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1.
Clin Infect Dis ; 72(3): 539, 2021 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-33527120

##### Asunto(s)
Epidemias , Hospitales , Humanos , New York , Prevalencia
2.
Rev Soc Bras Med Trop ; 54: e05532020, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33533818

##### RESUMEN

INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 has been transmitted to more than 200 countries, with 92.5 million cases and 1,981,678 deaths. METHODS: This study applied a mathematical model to estimate the increase in the number of cases in São Paulo state, Brazil during four epidemic periods and the subsequent 300 days. We used different types of dynamic transmission models to measure the effects of social distancing interventions, based on local contact patterns. Specifically, we used a model that incorporated multiple transmission pathways and an environmental class that represented the pathogen concentration in the environmental reservoir and also considered the time that an individual may sustain a latent infection before becoming actively infectious. Thus, this model allowed us to show how the individual quarantine and active monitoring of contacts can influence the model parameters and change the rate of exposure of susceptible individuals to those who are infected. RESULTS: The estimated basic reproductive number, R o , was 3.59 (95% confidence interval [CI]: 3.48 - 3.72). The mathematical model data prediction coincided with the real data mainly when the social distancing measures were respected. However, a lack of social distancing measures caused a significant increase in the number of infected individuals. Thus, if social distancing measures are not respected, we estimated a difference of at least 100,000 cases over the next 300 days. CONCLUSIONS: Although the predictive capacity of this model was limited by the accuracy of the available data, our results showed that social distancing is currently the best non-pharmacological measure.

##### Asunto(s)
Epidemias , Brasil/epidemiología , Humanos , Cuarentena
3.
Science ; 371(6530): 680-681, 2021 02 12.
Artículo en Inglés | MEDLINE | ID: mdl-33574202

##### Asunto(s)
Epidemias , Brotes de Enfermedades , Humanos , Reino Unido/epidemiología
4.
BMC Public Health ; 21(1): 257, 2021 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-33522928

##### RESUMEN

BACKGROUND: To inform researchers about the methodology and results of epidemic estimation studies performed for COVID-19 epidemic in Iran, we aimed to perform a rapid review. METHODS: We searched for and included published articles, preprint manuscripts and reports that estimated numbers of cumulative or daily deaths or cases of COVID-19 in Iran. We found 131 studies and included 29 of them. RESULTS: The included studies provided outputs for a total of 84 study-model/scenario combinations. Sixteen studies used 3-4 compartmental disease models. At the end of month two of the epidemic (2020-04-19), the lowest (and highest) values of predictions were 1,777 (388,951) for cumulative deaths, 20,588 (2,310,161) for cumulative cases, and at the end of month four (2020-06-20), were 3,590 (1,819,392) for cumulative deaths, and 144,305 (4,266,964) for cumulative cases. Highest estimates of cumulative deaths (and cases) for latest date available in 2020 were 418,834 on 2020-12-19 (and 41,475,792 on 2020-12-31). Model estimates predict an ominous course of epidemic progress in Iran. Increase in percent population using masks from the current situation to 95% might prevent 26,790 additional deaths (95% confidence interval 19,925-35,208) by the end of year 2020. CONCLUSIONS: Meticulousness and degree of details reported for disease modeling and statistical methods used in the included studies varied widely. Greater heterogeneity was observed regarding the results of predicted outcomes. Consideration of minimum and preferred reporting items in epidemic estimation studies might better inform future revisions of the available models and new models to be developed. Not accounting for under-reporting drives the models' results misleading.

##### Asunto(s)
/epidemiología , Epidemias , Humanos , Irán/epidemiología
5.
Math Biosci Eng ; 18(1): 950-967, 2021 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-33525127

