Modeling the impact of child vaccination (5-11 y) on overall COVID-19 related hospitalizations and mortality in a context of omicron variant predominance and different vaccination coverage paces in Brazil.

Background: Developing countries have experienced significant COVID-19 disease burden. With the emergence of new variants, particularly omicron, the disease burden in children has increased. When the first COVID-19 vaccine was approved for use in children aged 5-11 years of age, very few countries recommended vaccination due to limited risk-benefit evidence for vaccination of this population. In Brazil, ranking second in the global COVID-19 death toll, the childhood COVID-19 disease burden increased significantly in early 2022. This prompted a risk-benefit assessment of the introduction and scaling-up of COVID-19 vaccination of children. Methods: To estimate the potential impact of vaccinating children aged 5-11 years with mRNA-based COVID-19 vaccine in the context of omicron dominance, we developed a discrete-time SEIR-like model stratified in age groups, considering a three-month time horizon. We considered three scenarios: No vaccination, slow, and maximum vaccination paces. In each scenario, we estimated the potential reduction in total COVID-19 cases, hospitalizations, deaths, hospitalization costs, and potential years of life lost, considering the absence of vaccination as the base-case scenario. Findings: We estimated that vaccinating at a maximum pace could prevent, between mid-January and April 2022, about 26,000 COVID-19 hospitalizations, and 4200 deaths in all age groups; of which 5400 hospitalizations and 410 deaths in children aged 5-11 years. Continuing vaccination at a slow/current pace would prevent 1450 deaths and 9700 COVID-19 hospitalizations in all age groups in this same time period; of which 180 deaths and 2390 hospitalizations in children only. Interpretation: Maximum vaccination of children results in a significant reduction of COVID-19 hospitalizations and deaths and should be enforced in developing countries with significant disease incidence in children. Funding: This manuscript was funded by the Brazilian Council for Scientific and Technology Development (CNPq - Process # 402834/2020-8).

Estimating the impact of implementation and timing of the COVID-19 vaccination programme in Brazil: a counterfactual analysis.

Background: Vaccines developed between 2020 and 2021 against the SARS-CoV-2 virus were designed to diminish the severity and prevent deaths due to COVID-19. However, estimates of the effectiveness of vaccination campaigns in achieving these goals remain a methodological challenge. In this work, we developed a Bayesian statistical model to estimate the number of deaths and hospitalisations averted by vaccination of older adults (above 60 years old) in Brazil. Methods: We fit a linear model to predict the number of deaths and hospitalisations of older adults as a function of vaccination coverage in this group and casualties in younger adults. We used this model in a counterfactual analysis, simulating alternative scenarios without vaccination or with faster vaccination roll-out. We estimated the direct effects of COVID-19 vaccination by computing the difference between hypothetical and realised scenarios. Findings: We estimated that more than 165,000 individuals above 60 years of age were not hospitalised due to COVID-19 in the first seven months of the vaccination campaign. An additional contingent of 104,000 hospitalisations could have been averted if vaccination had started earlier. We also estimated that more than 58 thousand lives were saved by vaccinations in the period analysed for the same age group and that an additional 47 thousand lives could have been saved had the Brazilian government started the vaccination programme earlier. Interpretation: Our estimates provided a lower bound for vaccination impacts in Brazil, demonstrating the importance of preventing the suffering and loss of older Brazilian adults. Once vaccines were approved, an early vaccination roll-out could have saved many more lives, especially when facing a pandemic. Funding: The Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brazil (Finance Code 001 to F.M.D.M. and L.S.F.), Conselho Nacional de Desenvolvimento Científico e Tecnológico - Brazil (grant number: 315854/2020-0 to M.E.B., 141698/2018-7 to R.L.P.d.S., 313055/2020-3 to P.I.P., 311832/2017-2 to R.A.K.), Fundação de Amparo à Pesquisa do Estado de São Paulo - Brazil (contract number: 2016/01343-7 to R.A.K.), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro - Brazil (grant number: E-26/201.277/2021 to L.S.B.) and Inova Fiocruz/Fundação Oswaldo Cruz - Brazil (grant number: 48401485034116) to L.S.B., O.G.C. and M.G.d.F.C. The funding agencies had no role in the conceptualization of the study.

