Author
Patricia Asfora Falabella Leme
Other affiliations: Universidade Federal de Minas Gerais
Bio: Patricia Asfora Falabella Leme is an academic researcher from State University of Campinas. The author has contributed to research in topics: Viral shedding & Coronavirus. The author has an hindex of 3, co-authored 7 publications receiving 368 citations. Previous affiliations of Patricia Asfora Falabella Leme include Universidade Federal de Minas Gerais.
Topics: Viral shedding, Coronavirus
Papers
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University of Oxford1, University of São Paulo2, Federal University of Rio de Janeiro3, Université libre de Bruxelles4, Katholieke Universiteit Leuven5, Imperial College London6, University of Auvergne7, State University of Campinas8, Fundação Getúlio Vargas9, University of Edinburgh10, University of London11, University of Birmingham12, Universidade Federal de Minas Gerais13, DaimlerChrysler Aerospace14, Federal University of Uberlandia15, Federal University of Roraima16, Royal Veterinary College17, Faculdade de Medicina de São José do Rio Preto18, University of Southampton19
TL;DR: New light is shed on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and evidence that current interventions remain insufficient to keep virus transmission under control in this country is provided.
Abstract: Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in Sao Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.
286 citations
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05 Aug 2020
TL;DR: New light is shed on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil, and evidence that current interventions remain insufficient to keep virus transmission under control in the country is provided.
Abstract: Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1–1.6 in Sao Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within-state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average travelled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil, and provide evidence that current interventions remain insufficient to keep virus transmission under control in the country.
138 citations
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University of Oxford1, University of São Paulo2, Federal University of Rio de Janeiro3, Université libre de Bruxelles4, Imperial College London5, State University of Campinas6, University of Edinburgh7, University of London8, University of Birmingham9, Universidade Federal de Minas Gerais10, DaimlerChrysler Aerospace11, Federal University of Uberlandia12, Federal University of Roraima13, Royal Veterinary College14, Faculdade de Medicina de São José do Rio Preto15, University of Southampton16
TL;DR: Light is shed on the role of large and highly connected populated centres in the rapid ignition and establishment of SARS-CoV-2, and evidence that current interventions remain insufficient to keep virus transmission under control in Brazil is provided.
Abstract: Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Due to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus transmission and epidemic spread remain challenging. We investigate the impact of NPIs in Brazil using epidemiological, mobility and genomic data. Mobility-driven transmission models for Sao Paulo and Rio de Janeiro cities show that the reproduction number (Rt) reached below 1 following NPIs but slowly increased to values between 1 to 1.3 (1.0 - -1.6). Genome sequencing of 427 new genomes and analysis of a geographically representative genomic dataset from 21 of the 27 Brazilian states identified >100 international introductions of SARS-CoV-2 in Brazil. We estimate that three clades introduced from Europe emerged between 22 and 27 February 2020, and were already well-established before the implementation of NPIs and travel bans. During this first phase of the epidemic establishment of SARS-CoV-2 in Brazil, we find that the virus spread mostly locally and within-state borders. Despite sharp decreases in national air travel during this period, we detected a 25% increase in the average distance travelled by air passengers during this time period. This coincided with the spread of SARS-CoV-2 from large urban centers to the rest of the country. In conclusion, our results shed light on the role of large and highly connected populated centres in the rapid ignition and establishment of SARS-CoV-2, and provide evidence that current interventions remain insufficient to keep virus transmission under control in Brazil.
73 citations
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TL;DR: Improved and continued protection measures are necessary to mitigate the risk for reinfection among healthcare workers in Campinas, Brazil.
Abstract: We documented 4 cases of severe acute respiratory syndrome coronavirus 2 reinfection by non-variant of concern strains among healthcare workers in Campinas, Brazil. We isolated infectious particles from nasopharyngeal secretions during both infection episodes. Improved and continued protection measures are necessary to mitigate the risk for reinfection among healthcare workers.
16 citations
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16 Nov 2020TL;DR: A pesquisa qualitativa de carater participativo e com dimensao formativa for ampliar a possibilidade de aperfeicoamento do programa pelos sujeitos envolvidos a partir de elementos oriundos de their pratica, partindo do entendimento dos seus groups of interesse, formados pela equipe, usuarios, gestores e profissionais encaminhadores as mentioned in this paper.