##### RESUMEN

In this paper, deterministic and stochastic models are proposed to study the transmission dynamics of the Coronavirus Disease 2019 (COVID-19) in Wuhan, China. The deterministic model is formulated by a system of ordinary differential equations (ODEs) that is built upon the classical SEIR framework. The stochastic model is formulated by a continuous-time Markov chain (CTMC) that is derived based on the ODE model with constant parameters. The nonlinear CTMC model is approximated by a multitype branching process to obtain an analytical estimate for the probability of a disease outbreak. The local and global dynamics of the disease are analyzed by using the deterministic model with constant parameters, and the result indicates that the basic reproduction number $\mathcal{R}_0$ serves as a sharp disease threshold: the disease dies out if $\mathcal{R}_0\le 1$ and persists if $\mathcal{R}_0 > 1$. In contrast to the deterministic dynamics, the stochastic dynamics indicate that the disease may not persist when $\mathcal{R}_0 > 1$. Parameter estimation and validation are performed to fit our ODE model to the public reported data. Our result indicates that both the exposed and infected classes play an important role in shaping the epidemic dynamics of COVID-19 in Wuhan, China. In addition, numerical simulations indicate that a second wave of the ongoing pandemic is likely to occur if the prevention and control strategies are not implemented properly.

##### Asunto(s)
/epidemiología , Epidemias , Número Básico de Reproducción , China/epidemiología , Humanos , Cadenas de Markov , Modelos Teóricos , Pandemias , Probabilidad , Procesos Estocásticos , Factores de Tiempo
6.
J R Soc Interface ; 18(175): 20200683, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33530857

##### RESUMEN

SARS-CoV-2 is an international public health emergency; high transmissibility and morbidity and mortality can result in the virus overwhelming health systems. Combinations of social distancing, and test, trace, and isolate strategies can reduce the number of new infections per infected individual below 1, thus driving declines in case numbers, but may be both challenging and costly. These interventions must also be maintained until development and (now likely) mass deployment of a vaccine (or therapeutics), since otherwise, many susceptible individuals are still at risk of infection. We use a simple analytical model to explore how low levels of infection, combined with vaccination, determine the trajectory to community immunity. Understanding the repercussions of the biological characteristics of the viral life cycle in this scenario is of considerable importance. We provide a simple description of this process by modelling the scenario where the effective reproduction number [Formula: see text] is maintained at 1. Since the additional complexity imposed by the strength and duration of transmission-blocking immunity is not yet clear, we use our framework to probe the impact of these uncertainties. Through intuitive analytical relations, we explore how the necessary magnitude of vaccination rates and mitigation efforts depends crucially on the durations of natural and vaccinal immunity. We also show that our framework can encompass seasonality or preexisting immunity due to epidemic dynamics prior to strong mitigation measures. Taken together, our simple conceptual model illustrates the importance of individual and vaccinal immunity for community immunity, and that the quantification of individuals immunized against SARS-CoV-2 is paramount.

##### Asunto(s)
/inmunología , Inmunidad Colectiva , Vacunación , Número Básico de Reproducción , Epidemias , Humanos , Sistema Inmunológico , Salud Pública , Estaciones del Año
7.
Mem Inst Oswaldo Cruz ; 115: e200278, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33566939

##### RESUMEN

BACKGROUND: The impact of arbovirus cocirculation in Brazil is unknown. Dengue virus (DENV) reinfection may result in more intense viraemia or immunopathology, leading to more severe disease. The Zika virus (ZIKV) epidemic in the Americas provided pathogenicity evidence that had not been previously observed in flavivirus infections. In contrast to other flaviviruses, electron microscopy studies have shown that ZIKV may replicate in viroplasm-like structures. Flaviviruses produce an ensemble of structurally different virions, collectively contributing to tissue tropism and virus dissemination. OBJECTIVES AND METHODS: In this work, the Aedes albopictus mosquito cell lineage (C6/36 cells) and kidney epithelial cells from African green monkeys (Vero cells) were infected with samples of the main circulating arboviruses in Brazil [DENV-1, DENV-2, DENV-3, DENV-4, ZIKV, Yellow Fever virus (YFV) and Chikungunya virus (CHIKV)], and ultrastructural studies by transmission electron microscopy were performed. FINDINGS: We observed that ZIKV, the DENV serotypes, YFV and CHIKV particles are spherical. ZIKV, DENV-1, -2, -3 and -4 presented diameters of 40-50 nm, and CHIKV presented approximate diameters of 50-60 nm. Viroplasm-like structures was observed in ZIKV replication cycle. MAIN CONCLUSIONS: The morphogenesis of these arboviruses is similar to what has been presented in previous studies. However, we understand that further studies are needed to investigate the relationship between viroplasm-like structures and ZIKV replication dynamics.