Modelling the impact of school reopening and contact tracing strategies on Covid-19 dynamics in different epidemiologic settings in Brazil.

We simulate the impact of school reopening during the COVID-19 pandemic in three major urban centers in Brazil to identify the epidemiological indicators and the best timing for the return of in-school activities and the effect of contact tracing as a mitigation measure. Our goal is to offer guidelines for evidence-based policymaking. We implement an extended SEIR model stratified by age and considering contact networks in different settings - school, home, work, and community, in which the infection transmission rate is affected by various intervention measures. After fitting epidemiological and demographic data, we simulate scenarios with increasing school transmission due to school reopening, and also estimate the number of hospitalization and deaths averted by the implementation of contact tracing. Reopening schools results in a non-linear increase in reported COVID-19 cases and deaths, which is highly dependent on infection and disease incidence at the time of reopening. When contact tracing and quarantining are restricted to school and home settings, a large number of daily tests is required to produce significant effects in reducing the total number of hospitalizations and deaths. Policymakers should carefully consider the epidemiological context and timing regarding the implementation of school closure and return of in-person school activities. While contact tracing strategies prevent new infections within school environments, they alone are not sufficient to avoid significant impacts on community transmission.

Modelling optimal vaccination strategies against COVID-19 in a context of Gamma variant predominance in Brazil.

INTRODUCTION: Brazil experienced moments of collapse in its health system throughout 2021, driven by the emergence of variants of concern (VOC) combined with an inefficient initial vaccination strategy against Covid-19. OBJECTIVES: To support decision-makers in formulating COVID-19 immunization policy in the context of limited vaccine availability and evolving variants over time, we evaluate optimal strategies for Covid-19 vaccination in Brazil in 2021, when vaccination was rolled out during Gamma variant predominance. METHODS: Using a discrete-time epidemic model we estimate Covid-19 deaths averted, considering the currently Covid-19 vaccine products and doses available in Brazil; vaccine coverage by target population; and vaccine effectiveness estimates. We evaluated a 5-month time horizon, from early August to the end of December 2021. Optimal vaccination strategies compared the outcomes in terms of averted deaths when varying dose intervals from 8 to 12 weeks, and choosing the minimum coverage levels per age group required prior to expanding vaccination to younger target populations. We also estimated dose availability required over time to allow the implementation of optimal strategies. RESULTS: To maximize the number of averted deaths, vaccine coverage of at least 80 % should be reached in older age groups before starting vaccination into subsequent younger age groups. When evaluating varying dose intervals for AZD1222, reducing the dose interval from 12 to 8 weeks for the primary schedule would result in fewer COVID-19 deaths, but this can only be implemented if accompanied by an increase in vaccine supply of at least 50 % over the coming six-months in Brazil. CONCLUSION: Covid-19 immunization strategies should be tailored to local vaccine product availability and supply over time, circulating variants of concern, and vaccine coverage in target population groups. Modelling can provide valuable and timely evidence to support the implementation of vaccination strategies considering the local context, yet following international and regional technical evidence-based guidance.

Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2.

The SARS-CoV-2 pandemic is a major concern all over the world and, as vaccines became available at the end of 2020, optimal vaccination strategies were subjected to intense investigation. Considering their critical role in reducing disease burden, the increasing demand outpacing production, and that most currently approved vaccines follow a two-dose regimen, the cost-effectiveness of delaying the second dose to increment the coverage of the population receiving the first dose is often debated. Finding the best solution is complex due to the trade-off between vaccinating more people with lower level of protection and guaranteeing higher protection to a fewer number of individuals. Here we present a novel extended age-structured SEIR mathematical model that includes a two-dose vaccination schedule with a between-doses delay modelled through delay differential equations and linear optimization of vaccination rates. By maintaining the minimum stock of vaccines under a given production rate, we evaluate the dose interval that minimizes the number of deaths. We found that the best strategy depends on an interplay between the vaccine production rate and the relative efficacy of the first dose. In the scenario of low first-dose efficacy, it is always better to vaccinate the second dose as soon as possible, while for high first-dose efficacy, the best strategy of time window depends on the production rate and also on second-dose efficacy provided by each type of vaccine. We also found that the rate of spread of the infection does not affect significantly the thresholds of the best window, but is an important factor in the absolute number of total deaths. These conclusions point to the need to carefully take into account both vaccine characteristics and roll-out speed to optimize the outcome of vaccination strategies.

