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Mendes-Correa MC, Ghilardi FDR, Salomão MC, Villas-Boas LS, Paula AVD, Paiao HGO, Costa ACD, Tozetto-Mendoza TR, Freire W, Sales FCS, Claro IM, Sabino EC, Faria NR, Witkin SS. SARS-CoV-2 shedding, infectivity, and evolution in an immunocompromised adult patient. Rev Inst Med Trop Sao Paulo 2024; 66:e28. [PMID: 38747849 PMCID: PMC11095242 DOI: 10.1590/s1678-9946202466028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/25/2024] [Indexed: 05/19/2024] Open
Abstract
This study aimed to provide further insight into the evolutionary dynamics of SARS-CoV-2 by analyzing the case of a 40-year-old man who had previously undergone autologous hematopoietic stem cell transplantation due to a diffuse large B-cell lymphoma. He developed a persistent SARS-CoV-2 infection lasting at least 218 days and did not manifest a humoral immune response to the virus during this follow-up period. Whole-genome sequencing and viral cultures confirmed a persistent infection with a replication-positive virus that had undergone genetic variation for at least 196 days after symptom onset.
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Affiliation(s)
- Maria Cassia Mendes-Correa
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Fábio de Rose Ghilardi
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
| | - Matias Chiarastelli Salomão
- Hospital 9 de Julho, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, São Paulo, São Paulo, Brazil
| | - Lucy Santos Villas-Boas
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Anderson Vicente de Paula
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Heuder Gustavo Oliveira Paiao
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Tânia Regina Tozetto-Mendoza
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Wilton Freire
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
| | - Flavia Cristina Silva Sales
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
| | - Ingra Morales Claro
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-46), São Paulo, São Paulo, Brazil
- Imperial College, Department of Infectious Disease Epidemiology, London, United Kindgom
- University of Oxford, Department of Zoology, Oxford, United Kindgom
| | - Steven Sol Witkin
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), São Paulo, São Paulo, Brazil
- Weill Cornell Medicine, Department of Obstetrics and Gynecology, New York, New York, USA
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2
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Machado LC, Dezordi FZ, de Lima GB, de Lima RE, Silva LCA, Pereira LDM, da Silva AF, Silva Neto AMD, Oliveira ALSD, Armstrong ADC, Pessoa-E-Silva R, Loyo RM, Silva BDO, de Almeida AR, da Rocha Pitta MG, Santos FDADS, Mendonça Siqueira M, Resende PC, Delatorre E, Naveca FG, Miyajima F, Gräf T, do Carmo RF, Pereira MC, Campos TDL, Bezerra MF, Paiva MHS, Wallau GDL. Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco-Brazil. Microbiol Spectr 2024:e0421823. [PMID: 38651879 DOI: 10.1128/spectrum.04218-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving a large death toll. As of January 2023, Brazil is among the countries with the highest number of registered deaths. Nonpharmacological and pharmacological interventions have been heterogeneously implemented in the country, which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics. Here, we investigate the spatiotemporal dispersion of SARS-CoV-2 lineages in the Pernambuco state (Northeast Brazil) throughout the distinct epidemiological scenarios that unfolded in the first 2 years of the pandemic. We generated a total of 1,389 new SARS-CoV-2 genomes from June 2020 to August 2021. This sampling captured the arrival, communitary transmission, and the circulation of the B1.1, B.1.1.28, and B.1.1.33 lineages; the emergence of the former variant of interest P.2; and the emergence and fast replacement of all previous variants by the more transmissible variant of concern P.1 (Gamma). Based on the incidence and lineage spread pattern, we observed an East-to-West to inner state pattern of transmission, which is in agreement with the transmission of more populous metropolitan areas to medium- and small-size country-side cities in the state. Such transmission patterns may be partially explained by the main routes of traffic across municipalities in the state. Our results highlight that the fine-grained intrastate analysis of lineages and incidence spread can provide actionable insights for planning future nonpharmacological intervention for air-borne transmissible human pathogens.IMPORTANCEDuring the COVID-19 pandemic, Brazil was one of the most affected countries, mainly due its continental-size, socioeconomic differences among regions, and heterogeneous implementation of intervention methods. In order to investigate SARS-CoV-2 dynamics in the state of Pernambuco, we conducted a spatiotemporal dispersion study, covering the period from June 2020 to August 2021, to comprehend the dynamics of viral transmission during the first 2 years of the pandemic. Throughout this study, we were able to track three significant epidemiological waves of transmission caused by B1.1, B.1.1.28, B.1.1.33, P.2, and P.1 lineages. These analyses provided valuable insights into the evolution of the epidemiological landscape, contributing to a deeper understanding of the dynamics of virus transmission during the early years of the pandemic in the state of Pernambuco.