##### Asunto(s)
Arbovirus , Fiebre Chikungunya , Dengue , Epidemias , Fiebre Amarilla , Infección por el Virus Zika , Virus Zika , Animales , Brasil/epidemiología , Fiebre Chikungunya/epidemiología , Chlorocebus aethiops , Dengue/epidemiología , Células Vero , Infección por el Virus Zika/epidemiología
8.
Artículo en Ruso | MEDLINE | ID: mdl-33591677

##### RESUMEN

Since the ancient times, epidemics affect the processes proceeding in various spheres of life of human society. Hence, steadfast attention of historians to this biological phenomenon and its investigation. Quite a lot of of research studies is devoted to the first-rate epidemics, for instance, the famous «Black Death¼ in the middle of XIV century. At the same time, far from all such occurrences were properly interpreted in historical literature. Among little-studied and factually unknown epidemics, the pestilence, the plague, that struck the Russian state in the second half of 60s-early 70s of XVI century, stands out for. The article considers this occurrence, demonstrates its origin, time and geographical limits and also analyzes its consequences.

##### Asunto(s)
Epidemias , Peste , Animales , Personal de Salud , Caballos , Humanos , Peste/epidemiología , Federación de Rusia/epidemiología
9.
Brasília, D.F.; OPAS; 2021-02-19. (OPAS-W/BRA/PHE/COVID-19/21-0009).
No convencional en Portugués | PAHO-IRIS | ID: phr2-53295

##### RESUMEN

Esta orientação provisória reúne as informações sobre recursos humanos para a COVID-19 para que os gestores e formuladores de políticas de saúde em nível nacional, subnacional e de unidades de saúde planejem, gerenciem e preservem a força de trabalho necessária para manejo da pandemia da COVID-19 e mantenham os serviços essenciais de saúde. Esta orientação identifica as recomendações em nível individual, gerencial, organizacional e de sistema, reunindo em um único documento de referência as evidências iniciais das opções de políticas para a força de trabalho em saúde e para a pandemia em orientações sobre a COVID-19 publicadas pela Organização Mundial da Saúde (OMS). Ela será atualizada regularmente, beneficiando-se de ampla consulta aos departamentos e escritórios regionais da OMS, organizações internacionais, universidades e associações profissionais ativas na resposta à pandemia.

##### Asunto(s)
Infecciones por Coronavirus , Infecciones por Coronavirus , Coronavirus , Betacoronavirus , Control de Infecciones , Personal de Salud , Pandemias , Epidemias , Orientación , Salud Mental
10.
Brasília, D.F.; OPAS; 2021-02-11. (OPAS-W/BRA/PHE/COVID-19/21-0007).
No convencional en Portugués | PAHO-IRIS | ID: phr2-53265

##### Asunto(s)
Infecciones por Coronavirus , Pandemias , Epidemias , Coronavirus , Infecciones por Coronavirus , Betacoronavirus , Urgencias Médicas , Laboratorios , Virus del SRAS
11.
JAMA Netw Open ; 4(2): e2037069, 2021 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-33533933