Percolation across households in mechanistic models of non-pharmaceutical interventions in SARS-CoV-2 disease dynamics.

Since the emergence of the novel coronavirus disease 2019 (COVID-19), mathematical modelling has become an important tool for planning strategies to combat the pandemic by supporting decision-making and public policies, as well as allowing an assessment of the effect of different intervention scenarios. A proliferation of compartmental models were developed by the mathematical modelling community in order to understand and make predictions about the spread of COVID-19. While compartmental models are suitable for simulating large populations, the underlying assumption of a well-mixed population might be problematic when considering non-pharmaceutical interventions (NPIs) which have a major impact on the connectivity between individuals in a population. Here we propose a modification to an extended age-structured SEIR (susceptible-exposed-infected-recovered) framework, with dynamic transmission modelled using contact matrices for various settings in Brazil. By assuming that the mitigation strategies for COVID-19 affect the connections among different households, network percolation theory predicts that the connectivity among all households decreases drastically above a certain threshold of removed connections. We incorporated this emergent effect at population level by modulating home contact matrices through a percolation correction function, with the few additional parameters fitted to hospitalisation and mortality data from the city of São Paulo. Our model with percolation effects was better supported by the data than the same model without such effects. By allowing a more reliable assessment of the impact of NPIs, our improved model provides a better description of the epidemiological dynamics and, consequently, better policy recommendations.

Brazil in the face of new SARS-CoV-2 variants: emergencies and challenges in public health.

This article discusses the epidemic situation of Covid-19 in Brazil, in the face of the emergence of a new strain called P.1, which is more transmissible and may be associated with reinfection. Given the collapse of hospital care in Manaus in January 2021 and the results of three recent preprints, each that reports increased transmissibility of the P.1 variant, we propose some urgent measures. Genomic surveillance based on multi-step diagnostics, starting with RT-PCR type tests and up to sequencing, should be established. Efforts to identify reinfections associated with this variant and the update of its definition in protocols should be prioritized, and studies on the efficacy of currently available vaccines in Brazil concerning the new variant should be conducted. We also propose improving the Brazilian health surveillance system such that genomic surveillance is coordinated and thereby better able to respond to future emergencies in a more timely fashion. We call on the public agents involved in health surveillance to share data and information regarding the epidemic in a clear, fast and transparent way. Finally, we propose a greater engagement in inter-institutional cooperation of all those involved in the response and production of knowledge about the pandemic in our country.

Letter to the Scientific Community: Brazil in face of the new SARS-CoV-2 variants / Carta à Comunidade Científica: o Brasil frente às novas variantes de SARSCoV- 2

This letter discusses the epidemic situation of Covid-19 in Brazil, in the face of the emergence of a new strain, called P1, more transmissible and with possible associated reinfection.  Given the collapse of hospital care in Manaus in January 2021 and the results of three recent preprints, all of which found increased transmissibility of the P.1 variant, we propose some urgent actions: the establishment of genomic surveillance based on multi-step diagnostics, starting with RT-PCR type tests  to sequencing; an immediate effort to identify reinfections associated with the new variant, updating its definition protocols; and studies on the efficacy of currently available vaccines in Brazil in respect to the new variant.  We also propose the improvement of the Brazilian health surveillance system, which should be articulated with genomic surveillance, in order to respond more timely to future emergencies. We call on the public agents involved in health surveillance to share data and information regarding the epidemic in a clear, fast and transparent way. Finally, we propose a greater engagement in inter-institutional cooperation of all those involved in the response and production of knowledge about the pandemic in our country.

