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1.
Yearb Med Inform ; 30(1): 105-125, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34479384

##### Assuntos
COVID-19 , Sistemas de Informação , Informática Médica , Telemedicina , Inteligência Artificial , COVID-19/diagnóstico , Teste para COVID-19 , Busca de Comunicante , Sistemas de Apoio a Decisões Clínicas , Registros Eletrônicos de Saúde , Epidemias , Troca de Informação em Saúde , Interoperabilidade da Informação em Saúde , Humanos , Disseminação de Informação
2.
Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi ; 33(4): 373-379, 2021 Aug 20.
Artigo em Chinês | MEDLINE | ID: mdl-34505444

##### RESUMO

OBJECTIVE: To analyze the epidemiological characteristics and diagnosis of imported malaria before and after malaria elimination in Nanjing City of Jiangsu Province, so as to provide the scientific evidence for formulating the malaria control strategy after malaria elimination. METHODS: Data pertaining to the epidemic situation and individual investigation of malaria in Nanjing City before (from 2012 to 2016) and after malaria elimination (from 2017 to 2020) were captured from the National Notifiable Communicable Disease Reporting System and the Information System for Parasitic Diseases Control and Prevention and were analyzed statistically. RESULTS: A total of 178 malaria cases were reported in Nanjing City from 2012 to 2020, and all were imported cases. There were 99 malaria cases reported before malaria elimination in Nanjing City, including 78 cases with Plasmodium falciparum malaria (78.79%), 5 cases with P. vivax malaria (5.05%), 10 cases with P. ovale malaria (10.10%), 3 cases with P. malariae malaria (3.03%) and 3 cases with mixed infections (3.03%), and 79 malaria cases reported after elimination, including 63 cases with P. falciparum malaria (79.75%), 5 cases with P. vivax malaria (6.33%), 9 cases with P. ovale malaria (11.39%), 2 cases with P. malariae malaria (2.53%). There was no significant difference in the proportion of each type of malaria cases in Nanjing City before and after malaria elimination (χ2 =2.400, P > 0.05). Malaria cases mainly acquired Plasmodium infections in African regions, and no significant difference was seen in the proportion of malaria cases returning to Nanjing City from African countries before and after malaria elimination (χ2 = 0.093, P > 0.05). The number of malaria cases peaked in Nanjing City in January and during the period from May to July before elimination, and there was no apparent seasonal variation in the distribution of malaria cases after elimination. The proportion of malaria cases living in Nanjing City was significantly greater after malaria elimination than before elimination (72.15% vs. 55.56%; χ2 = 5.187, P = 0.023). The proportions of businessmen and international students were both 5.05% before malaria elimination, and increased to 15.19% and 13.92% after elimination, respectively (χ2 = 5.229 and 4.229, both P values < 0.05). The percentage of definitive diagnosis of malaria at initial diagnosis was 18.75% in county-level hospitals before malaria elimination and increased to 61.11% after elimination (χ2 = 6.275, P = 0.012), while the proportion of malaria cases with definitive diagnoses in county-level hospitals was 4.04% before malaria elimination and increased to 13.92% after elimination (χ2 = 5.562, P = 0.018). During the period from 2012 to 2020, the proportion of malaria cases with definitive diagnoses within 1 to 3 days post-admission increased from 27.27% in Nanjing City before malaria elimination to 45.57% after elimination (χ2 = 6.433, P = 0.011). CONCLUSIONS: The epidemic situation of imported malaria remains serious in Nanjing City during the post-elimination stage, and malaria parasite infections predominantly occur in African regions. In addition, there are changes in regional and occupational distributions of malaria cases and the diagnostic capability of malaria increases in county-level hospitals in Nanjing City after malaria elimination. Further improvements in the malaria surveillance system and the diagnostic and treatment capability of malaria in medical institutions at each level are required to consolidate malaria elimination achievements in Nanjing City.