##### RESUMEN

Importance: New York State has been an epicenter for both the US coronavirus disease 2019 (COVID-19) and HIV/AIDS epidemics. Persons living with diagnosed HIV may be more prone to COVID-19 infection and severe outcomes, yet few studies have assessed this possibility at a population level. Objective: To evaluate the association between HIV diagnosis and COVID-19 diagnosis, hospitalization, and in-hospital death in New York State. Design, Setting, and Participants: This cohort study, conducted in New York State, including New York City, between March 1 and June 15, 2020, matched data from HIV surveillance, COVID-19 laboratory-confirmed diagnoses, and hospitalization databases to provide a full population-level comparison of COVID-19 outcomes between persons living with diagnosed HIV and persons living without diagnosed HIV. Exposures: Diagnosis of HIV infection through December 31, 2019. Main Outcomes and Measures: The main outcomes were COVID-19 diagnosis, hospitalization, and in-hospital death. COVID-19 diagnoses, hospitalizations, and in-hospital death rates comparing persons living with diagnosed HIV with persons living without dianosed HIV were computed, with unadjusted rate ratios and indirect standardized rate ratios (sRR), adjusting for sex, age, and region. Adjusted rate ratios (aRRs) for outcomes specific to persons living with diagnosed HIV were assessed by age, sex, region, race/ethnicity, transmission risk, and CD4+ T-cell count-defined HIV disease stage, using Poisson regression models. Results: A total of 2988 persons living with diagnosed HIV (2109 men [70.6%]; 2409 living in New York City [80.6%]; mean [SD] age, 54.0 [13.3] years) received a diagnosis of COVID-19. Of these persons living with diagnosed HIV, 896 were hospitalized and 207 died in the hospital through June 15, 2020. After standardization, persons living with diagnosed HIV and persons living without diagnosed HIV had similar diagnosis rates (sRR, 0.94 [95% CI, 0.91-0.97]), but persons living with diagnosed HIV were hospitalized more than persons living without diagnosed HIV, per population (sRR, 1.38 [95% CI, 1.29-1.47]) and among those diagnosed (sRR, 1.47 [95% CI, 1.37-1.56]). Elevated mortality among persons living with diagnosed HIV was observed per population (sRR, 1.23 [95% CI, 1.07-1.40]) and among those diagnosed (sRR, 1.30 [95% CI, 1.13-1.48]) but not among those hospitalized (sRR, 0.96 [95% CI, 0.83-1.09]). Among persons living with diagnosed HIV, non-Hispanic Black individuals (aRR, 1.59 [95% CI, 1.40-1.81]) and Hispanic individuals (aRR, 2.08 [95% CI, 1.83-2.37]) were more likely to receive a diagnosis of COVID-19 than White individuals, but they were not more likely to be hospitalized once they received a diagnosis or to die once hospitalized. Hospitalization risk increased with disease progression to HIV stage 2 (aRR, 1.29 [95% CI, 1.11-1.49]) and stage 3 (aRR, 1.69 [95% CI, 1.38-2.07]) relative to stage 1. Conclusions and Relevance: In this cohort study, persons living with diagnosed HIV experienced poorer COVID-related outcomes relative to persons living without diagnosed HIV; Previous HIV diagnosis was associated with higher rates of severe disease requiring hospitalization, and hospitalization risk increased with progression of HIV disease stage.

##### Asunto(s)
/epidemiología , Comorbilidad , Infecciones por VIH/epidemiología , Mortalidad Hospitalaria , Hospitalización , Hospitales , Pandemias , Adulto , Afroamericanos , Anciano , Estudios de Cohortes , Epidemias , Grupo de Ascendencia Continental Europea , Femenino , Infecciones por VIH/complicaciones , Hispanoamericanos , Humanos , Masculino , Persona de Mediana Edad , New York/epidemiología , Ciudad de Nueva York/epidemiología
12.
Lancet HIV ; 8(2): e106-e113, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33539757

##### RESUMEN

Ending the AIDS epidemic by 2030 will require addressing stigma more systematically and at a larger scale than current efforts. Existing global evidence shows that stigma is a barrier to achieving each of the 90-90-90 targets; it undermines HIV testing, linkage to care, treatment adherence, and viral load suppression. However, findings from both research studies and programmatic experience have helped to inform the growing body of knowledge regarding how to reduce stigma, leading to key principles for HIV stigma reduction. These principles include immediately addressing actionable drivers of stigma, centring groups affected by stigma at the core of the response, and engaging opinion leaders and building partnerships between affected groups and opinion leaders. Although there is still room to strengthen research on stigma measurement and reduction, in particular for intersectional stigma, the proliferation of evidence over the past several decades on how to measure and address stigma provides a solid foundation for immediate and comprehensive action.

##### Asunto(s)
Síndrome de Inmunodeficiencia Adquirida/prevención & control , Síndrome de Inmunodeficiencia Adquirida/psicología , Epidemias/prevención & control , Miedo/psicología , Estigma Social , Síndrome de Inmunodeficiencia Adquirida/diagnóstico , Síndrome de Inmunodeficiencia Adquirida/virología , Fármacos Anti-VIH/uso terapéutico , Femenino , VIH/efectos de los fármacos , VIH/crecimiento & desarrollo , VIH/patogenicidad , Humanos , Masculino , Cooperación del Paciente/psicología , Cooperación del Paciente/estadística & datos numéricos , Aislamiento Social/psicología , Cumplimiento y Adherencia al Tratamiento/psicología , Cumplimiento y Adherencia al Tratamiento/estadística & datos numéricos , Carga Viral/efectos de los fármacos
13.
Hist Philos Life Sci ; 43(1): 18, 2021 Feb 10.
Artículo en Inglés | MEDLINE | ID: mdl-33566215