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Affiliation(s)
- Lais Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
| | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Gustavo Barbosa de Lima
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Raul Emídio de Lima
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Lilian Caroliny Amorim Silva
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Leandro de Mattos Pereira
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | | | - André Luiz Sá de Oliveira
- Núcleo de Estatística e Geoprocessamento, Instituto Aggeu Magalhães (IAM)- Fundação Oswaldo Cruz Pernambuco- FIOCRUZ-PE, Recife, Brazil
| | | | - Rômulo Pessoa-E-Silva
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Rodrigo Moraes Loyo
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Barbara de Oliveira Silva
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Anderson Rodrigues de Almeida
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Maira Galdino da Rocha Pitta
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Manaus, Amazonas, Brazil
| | - Fabio Miyajima
- Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceará, Fortaleza, Ceará, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | | | - Michelly Cristiny Pereira
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Tulio de Lima Campos
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Matheus Filgueira Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Marcelo Henrique Santos Paiva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste, Caruaru, Brazil
| | - Gabriel da Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
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da Rocha CBA, Machado LMG, Silva PRDS, de Freitas BHBM, Battisti IDE, Soares Dos Santos E, Ferreira SMB. Morbidity trend and space-time clusters of COVID-19 occurrence in children and adolescents. J Pediatr (Rio J) 2024; 100:196-203. [PMID: 37952930 PMCID: PMC10943318 DOI: 10.1016/j.jped.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
OBJECTIVE To analyze the morbidity trend and space-time distribution clusters of confirmed COVID-19 cases in children and adolescents. METHOD An ecological study of COVID-19 cases confirmed in the Information System from 2020 to 2022 in the age group from 0 to 19 years old, residents in Mato Grosso municipalities, Brazilian Midwest region. A trend analysis of the monthly morbidity rate of cases/100,000 inhabitants was used, following Prais-Winsten's regression. A space-time distribution of the Bayesian incidence rate per 100,000 inhabitants was performed, in addition to a space-time scan to identify high-risk clusters. RESULTS Of all 79,592 COVID-19 cases studied, 51.6% were in females and 44.21% in people aged 15-19 years old. The mean monthly rate was 265.87 cases per 100,000 inhabitants, with a stationary trend in the period analyzed (Monthly Percentage Variation [MPV]) = 12.15; CI95%[MPV]: -0.73;26.70). The morbidity rate due to COVID-19 was higher in the female gender (283.14/100,000 inhabitants) and in the age group from 15 to 19 years old (485.90/100,000 inhabitants). An increasing trend was observed with a greater monthly time variation of 14.42% (CI95%[MPV]: 1.28;29.28)] among those aged from 10 to 14 years old. The primary cluster, which was also the one with the highest Relative Risk (RR = 5,16, p-value = 0.001), included 19 municipalities located in the North health macro-region. CONCLUSION The findings indicated a monthly stationary trend in the study population, an increase in the age group from 10 to 14 years old, and areas at a higher risk for the disease in the North health macro-region of the state.