##### Assuntos
Epidemias , Malária Falciparum , Malária Vivax , Malária , China/epidemiologia , Cidades , Humanos , Malária/diagnóstico , Malária/epidemiologia , Malária/prevenção & controle
3.
J Res Health Sci ; 21(2): e00517, 2021 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-34465640

##### RESUMO

BACKGROUND: The basic reproduction number (R0) is an important concept in infectious disease epidemiology and the most important parameter to determine the transmissibility of a pathogen. This study aimed to estimate the nine-month trend of time-varying R of COVID-19 epidemic using the serial interval (SI) and Markov Chain Monte Carlo in Lorestan, west of Iran. STUDY DESIGN: Descriptive study. METHODS: This study was conducted based on a cross-sectional method. The SI distribution was extracted from data and log-normal, Weibull, and Gamma models were fitted. The estimation of time-varying R0, a likelihood-based model was applied, which uses pairs of cases to estimate relative likelihood. RESULTS: In this study, Rt was estimated for SI 7-day and 14-day time-lapses from 27 February-14 November 2020. To check the robustness of the R0 estimations, sensitivity analysis was performed using different SI distributions to estimate the reproduction number in 7-day and 14-day time-lapses. The R0 ranged from 0.56 to 4.97 and 0.76 to 2.47 for 7-day and 14-day time-lapses. The doubling time was estimated to be 75.51 days (95% CI: 70.41, 81.41). CONCLUSION: Low R0 of COVID-19 in some periods in Lorestan, west of Iran, could be an indication of preventive interventions, namely quarantine and isolation. To control the spread of the disease, the reproduction number should be reduced by decreasing the transmission and contact rates and shortening the infectious period.

##### Assuntos
Número Básico de Reprodução , COVID-19/epidemiologia , Epidemias , COVID-19/prevenção & controle , COVID-19/transmissão , COVID-19/virologia , Estudos Transversais , Humanos , Irã (Geográfico)/epidemiologia , Funções Verossimilhança , Cadeias de Markov , Método de Monte Carlo , Pandemias , SARS-CoV-2
4.
F1000Res ; 10: 315, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34504684

##### RESUMO

Background: The start of 2021 was marked by the initiation of a global vaccination campaign against the novel coronavirus SARS-CoV-2. Formulating an optimal distribution strategy under social and economic constraints is challenging. Optimal distribution is additionally constrained by the potential emergence of vaccine resistance. Analogous to chronic low-dose antibiotic exposure, recently inoculated individuals who are not yet immune play an outsized role in the emergence of resistance. Classical epidemiological modelling is well suited to explore how the behavior of the inoculated population impacts the total number of infections over the entirety of an epidemic. Methods: A deterministic model of epidemic evolution is analyzed, with seven compartments defined by their relationship to the emergence of vaccine-resistant mutants and representing three susceptible populations, three infected populations, and one recovered population. This minimally computationally intensive design enables simulation of epidemics across a broad parameter space. The results are used to identify conditions minimizing the cumulative number of infections. Results: When an escape variant is only modestly less infectious than the originating strain within a naïve population, there exists an optimal rate of vaccine distribution. Exceeding this rate increases the cumulative number of infections due to vaccine escape. Analysis of the model also demonstrates that inoculated individuals play a major role in the mitigation or exacerbation of vaccine-resistant outbreaks. Modulating the rate of host-host contact for the inoculated population by less than an order of magnitude can alter the cumulative number of infections by more than 20%. Conclusions: Mathematical modeling shows that optimization of the vaccination rate and limiting post-vaccination contacts can perceptibly affect the course of an epidemic. The consideration of limitations on post-vaccination contacts remains relevant for the entire duration of any vaccination campaign including the current status of SARS-CoV-2 vaccination.