##### RESUMEN

Since the February 2020 publication of the article 'Flattening the curve' in The Economist, political leaders worldwide have used this expression to legitimize the introduction of social distancing measures in fighting Covid-19. In fact, this expression represents a complex combination of three components: the shape of the epidemic curve, the social distancing measures and the reproduction number [Formula: see text]. Each component has its own history, each with a different history of control. Presenting the control of the epidemic as flattening the curve is in fact flattening the underlying natural-social complexity. The curve that needs to be flattened is presented as a bell-shaped curve, implicitly suggesting that the pathogen's spread is subject only to natural laws. The [Formula: see text] value, however, is, fundamentally, a metric of how a pathogen behaves within a social context, namely its numerical value is affected by sociopolitical influences. The jagged and erratic empirical curve of Covid-19 illustrates this. Although the virus has most likely infected only a small portion of the total susceptible population, it is clear its shape has changed drastically. This changing shape is largely due to sociopolitical factors. These include shifting formal laws and policies, shifting individual behaviors as well as shifting various other social norms and practices. This makes the course of Covid-19 curve both erratic and unpredictable.

##### Asunto(s)
Número Básico de Reproducción , Epidemias , /fisiología , /epidemiología , Humanos
14.
Zhonghua Yu Fang Yi Xue Za Zhi ; 55(1): 120-122, 2021 Jan 06.
Artículo en Chino | MEDLINE | ID: mdl-33455143

##### RESUMEN

To Track the source of the infection through an investigation of a clustering of coronavirus disease 2019(COVID-19), and provide scientific basis and Strategy for the effective control of the aggregated epidemic situation of COVID-19. Field epidemiological method was used to survey the cases and related close contacts in a family clustering epidemic of COVID-19 in Dandong city of Liaoning Province. We obtained survey data for a descriptive analysis.Real time RT-PCR technique was used to detect 2019-nCoV nucleic acid in samples collected from cases and related close contacts combined with serum specific antibody detection. A total of 3 confirmed cases and 2 asymptomatic infection cases were discovered in the clustering epidemic, with 34 close contacts.Of eight close family contacts visiting from other province, one patient was on the same flight as the confirmed case, and her antibody IgG was positive. The family clustering was caused by past infection case who visited her friend through Wuhan from other provinces to local area.

##### Asunto(s)
Epidemias , China/epidemiología , Ciudades , Femenino , Humanos , Reacción en Cadena en Tiempo Real de la Polimerasa
15.
Science ; 371(6526): 230-231, 2021 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-33446540

##### Asunto(s)
Epidemias , Brasil , Humanos , Inmunidad Colectiva , Incidencia , Vacunación
16.
BMC Public Health ; 21(1): 106, 2021 01 09.
Artículo en Inglés | MEDLINE | ID: mdl-33422035

##### RESUMEN

BACKGROUND: Public health workers at the Chinese Centre for Disease Control and Prevention (China CDC) and primary health care institutes (PHIs) were among the main workers who implemented prevention, control, and containment measures. However, their efforts and health status have not been well documented. We aimed to investigate the working conditions and health status of front line public health workers in China during the COVID-19 epidemic. METHODS: Between 18 February and 1 March 2020, we conducted an online cross-sectional survey of 2,313 CDC workers and 4,004 PHI workers in five provinces across China experiencing different scales of COVID-19 epidemic. We surveyed all participants about their work conditions, roles, burdens, perceptions, mental health, and self-rated health using a self-constructed questionnaire and standardised measurements (i.e., Patient Health Questionnaire and General Anxiety Disorder scale). To examine the independent associations between working conditions and health outcomes, we used multivariate regression models controlling for potential confounders. RESULTS: The prevalence of depression, anxiety, and poor self-rated health was 21.3, 19.0, and 9.8%, respectively, among public health workers (27.1, 20.6, and 15.0% among CDC workers and 17.5, 17.9, and 6.8% among PHI workers). The majority (71.6%) made immense efforts in both field and non-field work. Nearly 20.0% have worked all night for more than 3 days, and 45.3% had worked throughout the Chinese New Year holiday. Three risk factors and two protective factors were found to be independently associated with all three health outcomes in our final multivariate models: working all night for >3 days (multivariate odds ratio [ORm]=1.67~1.75, p<0.001), concerns about infection at work (ORm=1.46~1.89, p<0.001), perceived troubles at work (ORm=1.10~1.28, p<0.001), initiating COVID-19 prevention work after January 23 (ORm=0.78~0.82, p=0.002~0.008), and ability to persist for > 1 month at the current work intensity (ORm=0.44~0.55, p<0.001). CONCLUSIONS: Chinese public health workers made immense efforts and personal sacrifices to control the COVID-19 epidemic and faced the risk of mental health problems. Efforts are needed to improve the working conditions and health status of public health workers and thus maintain their morale and effectiveness during the fight against COVID-19.