Esta carta discute a situação epidêmica da Covid-19 no Brasil frente aoaparecimento de uma nova linhagem, chamada P1, mais transmissível e compossível re-infecção associada. Tendo em vista o colapso do atendimentohospitalar em Manaus em janeiro de 2021 e os resultados de três preprintsrecentes, todos encontrando maior transmissibilidade da variante P.1, propomos algumas ações urgentes: o estabelecimento de uma vigilância genômica baseada em diagnóstico em múltiplos passos, iniciando com os testes do tipo RT-PCR até o sequenciamento; um esforço imediato na identificação de re-infecções associadas à nova variante, atualizando os seus protocolos de definição; e estudos sobre a eficácia das vacinas atualmente disponíveis no Brasil na vigência da nova variante. Propomos, ademais, o aprimoramento do sistema de vigilância em saúde brasileiro, que seja articulado com a vigilância genômica, de forma a responder mais oportunamente a emergências futuras. Chamamos os agentes públicos implicados na vigilância em saúde para que compartilhem dados e informações referentes à epidemia de forma clara, rápida e transparente. Finalmente propomos um maior engajamento na cooperação inter-institucional de todos os envolvidos na resposta e produção de conhecimento sobre a pandemia em nosso país.

A mathematical model for zoonotic transmission of malaria in the Atlantic Forest: Exploring the effects of variations in vector abundance and acrodendrophily.

Transmission foci of autochthonous malaria caused by Plasmodium vivax-like parasites have frequently been reported in the Atlantic Forest in Southeastern and Southern Brazil. Evidence suggests that malaria is a zoonosis in these areas as human infections by simian Plasmodium species have been detected, and the main vector of malaria in the Atlantic Forest, Anopheles (Kerteszia) cruzii, can blood feed on human and simian hosts. In view of the lack of models that seek to predict the dynamics of zoonotic transmission in this part of the Atlantic Forest, the present study proposes a new deterministic mathematical model that includes a transmission compartment for non-human primates and parameters that take into account vector displacement between the upper and lower forest strata. The effects of variations in the abundance and acrodendrophily of An. cruzii on the prevalence of infected humans in the study area and the basic reproduction number (R0) for malaria were analyzed. The model parameters are based on the literature and fitting of the empirical data. Simulations performed with the model indicate that (1) an increase in the abundance of the vector in relation to the total number of blood-seeking mosquitoes leads to an asymptotic increase in both the proportion of infected individuals at steady state and R0; (2) the proportion of infected humans at steady state is higher when displacement of the vector mosquito between the forest strata increases; and (3) in most scenarios, Plasmodium transmission cannot be sustained only between mosquitoes and humans, which implies that non-human primates play an important role in maintaining the transmission cycle. The proposed model contributes to a better understanding of the dynamics of malaria transmission in the Atlantic Forest.

Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant.

Background: The SARS-CoV-2 variant of concern (VOC) P.1 (Gamma variant) emerged in the Amazonas State, Brazil, in November 2020. The epidemiological consequences of its mutations have not been widely studied, despite detection of P.1 in 36 countries, with local transmission in at least 5 countries. A range of mutations are seen in P.1, ten of them in the spike protein. It shares mutations with VOCs previously detected in the United Kingdom (B.1.1.7, Alpha variant) and South Africa (B.1.351, Beta variant). Methods: We estimated the transmissibility and reinfection of P.1 using a model-based approach, fitting data from the national health surveillance of hospitalized individuals and frequency of the P.1 variant in Manaus from December-2020 to February-2021. Results: Here we estimate that the new variant is about 2.6 times more transmissible (95% Confidence Interval: 2.4-2.8) than previous circulating variant(s). Manaus already had a high prevalence of individuals previously affected by the SARS-CoV-2 virus and our fitted model attributed 28% of Manaus cases in the period to reinfections by P.1, confirming the importance of reinfection by this variant. This value is in line with estimates from blood donors samples in Manaus city. Conclusions: Our estimates rank P.1 as one of the most transmissible among the SARS-CoV-2 VOCs currently identified, and potentially as transmissible as the posteriorly detected VOC B.1.617.2 (Delta variant), posing a serious threat and requiring measures to control its global spread.