##### Assuntos
COVID-19 , Epidemias , Vacinas contra COVID-19 , Humanos , SARS-CoV-2 , Vacinação
5.
Brasília, D.F.; OPAS; 2021-09-17. (OPAS-W/BRA/PHE/COVID-19/21-0074).
Não convencional em Português | PAHO-IRIS | ID: phr2-54855

##### RESUMO

Este informe científico substitui o Informe Científico da Organização Mundial da Saúde (OMS) intitulado Immunity passports in the context of COVID-19 [Passaportes de imunidade no contexto da COVID-19], publicado em 24 de abril de 2020.A atualização aborda aquilo que já se sabe sobre a imunidade contra o SARS-CoV-2 decorrente da infecção natural. Foi realizada uma rápida revisão sobre o assunto e buscas regulares foram realizadas em periódicos científicos por artigos sobre imunidade contra a COVID-19, a fim de garantir a inclusão de todos os estudos grandes e robustos disponíveis na literatura no momento em que este documento foi redigido.

##### Assuntos
COVID-19 , Coronavirus , Infecções por Coronavirus , Imunidade , Epidemias , Pandemias , SARS-CoV-2 , Betacoronavirus
6.
BMC Public Health ; 21(1): 1603, 2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34465334

##### RESUMO

BACKGROUND: The 2014-2015 Ebola epidemic in West Africa became a humanitarian crisis that exposed significant gaps in infection prevention and control (IPC) capacity in primary care facilities in Sierra Leone. Operational partners recognized the national gap and rapidly scaled-up an IPC training and infrastructure package. This prompted us to carry out a mixed-methods research study which aimed to evaluate adherence to IPC practices and understand how to improve IPC at the primary care level, where most cases of Ebola were initially presenting. The study was carried out during the national peak of the epidemic. DISCUSSION: We successfully carried out a rapid response research study that produced several expected and unexpected findings that were used to guide IPC measures during the epidemic. Although many research challenges were similar to those found when conducting research in low-resource settings, the presence of Ebola added risks to safety and security of data collectors, as well as a need to balance research activities with the imperative of response to a humanitarian crisis. A participatory approach that attempted to unify levels of the response from community upwards helped overcome the risk of lack of trust in an environment where Ebola had damaged relations between communities and the health system. CONCLUSION: In the context of a national epidemic, research needs to be focused, appropriately resourced, and responsive to needs. The partnership between local academics and a humanitarian organization helped facilitate access to study sites and approvals that allowed the research to be carried out quickly and safely, and for findings to be shared in response forums with the best chance of being taken up in real-time.

##### Assuntos
Epidemias , Doença pelo Vírus Ebola , Instituições de Assistência Ambulatorial , Surtos de Doenças/prevenção & controle , Epidemias/prevenção & controle , Doença pelo Vírus Ebola/epidemiologia , Doença pelo Vírus Ebola/prevenção & controle , Humanos , Atenção Primária à Saúde , Serra Leoa/epidemiologia
7.
BMC Public Health ; 21(1): 1632, 2021 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-34488689

##### RESUMO

BACKGROUND: Public health campaigns aim to promote awareness, increase knowledge, and encourage a target population to adopt desirable attitudes and behaviors. Assessing their reach from a multidimensional perspective through information technology can facilitate the development of more effective campaigns in public health response. METHODS: We scrutinized seven data sources from different perspectives to assess a health campaign launched in Brazil named "Syphilis No!". This campaign is part of an Agenda for strategic actions to reduce syphilis in Brazil which includes dissemination of educommunication materials to remind people of the importance of syphilis prevention, emphasizing "test, treat and cure" concept. We developed a multidimensional analysis framework and implemented an information system to process the data from a time series perspective, and assessed the effects over time, both before and after the campaign. We descriptively analyzed data related to the campaign, including e-news, search engine activity, online courses, serological tests, medication distribution and case notification rates. FINDINGS: Regarding search engine activity, we observed the highest volume of search during the first week of campaigns in 2018 (between November 25th and December 7th). Nevertheless, analyzing this data in a trend plot revealed sustained growth until the end of 2019. From March 2018, the amount of e-news posts related to syphilis in Brazil, indexed by Google, followed an increasing slope, with a record peak in October 2019. In addition, data showed that 12 new online courses related to syphilis disease were available on the AVASUS Platform Learning Management System (LMS), to support efforts to promote lifelong learning for health professionals, teachers, and students. These courses reached more than 22,000 students between February 2019 and September 2020. Serological test data showed that the number of tests carried out in 2019 were 375·18% more than in 2015, even accounting for population growth. Finally, starting from the middle of 2018, the syphilis case notification rates followed a decreasing curve. INTERPRETATION: From this perspective, the "Syphilis No!" Project was a positive influence, inducing policy to fight syphilis in Brazil by supporting the implementation of a testing, treatment, and cure agenda (#TesteTrateCure). Certainly, this inference was made by analyzing multidimensional aspects and because, prior to 2018, the country had largely neglected this disease, with no records of communication actions during that period.