##### Asunto(s)
/epidemiología , Epidemias , Personal de Salud/psicología , Personal de Salud/estadística & datos numéricos , Estado de Salud , Salud Pública , Trabajo/estadística & datos numéricos , Adulto , China/epidemiología , Estudios Transversales , Femenino , Humanos , Masculino , Persona de Mediana Edad , Encuestas y Cuestionarios
17.
BMC Public Health ; 21(1): 105, 2021 01 09.
Artículo en Inglés | MEDLINE | ID: mdl-33422049

##### RESUMEN

BACKGROUND: When a new or re-emergent pathogen, such as SARS-CoV-2, causes a major outbreak, rapid access to pertinent research findings is crucial for planning strategies and decision making. We researched whether the speed of sharing research results in the COVID-19 epidemic was higher than the SARS and Ebola epidemics. We also researched whether there is any difference in the most frequent topics investigated before and after the COVID-19, SARS, and Ebola epidemics started. METHODS: We used PubMed database search tools to determine the time-period it took for the number of articles to rise after the epidemics started and the most frequent topics assigned to the articles. RESULTS: The main results were, first, the rise in the number of articles occurred 6 weeks after the COVID-19 epidemic started whereas, this rise occurred 4 months after the SARS and 7 months after the Ebola epidemics started. Second, etiology, statistics & numerical data, and epidemiology were the three most frequent topics investigated in the COVID-19 epidemic. However, etiology, microbiology, and genetics in the SARS epidemic, and statistics & numerical data, epidemiology, and prevention & control in the Ebola epidemic were more frequently studied compared with other topics. Third, some topics were studied more frequently after the epidemics started. CONCLUSIONS: The speed of sharing results in the COVID-19 epidemic was much higher than the SARS and Ebola epidemics, and that there is a difference in the most frequent articles' topics investigated in these three epidemics. Due to the value of time in controlling epidemics spread, the study highlights the necessity of defining more solutions for rapidly providing pertinent research findings in fighting against the next public health emergency.

##### Asunto(s)
/epidemiología , Epidemias , Difusión de la Información , Investigación , Fiebre Hemorrágica Ebola/epidemiología , Humanos , Síndrome Respiratorio Agudo Grave/epidemiología
18.
PLoS One ; 16(1): e0244706, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33406106

##### RESUMEN

Without vaccines and treatments, societies must rely on non-pharmaceutical intervention strategies to control the spread of emerging diseases such as COVID-19. Though complete lockdown is epidemiologically effective, because it eliminates infectious contacts, it comes with significant costs. Several recent studies have suggested that a plausible compromise strategy for minimizing epidemic risk is periodic closure, in which populations oscillate between wide-spread social restrictions and relaxation. However, no underlying theory has been proposed to predict and explain optimal closure periods as a function of epidemiological and social parameters. In this work we develop such an analytical theory for SEIR-like model diseases, showing how characteristic closure periods emerge that minimize the total outbreak, and increase predictably with the reproductive number and incubation periods of a disease- as long as both are within predictable limits. Using our approach we demonstrate a sweet-spot effect in which optimal periodic closure is maximally effective for diseases with similar incubation and recovery periods. Our results compare well to numerical simulations, including in COVID-19 models where infectivity and recovery show significant variation.