Brazil in the face of new SARS-CoV-2 variants: emergencies and challenges in public health / O Brasil perante as novas variantes de SARS-CoV-2: emergências e desafios em saúde pública

ABSTRACT: This article discusses the epidemic situation of Covid-19 in Brazil, in the face of the emergence of a new strain called P.1, which is more transmissible and may be associated with reinfection. Given the collapse of hospital care in Manaus in January 2021 and the results of three recent preprints, each that reports increased transmissibility of the P.1 variant, we propose some urgent measures. Genomic surveillance based on multi-step diagnostics, starting with RT-PCR type tests and up to sequencing, should be established. Efforts to identify reinfections associated with this variant and the update of its definition in protocols should be prioritized, and studies on the efficacy of currently available vaccines in Brazil concerning the new variant should be conducted. We also propose improving the Brazilian health surveillance system such that genomic surveillance is coordinated and thereby better able to respond to future emergencies in a more timely fashion. We call on the public agents involved in health surveillance to share data and information regarding the epidemic in a clear, fast and transparent way. Finally, we propose a greater engagement in inter-institutional cooperation of all those involved in the response and production of knowledge about the pandemic in our country.

RESUMO: Este artigo discute a situação epidêmica da COVID-19 no Brasil diante do aparecimento de uma nova linhagem, chamada P.1, mais transmissível e com possível reinfecção associada. Tendo em vista o colapso do atendimento hospitalar em Manaus em janeiro de 2021 e os resultados de três preprints recentes, dos quais todos encontraram maior transmissibilidade da variante P.1, propomos algumas ações urgentes: o estabelecimento de uma vigilância genômica baseada em diagnóstico em múltiplos passos, iniciando com os testes do tipo transcrição reversa seguida de reação em cadeia da polimerase (RT-PCR) até o sequenciamento; um esforço imediato na identificação de reinfecções associadas à nova variante, com a atualização dos protocolos de definição; e estudos sobre a eficácia das vacinas disponíveis no Brasil na vigência da nova variante. Propomos, ademais, o aprimoramento do sistema de vigilância em saúde brasileiro para que seja articulado com a vigilância genômica, de forma a responder mais oportunamente a emergências futuras. Chamamos os agentes públicos implicados na vigilância em saúde para que compartilhem dados e informações referentes à epidemia de forma clara, rápida e transparente. Finalmente propomos maior engajamento na cooperação interinstitucional de todos os envolvidos na resposta e produção de conhecimento sobre a pandemia em nosso país.

Biodiversity can help prevent malaria outbreaks in tropical forests.

BACKGROUND: Plasmodium vivax is a widely distributed, neglected parasite that can cause malaria and death in tropical areas. It is associated with an estimated 80-300 million cases of malaria worldwide. Brazilian tropical rain forests encompass host- and vector-rich communities, in which two hypothetical mechanisms could play a role in the dynamics of malaria transmission. The first mechanism is the dilution effect caused by presence of wild warm-blooded animals, which can act as dead-end hosts to Plasmodium parasites. The second is diffuse mosquito vector competition, in which vector and non-vector mosquito species compete for blood feeding upon a defensive host. Considering that the World Health Organization Malaria Eradication Research Agenda calls for novel strategies to eliminate malaria transmission locally, we used mathematical modeling to assess those two mechanisms in a pristine tropical rain forest, where the primary vector is present but malaria is absent. METHODOLOGY/PRINCIPAL FINDINGS: The Ross-Macdonald model and a biodiversity-oriented model were parameterized using newly collected data and data from the literature. The basic reproduction number ([Formula: see text]) estimated employing Ross-Macdonald model indicated that malaria cases occur in the study location. However, no malaria cases have been reported since 1980. In contrast, the biodiversity-oriented model corroborated the absence of malaria transmission. In addition, the diffuse competition mechanism was negatively correlated with the risk of malaria transmission, which suggests a protective effect provided by the forest ecosystem. There is a non-linear, unimodal correlation between the mechanism of dead-end transmission of parasites and the risk of malaria transmission, suggesting a protective effect only under certain circumstances (e.g., a high abundance of wild warm-blooded animals). CONCLUSIONS/SIGNIFICANCE: To achieve biological conservation and to eliminate Plasmodium parasites in human populations, the World Health Organization Malaria Eradication Research Agenda should take biodiversity issues into consideration.