##### Assuntos
Epidemias , Sífilis , Brasil/epidemiologia , Promoção da Saúde , Humanos , Saúde Pública , Sífilis/epidemiologia , Sífilis/prevenção & controle
8.
Artigo em Inglês | MEDLINE | ID: mdl-34501965

##### RESUMO

The spread of COVID-19 is having a serious impact on socioeconomic development, and increased environmental risk perception (ERP). ERP provide new ideas for the orderly recovery of society. However, there have been studies that often pay attention to individual factors, and less concerned about the external environment. In fact, ERP will be affected by the external environment and individual factors. We used a Python script to collect 65,277 valid Weibo comments during the COVID-19 epidemic in China to assess urban residents' environmental risk perception (ERP). SnowNLP emotion analysis was used to measure the ERP of 366 urban in China, and the structural proportion characteristics and spatial-temporal differentiation of ERP were analyzed. Then, an order logistic regression model was used to investigate the relationship between economic level, social security, medical facilities and ERP. The study investigated the Chinese cities have a higher ERP during the COVID-19 period, and it shows marked fluctuations. As COVID-19 spreads, the ERP shows a distribution pattern of "high in the southeast and low in the northwest" with Hu line as the boundary and "from high to low" with Wuhan as the high value center. COVID-19 serves as catalysts for ERP, the impact of COVID-19 is enhanced after socioeconomic factors are considered. The economic level effectively regulates ERP, except the stage of accelerating diffusion. ERP is effectively stabilized by social security and medical facilities. After considering all the variables simultaneously, we found that the mitigation effect of social security and medical facilities on ERP has improved.

##### Assuntos
COVID-19 , Epidemias , China/epidemiologia , Cidades , Humanos , Percepção , SARS-CoV-2
9.
Math Biosci Eng ; 18(5): 5505-5524, 2021 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-34517498

##### RESUMO

Based on the SIQR model, we consider the influence of time delay from infection to isolation and present a delayed differential equation (DDE) according to the characteristics of the COVID-19 epidemic phenomenon. First, we consider the existence and stability of equilibria in the above delayed SIQR model. Second, we analyze the existence of Hopf bifurcations associated with two equilibria, and we verify that Hopf bifurcations occur as delays crossing some critical values. Then, we derive the normal form for Hopf bifurcation by using the multiple time scales method for determining the stability and direction of bifurcation periodic solutions. Finally, numerical simulations are carried out to verify the analytic results.

##### Assuntos
COVID-19 , Epidemias , Simulação por Computador , Humanos , Modelos Biológicos , SARS-CoV-2
10.
Math Biosci Eng ; 18(5): 5865-5920, 2021 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-34517515

##### RESUMO

Infectious diseases have been one of the major causes of human mortality, and mathematical models have been playing significant roles in understanding the spread mechanism and controlling contagious diseases. In this paper, we propose a delayed SEIR epidemic model with intervention strategies and recovery under the low availability of resources. Non-delayed and delayed models both possess two equilibria: the disease-free equilibrium and the endemic equilibrium. When the basic reproduction number $R_0 = 1$, the non-delayed system undergoes a transcritical bifurcation. For the delayed system, we incorporate two important time delays: $\tau_1$ represents the latent period of the intervention strategies, and $\tau_2$ represents the period for curing the infected individuals. Time delays change the system dynamics via Hopf-bifurcation and oscillations. The direction and stability of delay induced Hopf-bifurcation are established using normal form theory and center manifold theorem. Furthermore, we rigorously prove that local Hopf bifurcation implies global Hopf bifurcation. Stability switching curves and crossing directions are analyzed on the two delay parameter plane, which allows both delays varying simultaneously. Numerical results demonstrate that by increasing the intervention strength, the infection level decays; by increasing the limitation of treatment, the infection level increases. Our quantitative observations can be useful for exploring the relative importance of intervention and medical resources. As a timing application, we parameterize the model for COVID-19 in Spain and Italy. With strict intervention policies, the infection numbers would have been greatly reduced in the early phase of COVID-19 in Spain and Italy. We also show that reducing the time delays in intervention and recovery would have decreased the total number of cases in the early phase of COVID-19 in Spain and Italy. Our work highlights the necessity to consider the time delays in intervention and recovery in an epidemic model.