##### Asunto(s)
Brotes de Enfermedades/prevención & control , Cuarentena/métodos , Gestión de Riesgos/métodos , /prevención & control , Control de Enfermedades Transmisibles/métodos , Enfermedades Transmisibles/psicología , Brotes de Enfermedades/estadística & datos numéricos , Epidemias/prevención & control , Epidemias/estadística & datos numéricos , Humanos , Modelos Teóricos , /patogenicidad
19.
Nucleic Acids Res ; 49(D1): D1-D9, 2021 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-33396976

##### RESUMEN

The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV-2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In metabolism and signalling, STRING, KEGG and WikiPathways are featured, along with returning KLIFS and new DKK and KinaseMD, all focused on kinases. IMG/M and IMG/VR update in the microbial and viral genome resources section, while human and model organism genomics resources include Flybase, Ensembl and UCSC Genome Browser. Cancer studies are covered by updates from canSAR and PINA, as well as newcomers CNCdatabase and Oncovar for cancer drivers. Plant comparative genomics is catered for by updates from Gramene and GreenPhylDB. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been substantially updated, revisiting nearly 1000 entries, adding 90 new resources and eliminating 86 obsolete databases, bringing the current total to 1641 databases. It is available at https://www.oxfordjournals.org/nar/database/c/.

##### Asunto(s)
Bases de Datos de Ácidos Nucleicos , Biología Molecular/estadística & datos numéricos , Ácidos Nucleicos , Publicaciones Periódicas como Asunto/estadística & datos numéricos , Investigación/estadística & datos numéricos , /genética , /epidemiología , /virología , Biología Computacional/métodos , Epidemias , Genómica/métodos , Humanos , Internet , Biología Molecular/métodos , Biología Molecular/normas , Publicaciones Periódicas como Asunto/normas , Investigación/normas , /fisiología
20.
BMC Genomics ; 22(1): 5, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33407110

##### RESUMEN

BACKGROUND: Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complexity of the sc datasets poses a great challenge in its utility and this problem is further exacerbated when working with larger datasets typically generated by consortium efforts. As the scale of single cell datasets continues to increase exponentially, there is an unmet technological need to develop database platforms that can evaluate key biological hypotheses by querying extensive single-cell datasets. Large single-cell datasets like Human Cell Atlas and COVID-19 cell atlas (collection of annotated sc datasets from various human organs) are excellent resources for profiling target genes involved in human diseases and disorders ranging from oncology, auto-immunity, as well as infectious diseases like COVID-19 caused by SARS-CoV-2 virus. SARS-CoV-2 infections have led to a worldwide pandemic with massive loss of lives, infections exceeding 7 million cases. The virus uses ACE2 and TMPRSS2 as key viral entry associated proteins expressed in human cells for infections. Evaluating the expression profile of key genes in large single-cell datasets can facilitate testing for diagnostics, therapeutics, and vaccine targets, as the world struggles to cope with the on-going spread of COVID-19 infections. MAIN BODY: In this manuscript we describe REVEAL: SingleCell, which enables storage, retrieval, and rapid query of single-cell datasets inclusive of millions of cells. The array native database described here enables selecting and analyzing cells across multiple studies. Cells can be selected using individual metadata tags, more complex hierarchical ontology filtering, and gene expression threshold ranges, including co-expression of multiple genes. The tags on selected cells can be further evaluated for testing biological hypotheses. One such example includes identifying the most prevalent cell type annotation tag on returned cells. We used REVEAL: SingleCell to evaluate the expression of key SARS-CoV-2 entry associated genes, and queried the current database (2.2 Million cells, 32 projects) to obtain the results in < 60 s. We highlighted cells expressing COVID-19 associated genes are expressed on multiple tissue types, thus in part explains the multi-organ involvement in infected patients observed worldwide during the on-going COVID-19 pandemic. CONCLUSION: In this paper, we introduce the REVEAL: SingleCell database that addresses immediate needs for SARS-CoV-2 research and has the potential to be used more broadly for many precision medicine applications. We used the REVEAL: SingleCell database as a reference to ask questions relevant to drug development and precision medicine regarding cell type and co-expression for genes that encode proteins necessary for SARS-CoV-2 to enter and reproduce in cells.

##### Asunto(s)
/genética , Receptores Virales/genética , Serina Endopeptidasas/genética , Análisis de la Célula Individual/métodos , /metabolismo , /virología , Células Cultivadas , Bases de Datos Genéticas , Epidemias , Perfilación de la Expresión Génica , Humanos , Receptores Virales/metabolismo , /fisiología , Internalización del Virus