Dynamics of COVID-19 in Amazonia: A history of government denialism and the risk of a third wave.

The city of Manaus (the capital of Brazil's state of Amazonas) has become a key location for understanding the dynamics of the global pandemic of COVID-19. Different groups of scientists have foreseen different scenarios, such as the second wave or that Manaus could escape such a wave by having reached herd immunity. Here we test five hypotheses that explain the second wave of COVID-19 in Manaus: 1) The greater transmissibility of the Amazonian (gamma or P.1) variant is responsible for the second wave; 2) SARS-CoV-2 infection levels during the first wave were overestimated by those foreseeing herd immunity, and the population remained below this threshold when the second wave began at the beginning of December 2020; 3) Antibodies acquired from infection by one lineage do not confer immunity against other lineages; 4) Loss of immunity has generated a feedback phenomenon among infected people, which could generate future waves, and 5) A combination of the foregoing hypotheses. We also evaluated the possibility of a third wave in Manaus despite advances in vaccination, the new wave being due to the introduction of the delta variant in the region and the loss of immunity from natural contact with the virus. We developed a multi-strain SEIRS (Susceptible-Exposed-Infected-Removed-Susceptible) model and fed it with data for Manaus on mobility, COVID-19 hospitalizations, numbers of cases and deaths. Our model contemplated the current vaccination rates for all vaccines applied in Manaus and the individual protection rates already known for each vaccine. Our results indicate that the SARS-CoV-2 gamma (P.1) strain that originated in the Amazon region is not the cause of the second wave of COVID-19 in Manaus, but rather this strain originated during the second wave and became predominant in January 2021. Our multi-strain SEIRS model indicates that neither the doubled transmission rate of the gamma variant nor the loss of immunity alone is sufficient to explain the sudden rise of hospitalizations in late December 2020. Our results also indicate that the most plausible explanation for the current second wave is a SARS-CoV-2 infection level at around 50% of the population in early December 2020, together with loss of population immunity and early relaxation of restrictive measures. The most-plausible model indicates that contact with one strain does not provide protection against other strains and that the gamma variant has a transmissibility rate twice that of the original SARS-CoV-2 strain. Our model also shows that, despite the advance of vaccination, and even if future vaccination advances at a steady pace, the introduction of the delta variant or other new variants could cause a new wave of COVID-19.

Brazil's COVID-19 Epicenter in Manaus: How Much of the Population Has Already Been Exposed and Are Vulnerable to SARS-CoV-2?

Is Brazil's COVID-19 epicenter really approaching herd immunity? A recent study estimated that in October 2020 three-quarters of the population of Manaus (the capital of the largest state in the Brazilian Amazon) had contact with SARS-CoV-2. We show that 46% of the Manaus population having had contact with SARS-CoV-2 at that time is a more plausible estimate, and that Amazonia is still far from herd immunity. The second wave of COVID-19 is now evident in Manaus. We predict that the pandemic of COVID-19 will continue throughout 2021, given the duration of naturally acquired immunity of only 240 days and the slow pace of vaccination. Manaus has a large percentage of the population that is susceptible (35 to 45% as of May 17, 2021). Against this backdrop, measures to restrict urban mobility and social isolation are still necessary, such as the closure of schools and universities, since the resumption of these activities in 2020 due to the low attack rates of SARS-CoV-2 was the main trigger for the second wave in Manaus.

Dynamics of COVID-19 in Amazonia: a history of government denialism and the risk of a third wave

The city of Manaus (the capital of Brazil’s state of Amazonas) has become a key location for understanding the dynamics of the global pandemic of COVID-19. Different groups of scientists have foreseen different scenarios, such as the second wave or that Manaus could escape such a wave by having reached herd immunity. Here we test five hypotheses that explain the second wave of COVID-19 in Manaus: 1) The greater transmissibility of the Amazonian (gamma or P.1) variant is responsible for the second wave; 2) SARS-CoV-2 infection levels during the first wave were overestimated by those foreseeing herd immunity, and the population remained below this threshold when the second wave began at the beginning of December 2020; 3) Antibodies acquired from infection by one lineage do not confer immunity against other lineages; 4) Loss of immunity has generated a feedback phenomenon among infected people, which could generate future waves, and 5) A combination of the foregoing hypotheses. We also evaluated the possibility of a third wave in Manaus despite advances in vaccination, the new wave being due to the introduction of the delta variant in the region and the loss of immunity from natural contact with the virus. We developed a multi-strain SEIRS (Susceptible-Exposed-Infected-Removed-Susceptible) model and fed it with data for Manaus on mobility, COVID-19 hospitalizations, numbers of cases and deaths. Our model contemplated the current vaccination rates for all vaccines applied in Manaus and the individual protection rates already known for each vaccine. Our results indicate that the SARS-CoV-2 gamma (P.1) strain that originated in the Amazon region is not the cause of the second wave of COVID-19 in Manaus, but rather this strain originated during the second wave and became predominant in January 2021. Our multi-strain SEIRS model indicates that neither the doubled transmission rate of the gamma variant nor the loss of immunity alone is sufficient to explain the sudden rise of hospitalizations in late December 2020. Our results also indicate that the most plausible explanation for the current second wave is a SARS-CoV-2 infection level at around 50% of the population in early December 2020, together with loss of population immunity and early relaxation of restrictive measures. The most-plausible model indicates that contact with one strain does not provide protection against other strains and that the gamma variant has a transmissibility rate twice that of the original SARS-CoV-2 strain. Our model also shows that, despite the advance of vaccination, and even if future vaccination advances at a steady pace, the introduction of the delta variant or other new variants could cause a new wave of COVID-19.