##### Assuntos
COVID-19 , Epidemias , Simulação por Computador , Humanos , Modelos Biológicos , Modelos Teóricos , SARS-CoV-2 , Espanha/epidemiologia
11.
F1000Res ; 10: 447, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34484689

##### RESUMO

Background: It is often assumed that pathogens evolve towards reduced virulence, but counterexamples abound. Faced with a new pathogen, such as SARS-CoV-2, it is highly desirable to be able to forecast the case fatality rate (CFR) and overall disease burden into the future. Considerable effort has been invested towards the development of a mathematical framework for predicting virulence evolution. Although many approaches accurately recapitulate complex outcomes, most rely on an assumed trade-off between CFR and infection rate. It is often impractical to empirically validate this constraint for human pathogens. Methods: A compartment model with parameters tuning the degree to which symptomatic individuals are isolated and the duration of immunity is constructed and evaluated at both short timescales and at equilibrium (when it exists). Results: We reveal kinetic constraints where the variation of multiple parameters in concert leads to decreased CFR and increased pathogen fitness, whereas independent variation of the parameters decreases pathogen fitness. Smallpox, SARS-CoV-2, and influenza are analyzed as diverse representatives of human respiratory viruses. We show that highly virulent viruses, such as smallpox, are likely often constrained by host behavior, whereas moderately virulent viruses, such as SARS-CoV-2, appear to be typically constrained by the relationship between the duration of immunity and CFR. Conclusions: Evolution of human respiratory epidemics appears to be often kinetically constrained and a reduction in CFR should not be assumed. Our findings imply that, without continued public health intervention, SARS-CoV-2 is likely to continue presenting a substantial disease burden. The existence of a parameter regime admitting endemic equilibrium suggests that herd immunity is unachievable. However, we demonstrate that even partial isolation of symptomatic individuals can have a major effect not only by reducing the number of fatalities in the short term but also by potentially changing the evolutionary trajectory of the virus towards reduced CFR.

##### Assuntos
COVID-19 , Epidemias , Influenza Humana , Efeitos Psicossociais da Doença , Humanos , Influenza Humana/epidemiologia , SARS-CoV-2
12.
Front Public Health ; 9: 572415, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34485206

##### RESUMO

Objective: To understand the impact of COVID-19 epidemic on the mental health status of intensive care unit (ICU) practitioners in China, and to explore the relevant factors that may affect the mental health status of front-line medical workers so as to adopt efficient and comprehensive measures in a timely manner to protect the mental health of medical staff. Methods: The study covered most of the provinces in China, and a questionnaire survey was conducted based on the WeChat platform and the Wenjuanxing online survey tool. With the method of anonymous investigation, we chose ICU practitioners to participate in the investigation from April 5, 2020 to April 7, 2020. The respondents were divided into two groups according to strict criteria of inclusion and exclusion, those who participated in the rescue work of COVID-19 (COVID-19 group) and those who did not (non-COVID-19 group). The SCL-90 self-evaluation scale was used for the evaluation of mental health status of the subjects. Results: A total of 3,851 respondents completed the questionnaire. First, the overall mental health status of the targeted population, compared with the Chinese norm (n = 1,388), was reflected in nine related factor groups of the SCL-90 scale, and significant differences were found in every factor in both men and women, except for the interpersonal sensitivity in men. Second, the overall mental health of the non-COVID-19 group was worse than that of the COVID-19 group by the SCL-90 scale (OR = 1.98, 95% CI, 1.682-2.331). Third, we have revealed several influencing factors for their mental health in the COVID-19 group, current working status (P < 0.001), satisfaction of diet and accommodation (P < 0.05), occupational exposure (P = 0.005), views on the risk of infection (P = 0.034), and support of training (P = 0.01). Conclusion: The mental health status of the ICU practitioners in the COVID-19 group is better than that of the non-COVID-19 group, which could be attributed to a strengthened mentality and awareness of risks related to occupational exposure and enforced education on preventive measures for infectious diseases, before being on duty.