Abstract: RESUMO Trata-se da avaliacao de um programa de prevencao e tratamento de Doencas Cronicas Nao Transmissiveis (DCNT) oferecido a comunidade de uma universidade publica por ambulatorio localizado em suas dependencias. O processo avaliativo teve como objetivo apreender a dinâmica e compreender a forma de interacao entre os atores envolvidos no cotidiano do programa, partindo do entendimento dos seus grupos de interesse, formados pela equipe, usuarios, gestores e profissionais encaminhadores. Realizou-se pesquisa qualitativa de carater participativo e com dimensao formativa para ampliar a possibilidade de aperfeicoamento do programa pelos sujeitos envolvidos a partir de elementos oriundos de sua pratica. A Avaliacao de Quarta Geracao de Guba e Lincoln e o Metodo Paideia de Campos foram norteadores metodologicos da pesquisa. A analise do material empirico foi agrupada em tres nucleos tematicos: metodo de trabalho, equipe e gestao do programa. Constatou-se que uma escuta reflexiva dos profissionais e fator decisivo para ampliar a autonomia dos usuarios e sua adesao terapeutica; a realizacao de grupos educativos no local de trabalho favoreceu a captacao para tratamento e participacao dos usuarios, especialmente os do genero masculino; e os encontros dos grupos possibilitam diversos ganhos objetivos e subjetivos, como a interacao social entre pessoas de diferentes areas da universidade.
1 citations
Cited by
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Imperial College London1, University of São Paulo2, University of Oxford3, University of Edinburgh4, Federal University of Uberlandia5, Instituto Adolfo Lutz6, Universidade Federal de Minas Gerais7, State University of Campinas8, National Institute of Amazonian Research9, Harvard University10, University of California, Los Angeles11, Temple University12, University of Southampton13, University of Birmingham14, Katholieke Universiteit Leuven15, Royal Veterinary College16, University of Copenhagen17
TL;DR: In this article, the authors used a two-category dynamical model that integrates genomic and mortality data to estimate that P.1 may be 1.7-to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.
Abstract: Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
985 citations
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TL;DR: The SARS-CoV-2 virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection.
Abstract: Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits, and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, SARS-CoV-2 RNA has been detected in felids, mink, and dogs in the field. Here, we describe an in-depth investigation using whole-genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection. Despite enhanced biosecurity, early warning surveillance, and immediate culling of animals in affected farms, transmission occurred between mink farms in three large transmission clusters with unknown modes of transmission. Of the tested mink farm residents, employees, and/or individuals with whom they had been in contact, 68% had evidence of SARS-CoV-2 infection. Individuals for which whole genomes were available were shown to have been infected with strains with an animal sequence signature, providing evidence of animal-to-human transmission of SARS-CoV-2 within mink farms.
802 citations
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TL;DR: The emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic has been witnessed as mentioned in this paper.
Abstract: The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.
593 citations
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TL;DR: In this article, a conceptual framework for the interaction of the human innate immune system with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was provided to link the clinical observations with experimental findings that have been made during the first year of the pandemic.
422 citations
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TL;DR: The spread of COVID-19 in Manaus, Brazil, shows that a largely unmitigated epidemic can infect a high fraction of the population and cause high mortality, and confirms that when poorly controlled, CO VID-19 caninfect a large proportion of the Population, causing high mortality.
Abstract: SARS-CoV-2 spread rapidly in the Brazilian Amazon and the attack rate there is an estimate of the final size of a largely unmitigated epidemic. We use a convenience sample of blood donors to show that by June, one month after the epidemic peak in Manaus, capital of Amazonas state, 44% of the population had detectable IgG antibodies. Correcting for cases without a detectable antibody response and antibody waning, we estimate a 66% attack rate in June, rising to 76% in October. This is higher than in Sao Paulo, in southeastern Brazil, where the estimated attack rate in October is 29%. These results confirm that, when poorly controlled, COVID-19 can infect a high fraction of the population causing high mortality.
402 citations