the reliance of U.S. businesses on human interaction, detailed by industry and geographic location. We find that, before the pandemic hit, 43 million workers worked in occupations that rely heavily on face-to-face communication or require close physical proximity to other workers. Many of these workers lost their jobs since. Consistently with our model, employment losses have been largest in sectors that rely heavily on customer contact and where these contacts dropped the most: retail, hotels and restaurants, arts and entertainment and schools. Our results can help quantify the economic costs of social distancing.


Subject(s)
Commerce/trends , Coronavirus Infections/prevention & control , Employment/trends , Infection Control/economics , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Betacoronavirus/pathogenicity , Commerce/standards , Commerce/statistics & numerical data , Coronavirus Infections/economics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Datasets as Topic , Employment/economics , Employment/statistics & numerical data , Humans , Infection Control/methods , Infection Control/standards , Pandemics/economics , Pneumonia, Viral/economics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , United States
12.
Cytometry A ; 97(9): 882-886, 2020 09.
Article in English | MEDLINE | ID: covidwho-790373

ABSTRACT

Operating shared resource laboratories (SRLs) in times of pandemic is a challenge for research institutions. In a multiuser, high-turnover working space, the transmission of infectious agents is difficult to control. To address this challenge, imaging core facility managers being members of German BioImaging discussed how shared microscopes could be operated with minimal risk of spreading SARS-CoV-2 between users and staff. Here, we describe the resulting guidelines and explain their rationale, with a focus on separating users in space and time, protective face masks, and keeping surfaces virus-free. These recommendations may prove useful for other types of SRLs. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.


Subject(s)
Betacoronavirus/pathogenicity , Biomedical Research/organization & administration , Coronavirus Infections/prevention & control , Infection Control , Laboratories/organization & administration , Microscopy , Occupational Health , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Cooperative Behavior , Coronavirus Infections/transmission , Coronavirus Infections/virology , Decontamination , Equipment Contamination/prevention & control , Germany , Humans , Occupational Exposure/prevention & control , Personal Protective Equipment , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Protective Factors , Research Personnel/organization & administration , Risk Assessment , Risk Factors , Workflow
15.
Vet Rec ; 186(5): 144-145, 2020 02 08.
Article in English | MEDLINE | ID: covidwho-783626
16.
PLoS One ; 15(10): e0241405, 2020.
Article in English | MEDLINE | ID: covidwho-1024408

ABSTRACT

BACKGROUND: The first cases of COVID-19 caused by the SARS-CoV-2 virus were reported in China in December 2019. The disease has since spread globally. Many countries have instated measures to slow the spread of the virus. Information about the spread of the virus in a country can inform the gradual reopening of a country and help to avoid a second wave of infections. Our study focuses on Denmark, which is opening up when this study is performed (end-May 2020) after a lockdown in mid-March. METHODS: We perform a phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 genome sequences and put them into context using sequences from other countries. RESULTS: Our findings are consistent with several introductions of the virus to Denmark from independent sources. We identify several chains of mutations that occurred in Denmark. In at least one case we find evidence that the virus spread from Denmark to other countries. A number of the mutations found in Denmark are non-synonymous, and in general there is a considerable variety of strains. The proportions of the most common haplotypes remain stable after lockdown. CONCLUSION: Employing phylogenetic methods on Danish genome sequences of SARS-CoV-2, we exemplify how genetic data can be used to trace the introduction of a virus to a country. This provides alternative means for verifying existing assumptions. For example, our analysis supports the hypothesis that the virus was brought to Denmark by skiers returning from Ischgl. On the other hand, we identify transmission routes which suggest that Denmark was part of a network of countries among which the virus was being transmitted. This challenges the common narrative that Denmark only got infected from abroad. Our analysis concerning the ratio of haplotypes does not indicate that the major haplotypes appearing in Denmark have a different degree of virality.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/transmission , Genome, Viral , Mutation , Pneumonia, Viral/transmission , Coronavirus Infections/epidemiology , Denmark/epidemiology , Haplotypes , Humans , Pandemics , Phylogeny , Pneumonia, Viral/epidemiology
17.
PLoS One ; 15(10): e0241163, 2020.
Article in English | MEDLINE | ID: covidwho-1024405

ABSTRACT

The events of the recent SARS-CoV-2 epidemics have shown the importance of social factors, especially given the large number of asymptomatic cases that effectively spread the virus, which can cause a medical emergency to very susceptible individuals. Besides, the SARS-CoV-2 virus survives for several hours on different surfaces, where a new host can contract it with a delay. These passive modes of infection transmission remain an unexplored area for traditional mean-field epidemic models. Here, we design an agent-based model for simulations of infection transmission in an open system driven by the dynamics of social activity; the model takes into account the personal characteristics of individuals, as well as the survival time of the virus and its potential mutations. A growing bipartite graph embodies this biosocial process, consisting of active carriers (host) nodes that produce viral nodes during their infectious period. With its directed edges passing through viral nodes between two successive hosts, this graph contains complete information about the routes leading to each infected individual. We determine temporal fluctuations of the number of exposed and the number of infected individuals, the number of active carriers and active viruses at hourly resolution. The simulated processes underpin the latent infection transmissions, contributing significantly to the spread of the virus within a large time window. More precisely, being brought by social dynamics and exposed to the currently existing infection, an individual passes through the infectious state until eventually spontaneously recovers or otherwise is moves to a controlled hospital environment. Our results reveal complex feedback mechanisms that shape the dependence of the infection curve on the intensity of social dynamics and other sociobiological factors. In particular, the results show how the lockdown effectively reduces the spread of infection and how it increases again after the lockdown is removed. Furthermore, a reduced level of social activity but prolonged exposure of susceptible individuals have adverse effects. On the other hand, virus mutations that can gradually reduce the transmission rate by hopping to each new host along the infection path can significantly reduce the extent of the infection, but can not stop the spreading without additional social strategies. Our stochastic processes, based on graphs at the interface of biology and social dynamics, provide a new mathematical framework for simulations of various epidemic control strategies with high temporal resolution and virus traceability.


Subject(s)
Asymptomatic Infections , Betacoronavirus/genetics , Coronavirus Infections/transmission , Models, Statistical , Pneumonia, Viral/transmission , Coronavirus Infections/prevention & control , Coronavirus Infections/virology , Disease Susceptibility , Humans , Interpersonal Relations , Mutation , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Pneumonia, Viral/virology , Quarantine/methods , Stochastic Processes , Time Factors
20.
J Occup Environ Med ; 62(11): 953-958, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-1024152

ABSTRACT

OBJECTIVE: We study employee perspectives on return to physical workspaces to ultimately inform employers' and policy makers' decision making around the return to work during COVID-19. METHODS: We tested the three-component conceptual model using survey data collected in the United States in May 2020 from samples of energy workers (N = 333). RESULTS: Women, non-Caucasians, and employees living in multi-generational households were less willing to return. Concerns about childcare were negatively related to willingness to return, whereas organizational strategies for mitigating COVID-19 transmission at work were positively related to willingness to return. COVID-19 infections in an employees' network were also negatively related to employees' willingness to return. CONCLUSIONS: Blanket policies may miss the nuanced needs of different employee groups. Employers and policy makers should adopt flexible approaches to ensure a return to workspaces that addresses employee concerns and needs.


Subject(s)
Betacoronavirus , Coronavirus Infections/prevention & control , Infection Control/organization & administration , Organizational Policy , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Return to Work/psychology , Workplace/organization & administration , Adult , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Female , Humans , Male , Middle Aged , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , United States , Volition
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