##### Assuntos
COVID-19 , Epidemias , China/epidemiologia , Feminino , Nível de Saúde , Humanos , Unidades de Terapia Intensiva , Masculino , SARS-CoV-2
13.
Hist Cienc Saude Manguinhos ; 28(3): 869-874, 2021.
Artigo em Espanhol | MEDLINE | ID: mdl-34346995

##### RESUMO

This article describes the emergence of health concerns relating to the epidemics that occurred during the twentieth century in La Pampa, a province in Argentina. Epidemics such as smallpox drove such policies, which frequently originated in Buenos Aires, the country's capital. The spread of many epidemics was due to shortages: water, sewage and adequate refuse disposal, an insufficient number of health care workers, the presence of disease transmission vectors such as mosquitos, and, ultimately, poverty. The historical experience described in this text highlights the importance of analyzing the impact of SARS-CoV-2 beyond the big cities.

##### Assuntos
COVID-19/história , Epidemias/história , Varíola/história , Animais , Argentina/epidemiologia , COVID-19/epidemiologia , Criança , Cidades/epidemiologia , Cidades/história , Erradicação de Doenças/história , Erradicação de Doenças/organização & administração , Feminino , Pessoal de Saúde/história , Pessoal de Saúde/estatística & dados numéricos , Política de Saúde/história , Política de Saúde/legislação & jurisprudência , História do Século XX , Humanos , Índios Sul-Americanos/história , Índios Sul-Americanos/estatística & dados numéricos , Insetos Vetores , Masculino , Militares/história , Pobreza/história , Eliminação de Resíduos/história , Esgotos , Varíola/epidemiologia , Varíola/prevenção & controle , Vacinação/história , Vacinação/legislação & jurisprudência , Abastecimento de Água/história
14.
Psychiatry Res ; 304: 114132, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34348211

##### RESUMO

Few people have paid attention to community epidemic prevention workers in the postpandemic era of COVID-19. This study aimed to explore the prevalence and risk factors for mental health symptoms in community epidemic prevention workers during the postpandemic era. Mental health status was evaluated by the Patient Health Questionnaire-9, Generalized Anxiety Disorder-7, Chinese Perceived Stress Scale, Insomnia Severity Index, and Maslach Burnout Inventory-General Survey. The results showed that a considerable proportion of community epidemic prevention workers reported symptoms of depression (39.7%), anxiety (29.5%), high stress (51.1%), insomnia (30.8%), and burnout (53.3%). The prevalence of depression and anxiety in community epidemic prevention workers was higher than in community residents. Among community epidemic prevention workers, short sleep duration was a risk factor for depression, anxiety, high stress and insomnia. Concurrent engagement in work unrelated to epidemic prevention and current use of hypnotics were risk factors for depression, anxiety and insomnia. Our study suggests that during the postpandemic era, the mental health problems of community epidemic prevention workers are more serious than those of community residents. Several variables, such as short sleep duration and concurrent engagement in work unrelated to epidemic prevention, are associated with mental health among community epidemic prevention workers.

