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

We thank all members of Observatório COVID-19 BR and the CoMo Consortium for the collaborative work. The authors also thank the research funding agencies: São Paulo Research Foundation (FAPESP) – Brazil (grant number: 2019/26310-2 and 2017/26770-8 to CF, 2018/24037-4 to SP, 2018/23984-0 to VS and contract number: 2016/01343-7 to RAK), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) – Brazil (Finance Code 001 to LSF) and the Brazilian National Council for Scientific and Technological Development (CNPq) (grant number: 315854/2020-0 to MEB, 313055/2020-3 to PIP and 311832/2017-2 to RAK). RA is funded by the Bill and Melinda Gates Foundation (OPP1193472). LW is funded by the Li Ka Shing Foundation, Hong Kong. The CoMo Consortium has support from the Oxford University COVID-19 Research Response Fund (ref: 0009280).Peer reviewedPublisher PD

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

Funding: This work was supported by the Coordination of Superior Level Staff Improvement (CAPES), Brazil (Finance Code 001 to LSF and FMDM), National Council for Scientific and Technological Development (CNPq), Brazil (grant number: 315854/2020-0 to MEB, 141698/2018-7 to RLPS, 312559/2020-8 to MASMV and 311832/2017-2 to RAK), São Paulo Research Foundation (FAPESP), Brazil (grant #2019/26310-2 and #2017/26770-8 to CF, #2018/26512-1 to OC, #2018/24037-4 to SP, #2018/23984-0 to VS and contract #2016/01343-7 to RAK) and Swiss National Science Foundation (grant PCEFP3_181243 to VS). The Sound Foundation (Massachusetts, USA) provided financial support for the open-source publication of this work via a grant to The University of Oxford (UK) to support the work of members of the COVID-19 International Modeling (CoMo) Consortium. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Modeling the impact of school reopening and contact tracing strategies on COVID-19 dynamics in different epidemiologic settings in Brazil

This study was funded by the Brazilian National Council for Scientific and Technological Development (CNPq) - Process # 402834/2020-8 (request for proposals MCTIC/CNPq/FNDCT/MS/SCTIE/Decit Number 07/2020). The funding sources played no role in the study design; collection, analysis, or interpretation of the data; writing the report, or decision to submit the paper for publication. MEB received a technological and industrial scholarship from CNPq (grant number 315854/2020-0). LSF received a masters scholarship from Coordination of Superior Level Staff Improvement (CAPES) (finance code 001). SP was supported by Sao Paulo State Research Support Foundation (FAPESP) (grant number: 2018/24037-4). CF was supported by FAPESP (grant number: 2019/26310-2 and 2017/26770-8). RAK has been supported by CNPq (grant number: 311832/2017-2) and FAPESP (contract number: 2016/01343-7). PIP has been supported by CNPq (grant number: 313055/2020-3). RSK has been supported by CNPq (proc. 312378/2019-0). MQMR received a postdoctoral scholarship from CAPES (grant number 305269/2020-8). CMT has been supported by CNPq productivity fellowship and the National Institute of Science and Technology for Health Technology Assessment (IATS) (proc: 465518/2014-1). AMB received a technological and industrial scholarship from CNPq (grant number 402834/2020-8). LMS received a technological and industrial scholarship from CNPq (grant number 315866/2020-9). JAFD-F has been supported by CNPq productivity fellowship and the National Institutes for Science and Technology in Ecology, Evolution and Biodiversity Conservation (INCT-EEC), supported by MCTIC/CNPq (proc. 465610/2014-5) and FAPEG (proc. 201810267000023).Preprin

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 en- vironments, they alone are not sufficient to avoid significant impacts on community transmission

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

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

Brazil in the face of new SARS-CoV-2 variantsemergencies and challenges in public health

Peer reviewedPublisher PD

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 BrazilResearch in context

Summary: 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)