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Affiliation(s)
| | | | | | | | - Iara Denise Endruweit Battisti
- Universidade Federal da Fronteira Sul (UFFS), Programa de Pós-Graduação em Desenvolvimento e Políticas Públicas, Cerro Largo, RS, Brazil
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Teixeira DG, Rodrigues-Neto JF, da Cunha DCS, Jeronimo SMB. Understanding SARS-CoV-2 spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil. Infect Genet Evol 2024; 118:105556. [PMID: 38242186 DOI: 10.1016/j.meegid.2024.105556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
SARS-CoV-2 genome underwent mutations since it started circulating within the human population. The aim of this study was to understand the fluctuation of the spike clusters concomitant to the population immunity either due to natural infection and/or vaccination in a state of Brazil that had both high rate of natural infection and vaccination coverage. A total of 1725 SARS-CoV-2 sequences from the state of Rio Grande do Norte, Brazil, were retrieved from GISAID and subjected to cluster analysis. Immunoinformatics were used to predict T- and B-cell epitopes, followed by simulation to estimate either pro- or anti-inflammatory responses and to correlate with circulating variants. From March 2020 to June 2022, the state of Rio Grande do Norte reported 579,931 COVID-19 cases with a 1.4% fatality rate across the three major waves: May-Sept 2020, Feb-Aug 2021, and Jan-Mar 2022. Cluster 0 variants (wild type strain, Zeta) were prevalent in the first wave and Delta (AY.*), which circulated in Brazil in the latter half of 2021, featuring fewer unique epitopes. Cluster 1 (Gamma (P.1 + P.1.*)) dominated the first half of 2021. Late 2021 had two new clusters, Cluster 2 (Omicron, (B.1.1.529 + BA.*)), and Cluster 3 (BA.*) with the most unique epitopes, in addition to Cluster 4 (Delta sub lineages) which emerged in the second half of 2021 with fewer unique epitopes. Cluster 1 epitopes showed a high pro-inflammatory propensity, while others exhibited a balanced cytokine induction. The clustering method effectively identified Spike groups that may contribute to immune evasion and clinical presentation, and explain in part the clinical outcome.
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Affiliation(s)
- Diego Gomes Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - João Firmino Rodrigues-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Escola Multicampi de Ciências Médicas do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Caicó, Rio Grande do Norte, Brazil
| | - Dayse Caroline Severiano da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Selma Maria Bezerra Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Departmento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil; Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais, Natal, Rio Grande do Norte, Brazil.
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Freitas MTDS, Sena LOC, Fukutani KF, dos Santos CA, Neto FDCB, Ribeiro JS, dos Reis ES, Balbino VDQ, de Sá Paiva Leitão S, de Aragão Batista MV, Lipscomb MW, de Moura TR. The increase in SARS-CoV-2 lineages during 2020-2022 in a state in the Brazilian Northeast is associated with a number of cases. Front Public Health 2023; 11:1222152. [PMID: 38186707 PMCID: PMC10771345 DOI: 10.3389/fpubh.2023.1222152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 11/15/2023] [Indexed: 01/09/2024] Open
Abstract
SARS-CoV-2 has caused a high number of deaths in several countries. In Brazil, there were 37 million confirmed cases of COVID-19 and 700,000 deaths caused by the disease. The population size and heterogeneity of the Brazilian population should be considered in epidemiological surveillance due to the varied tropism of the virus. As such, municipalities and states must be factored in for their unique specificities, such as socioeconomic conditions and population distribution. Here, we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and their dynamics in each microregion from Sergipe state, northeastern Brazil, in the first 3 years of the pandemic. We analyzed 586 genomes sequenced between March 2020 and November 2022 extracted from the GISAID database. Phylogenetic analyses were carried out for each data set to reconstruct evolutionary history. Finally, the existence of a correlation between the number of lineages and infection cases by SARS-CoV-2 was evaluated. Aracaju, the largest city in northeastern Brazil, had the highest number of samples sequenced. This represented 54.6% (320) of the genomes, and consequently, the largest number of lineages identified. Studies also analyzed the relationship between mean lineage distributions and mean monthly infections, daily cases, daily deaths, and hospitalizations of vaccinated and unvaccinated patients. For this, a correlation matrix was created. Results revealed that the increase in the average number of SARS-CoV-2 variants was related to the average number of SARS-CoV-2 cases in both unvaccinated and vaccinated individuals. Thus, our data indicate that it is necessary to maintain epidemiological surveillance, especially in capital cities, since they have a high rate of circulation of resident and non-resident inhabitants, which contributes to the dynamics of the virus.