##### Assuntos
COVID-19 , Epidemias , Distúrbios do Início e da Manutenção do Sono , Ansiedade/epidemiologia , China/epidemiologia , Estudos Transversais , Depressão , Humanos , Saúde Mental , Prevalência , Fatores de Risco , SARS-CoV-2 , Distúrbios do Início e da Manutenção do Sono/epidemiologia
15.
Sci Rep ; 11(1): 17054, 2021 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-34462450

##### RESUMO

We investigate patterns of COVID-19 mortality across 20 Italian regions and their association with mobility, positivity, and socio-demographic, infrastructural and environmental covariates. Notwithstanding limitations in accuracy and resolution of the data available from public sources, we pinpoint significant trends exploiting information in curves and shapes with Functional Data Analysis techniques. These depict two starkly different epidemics; an "exponential" one unfolding in Lombardia and the worst hit areas of the north, and a milder, "flat(tened)" one in the rest of the country-including Veneto, where cases appeared concurrently with Lombardia but aggressive testing was implemented early on. We find that mobility and positivity can predict COVID-19 mortality, also when controlling for relevant covariates. Among the latter, primary care appears to mitigate mortality, and contacts in hospitals, schools and workplaces to aggravate it. The techniques we describe could capture additional and potentially sharper signals if applied to richer data.

##### Assuntos
COVID-19/mortalidade , Epidemias , COVID-19/epidemiologia , Análise de Dados , Humanos , Itália/epidemiologia , Dinâmica Populacional
16.
Hist Philos Life Sci ; 43(3): 105, 2021 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-34462807

##### RESUMO

The article takes the renewed popularity and interest in epidemiological modelling for Covid-19 as a point of departure to ask how modelling has historically shaped epidemiological reasoning. The focus lies on a particular model, developed in the late 1920s through a collaboration of the former field-epidemiologists and medical officer, Wade Hampton Frost, and the biostatistician and population ecologist Lowell Reed. Other than former approaches to epidemic theory in mathematical formula, the Reed-Frost epidemic theory was materialised in a simple mechanical analogue: a box with coloured marbles and a wooden trough. The article reconstructs how the introduction of this mechanical model has reshaped epidemiological reasoning by shifting the field from purely descriptive to analytical practices. It was not incidental that the history of this model coincided with the foundation of epidemiology as an academic discipline, as it valorised and institutionalised new theoretical contributions to the field. Through its versatility, the model shifted the field's focus from mono-causal explanations informed by bacteriology, eugenics or sanitary perspectives towards the systematic consideration of epidemics as a set of interdependent and dynamic variables.

##### Assuntos
Epidemias , Estudos Epidemiológicos , Epidemiologia/história , História do Século XX , Humanos , Modelos Teóricos
17.
Lancet ; 398(10302): 742-743, 2021 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-34454663
18.
Proc Biol Sci ; 288(1956): 20210900, 2021 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-34375554

##### RESUMO

There is increasing interest in the role that evolution may play in current and future pandemics, but there is often also considerable confusion about the actual evolutionary predictions. This may be, in part, due to a historical separation of evolutionary and medical fields, but there is a large, somewhat nuanced body of evidence-supported theory on the evolution of infectious disease. In this review, we synthesize this evolutionary theory in order to provide a framework for clearer understanding of the key principles. Specifically, we discuss the selection acting on zoonotic pathogens' transmission rates and virulence at spillover and during emergence. We explain how the direction and strength of selection during epidemics of emerging zoonotic disease can be understood by a three Ts framework: trade-offs, transmission, and time scales. Virulence and transmission rate may trade-off, but transmission rate is likely to be favoured by selection early in emergence, particularly if maladapted zoonotic pathogens have 'no-cost' transmission rate improving mutations available to them. Additionally, the optimal virulence and transmission rates can shift with the time scale of the epidemic. Predicting pathogen evolution, therefore, depends on understanding both the trade-offs of transmission-improving mutations and the time scales of selection.