The First Case of Immunity Loss and SARS-CoV-2 Reinfection by the Same Virus Lineage in Amazonia.

We report the first confirmed record of a SARS-CoV-2 immunity loss and reinfection for the Amazon region and for Brazil by the same virus lineage. The patient presented an asymptomatic condition the first time and an aggravated one after reinfection. We raise the possibility of a recessive genotype in the Amazonian population that does not generate an immune memory response to SARS-CoV-2.

Brazil’s COVID-19 epicenter in Manaus: how much of the population has already been exposed and are vulnerable to SARS-CoV-2?

Is Brazil’s COVID-19 epicenter really approaching herd immunity? A recent study estimated that in October 2020 three-quarters of the population of Manaus (the capital of the largest state in the Brazilian Amazon) had contact with SARS-CoV-2. We show that 46% of the Manaus population having had contact with SARS-CoV-2 at that time is a more plausible estimate, and that Amazonia is still far from herd immunity. The second wave of COVID-19 is now evident in Manaus. We predict that the pandemic of COVID-19 will continue throughout 2021, given the duration of naturally acquired immunity of only 240 days and the slow pace of vaccination. Manaus has a large percentage of the population that is susceptible (35 to 45% as of May 17, 2021). Against this backdrop, measures to restrict urban mobility and social isolation are still necessary, such as the closure of schools and universities, since the resumption of these activities in 2020 due to the low attack rates of SARS-CoV-2 was the main trigger for the second wave in Manaus.

The first case of immunity loss and SARS-CoV-2 reinfection by the same virus lineage in Amazonia

We report the first confirmed record of a SARS-CoV-2 immunity loss and reinfection for the Amazon region and for Brazil by the same virus lineage. The patient presented an asymptomatic condition the first time and an aggravated one after reinfection. We raise the possibility of a recessive genotype in the Amazonian population that does not generate an immune memory response to SARS-CoV-2.

Vertical social distancing policy is ineffective to contain the COVID-19 pandemic.

Considering numerical simulations, this study shows that the so-called vertical social distancing health policy is ineffective to contain the COVID-19 pandemic. We present the SEIR-Net model, for a network of social group interactions, as a development of the classic mathematical model of SEIR epidemics (Susceptible-Exposed-Infected (symptomatic and asymptomatic)-Removed). In the SEIR-Net model, we can simulate social contacts between groups divided by age groups and analyze different strategies of social distancing. In the vertical distancing policy, only older people are distanced, whereas in the horizontal distancing policy all age groups adhere to social distancing. These two scenarios are compared to a control scenario in which no intervention is made to distance people. The vertical distancing scenario is almost as bad as the control, both in terms of people infected and in the acceleration of cases. On the other hand, horizontal distancing, if applied with the same intensity in all age groups, significantly reduces the total infected people "flattening the disease growth curve". Our analysis considers the city of Belo Horizonte, Minas Gerais State, Brazil, but similar conclusions apply to other cities as well. Code implementation of the model in R-language is provided in the supplementary material.

Vertical social distancing policy is ineffective to contain the COVID-19 pandemic / A política de distanciamento social vertical é ineficaz para conter a pandemia da COVID-19 / La política de aislamiento social vertical es ineficaz para contener la pandemia de COVID-19

Abstract: Considering numerical simulations, this study shows that the so-called vertical social distancing health policy is ineffective to contain the COVID-19 pandemic. We present the SEIR-Net model, for a network of social group interactions, as a development of the classic mathematical model of SEIR epidemics (Susceptible-Exposed-Infected (symptomatic and asymptomatic)-Removed). In the SEIR-Net model, we can simulate social contacts between groups divided by age groups and analyze different strategies of social distancing. In the vertical distancing policy, only older people are distanced, whereas in the horizontal distancing policy all age groups adhere to social distancing. These two scenarios are compared to a control scenario in which no intervention is made to distance people. The vertical distancing scenario is almost as bad as the control, both in terms of people infected and in the acceleration of cases. On the other hand, horizontal distancing, if applied with the same intensity in all age groups, significantly reduces the total infected people "flattening the disease growth curve". Our analysis considers the city of Belo Horizonte, Minas Gerais State, Brazil, but similar conclusions apply to other cities as well. Code implementation of the model in R-language is provided in the supplementary material.

Resumo: O artigo demonstra através de simulações numéricas que a política do chamado distanciamento social vertical é ineficaz para conter a pandemia da COVID-19. Os autores apresentam o modelo SEIR-Net para uma rede de interações entre grupos sociais, enquanto desdobramento do modelo matemático clássico para epidemias, chamado SEIR (Suscetíveis-Expostos-Infectados (sintomáticos e assintomáticos)-Removidos). No modelo SEIR-Net, pode-se simular contatos sociais entre grupos, divididos por faixas etárias, e analisar diferentes estratégias de distanciamento social. Na política de distanciamento vertical, apenas os idosos ficam distanciados, ao contrário da política de distanciamento horizontal, em que todas as faixas etárias aderem ao distanciamento. O artigo compara esses dois cenários a um cenário controle, sem nenhuma intervenção para distanciar as pessoas umas das outras. O cenário do distanciamento vertical é quase tão ruim quanto aquele sem nenhum distanciamento, em termos tanto do número de infectados quanto da aceleração do número de casos. Por outro lado, o distanciamento horizontal, desde que aplicado com a mesma intensidade a todos os grupos etários, reduz significativamente o número total de infectados e "achata a curva de crescimento da doença". Nossa análise foi feita no Município de Belo Horizonte, Minas Gerais, Brasil, mas conclusões semelhantes se aplicam igualmente a outras cidades. O material suplementar do artigo fornece detalhes sobre a implementação do código do modelo na linguagem R.

Demostramos mediante simulaciones numéricas que la denominada política de salud de aislamiento social vertical es ineficaz para contener la pandemia de COVID-19. Presentamos el modelo SEIR-Net para interacciones de grupo en una red social, como una evolución del clásico modelo matemático SEIR epidemics (Susceptibles-Expuestos-Infectados (sintomáticos y asintomáticos)-Removidos). En el modelo SEIR-Net, podemos simular contactos sociales entre grupos divididos por grupos de edad y analizar diferentes estrategias de distanciamiento social. En la política de aislamiento vertical, solamente se aísla a los ancianos, frente a la política de aislamiento horizontal, donde todos los grupos de edad se adhieren al aislamiento social. Estos dos escenarios se compararon a un escenario de control, en el que no se realiza ninguna intervención para aislar a la gente. El escenario de aislamiento vertical es casi tan malo, como el escenario donde no se aplica ningún tipo de aislamiento, tanto en términos del número de infectados, como en la aceleración del número de casos. Por otro lado, el aislamiento horizontal, si se aplica con la misma intensidad en todos los grupos de edad, reduce significativamente el número total de infectados y "aplana la curva de crecimiento de la enfermedad". Nuestro análisis se realiza en la municipalidad de Belo Horizonte, Minas Gerais, Brasil, pero conclusiones similares se pueden aplicar también a otras ciudades. En el material complementario se facilita la implementación del código del modelo en R-language.

Cursos de graduação em medicina: uma análise a partir do sinaes / Undergraduate medical courses in Brazil: an analysis based on the sinaes system

Estudo descritivo analítico dos indicadores do Sistema Nacional de Avaliação da Educação Superior-Sinaes/Inep/MEC. Existem evidências de problemas metodológicos nos instrumentos do Exame Nacional de Desempenho dos Estudantes (Enade). Houve variação das matrizes de referência em 2004 e 2007, mudanças nas fórmulas e multicolinearidade no cálculo do Conceito Preliminar e do nível de dificuldade das provas, respectivamente 65 por cento em 2004 e 35 por cento em 2007. Nos dois períodos, quase metade das questões avaliou a capacidade de memorização (47 por cento e 42 por cento). A análise Cart apontou condição sociocultural, rede pública de ensino e percepção de alta oferta de formação complementar pela instituição como fatores associados ao melhor desempenho do concluinte. Tanto a nota no componente específico do concluinte como a diferença entre a nota de formação geral do concluinte e do ingressante são indicadores de forte discriminação de desempenho. Propõe-se um indicador multicritério dessas duas quantidades, que foi capaz de discriminar as instituições bem conceituadas da área médica. Matrizes de referência compatíveis e robustas são necessárias para o monitoramento de cursos que formem profissionais de excelência e que estejam conscientes de suas responsabilidades sociais.

This descriptive study of the indicators from the National System for the Evaluation of Higher Education-Sinaes/Inep/MEC. There is evidence of methodological problems in the construction of the instruments for the National Examination of Students' Performance (Enade). There was a variation in the reference matrices in 2004 and 2007, changes in the formulas, and multi-colinearity in calculation of the Preliminary Classification. In 2004, 65 percent of the questions were classified as "difficult", as compared to only 35 percent in 2007..Nearly half of the questions evaluated the capacity for memorization (47 percent and 42 percent). Cart analysis pointed to the following factors associated with better performance on the graduating student's: higher socioeconomic status, public institution, and high supply of complementary training by the institution. Both the graduating student's specific component grade and the difference between them and first-year student's overall classification appear as robust performance indicators. This study proposes a multiple-criteria indicator which proved capable of discriminating between highly rated institutions in the medical field. Consistent and robust reference matrices are necessary for monitoring courses that train excellent professionals who are aware of their social responsibilities.