##### Assuntos
Doenças Transmissíveis , Epidemias , Evolução Biológica , Doenças Transmissíveis/epidemiologia , Humanos , Virulência
19.
Microbiol Spectr ; 9(1): e0026121, 2021 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-34346744

##### RESUMO

The dynamics of quasispecies afford RNA viruses a great fitness on cell tropism and host range. To study the quasispecies features and the intra-host evolution of SARS-CoV-2, we collected nine confirmed patients and sequenced the haplotypes of spike gene using a single-molecule real-time platform. Fourteen samples were extracted from sputum, nasopharyngeal swabs, or stool, which in total produced 283,655 high-quality circular consensus sequences. We observed a stable quasispecies structure that one master mutant (mean abundance â¼0.70), followed by numerous minor mutants (mean abundance â¼1.21 × 10-3). Under high selective pressure, minor mutants may obtain a fitness advantage and become the master ones. The later predominant substitution D614G existed in the minor mutants of more than one early patient. An epidemic variant had a possibility to be independently originated from multiple hosts. The mutant spectrums covered â¼85% amino acid variations of public genomes (GISAID; frequency ≥ 0.1) and likely provided an advantage mutation pool for the current/future epidemic variants. Notably, 32 of 35 collected antibody escape substitutions were preexistent in the early quasispecies. Virus populations in different tissues/organs revealed potentially independent replications. The quasispecies complexity of sputum samples was significantly lower than that of nasopharyngeal swabs (P = 0.02). Evolution analysis revealed that three continuous S2 domains (HR1, CH, and CD) had undergone a positive selection. Cell fusion-related domains may play a crucial role in adapting to the intrahost immune system. Our findings suggested that future epidemiologic investigations and clinical interventions should consider the quasispecies information that has missed by routine single consensus genome. IMPORTANCE RNA virus population in a host does not consist of a consensus single haplotype but rather an ensemble of related sequences termed quasispecies. The dynamics of quasispecies afford SARS-CoV-2 a great ability on genetic fitness during intrahost evolution. The process is likely achieved by changing the genetic characteristics of key functional genes, such as the spike glycoprotein. Previous studies have applied the next-generation sequencing (NGS) technology to evaluate the quasispecies of SARS-CoV-2, and results indicated a low genetic diversity of the spike gene. However, the NGS platform cannot directly obtain the full haplotypes without assembling, and it is also difficult to predict the extremely low-frequency variations. Therefore, we introduced a single-molecule real-time technology to directly obtain the haplotypes of the RNA population and further study the quasispecies features and intrahost evolution of the spike gene.

##### Assuntos
Epidemias , Mutação , Quase-Espécies , SARS-CoV-2/classificação , SARS-CoV-2/genética , Adulto , Idoso , Sequência de Bases , COVID-19/virologia , Criança , Feminino , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Glicoproteína da Espícula de Coronavírus/genética
20.
Artigo em Inglês | MEDLINE | ID: mdl-34444166

##### RESUMO

The 2016-2017 Tanzania HIV Impact Survey (THIS) reported the accomplishments towards the 90-90-90 global HIV targets at 61-94-87, affirming the need to focus on the first 90 (i.e., getting 90% of people living with HIV (PLHIV) tested). We conducted a patient-pathway analysis to understand the gap observed, by assessing the alignment between where PLHIV seek healthcare and where HIV services are available in the Shinyanga region, Tanzania. We used existing and publicly available data from the National AIDS Control program, national surveys, registries, and relevant national reports. Region-wide, the majority (n = 458/722, 64%) of THIS respondents accessed their last HIV test at public sector facilities. There were 65.9%, 45.1%, and 74.1% who could also access antiretroviral therapy (ART), CD4 testing, and HIV viral load testing at the location of their last HIV test, respectively. In 2019, the viral suppression rate estimated among PLHIV on ART in the Shinyanga region was 91.5%. PLHIV access HIV testing mostly in public health facilities; our research shows that synergies can be achieved to improve access to services further down the cascade in this sector. Furthermore, effective engagement with the private sector (not-for-profit and for-profit) will help to achieve the last mile toward ending the HIV epidemic.

##### Assuntos
Epidemias , Infecções por HIV , Testes Diagnósticos de Rotina , Infecções por HIV/tratamento farmacológico , Infecções por HIV/epidemiologia , Humanos , População Rural , Tanzânia/epidemiologia
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