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Affiliation(s)
- Moises Thiago de Souza Freitas
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Brazil
- Parasitic Biology Graduate Program, Federal University of Sergipe, São Cristóvão, Brazil
| | - Ludmila Oliveira Carvalho Sena
- Health Foundation Parreiras Horta, Central Laboratory of Public Health (LACEN/SE), Sergipe State Health Secretariat, Aracaju, Brazil
| | - Kiyoshi Ferreira Fukutani
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Cliomar Alves dos Santos
- Health Foundation Parreiras Horta, Central Laboratory of Public Health (LACEN/SE), Sergipe State Health Secretariat, Aracaju, Brazil
| | | | - Julienne Sousa Ribeiro
- Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
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Tang CY, Li T, Haynes TA, McElroy JA, Ritter D, Hammer RD, Sampson C, Webby R, Hang J, Wan XF. Rural populations facilitated early SARS-CoV-2 evolution and transmission in Missouri, USA. Npj Viruses 2023; 1:7. [PMID: 38186942 PMCID: PMC10769004 DOI: 10.1038/s44298-023-00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/20/2023] [Indexed: 01/09/2024]
Abstract
In the United States, rural populations comprise 60 million individuals and suffered from high COVID-19 disease burdens. Despite this, surveillance efforts are biased toward urban centers. Consequently, how rurally circulating SARS-CoV-2 viruses contribute toward emerging variants remains poorly understood. In this study, we aim to investigate the role of rural communities in the evolution and transmission of SARS-CoV-2 during the early pandemic. We collected 544 urban and 435 rural COVID-19-positive respiratory specimens from an overall vaccine-naïve population in Southwest Missouri between July and December 2020. Genomic analyses revealed 53 SARS-CoV-2 Pango lineages in our study samples, with 14 of these lineages identified only in rural samples. Phylodynamic analyses showed that frequent bi-directional diffusions occurred between rural and urban communities in Southwest Missouri, and that four out of seven Missouri rural-origin lineages spread globally. Further analyses revealed that the nucleocapsid protein (N):R203K/G204R paired substitutions, which were detected disproportionately across multiple Pango lineages, were more associated with urban than rural sequences. Positive selection was detected at N:204 among rural samples but was not evident in urban samples, suggesting that viruses may encounter distinct selection pressures in rural versus urban communities. This study demonstrates that rural communities may be a crucial source of SARS-CoV-2 evolution and transmission, highlighting the need to expand surveillance and resources to rural populations for COVID-19 mitigation.
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Affiliation(s)
- Cynthia Y. Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tricia A. Haynes
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jane A. McElroy
- Family and Community Medicine, University of Missouriś, Columbia, MO, USA
| | - Detlef Ritter
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | - Richard D. Hammer
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | | | - Richard Webby
- Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA
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7
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Misra G, Manzoor A, Chopra M, Upadhyay A, Katiyar A, Bhushan B, Anvikar A. Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India. Sci Rep 2023; 13:14847. [PMID: 37684328 PMCID: PMC10491582 DOI: 10.1038/s41598-023-42065-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023] Open
Abstract
The various strains and mutations of SARS-CoV-2 have been tracked using several forms of genomic classification systems. The present study reports high-throughput sequencing and analysis of 99 SARS-CoV-2 specimens from Western Uttar Pradesh using sequences obtained from the GISAID database, followed by phylogeny and clade classification. Phylogenetic analysis revealed that Omicron lineages BA-2-like (55.55%) followed by Delta lineage-B.1.617.2 (45.5%) were predominantly circulating in this area Signature substitution at positions S: N501Y, S: D614G, S: T478K, S: K417N, S: E484A, S: P681H, and S: S477N were commonly detected in the Omicron variant-BA-2-like, however S: D614G, S: L452R, S: P681R and S: D950N were confined to Delta variant-B.1.617.2. We have also identified three escape variants in the S gene at codon position 19 (T19I/R), 484 (E484A/Q), and 681 (P681R/H) during the fourth and fifth waves in India. Based on the phylogenetic diversification studies and similar changes in other lineages, our analysis revealed indications of convergent evolution as the virus adjusts to the shifting immunological profile of its human host. To the best of our knowledge, this study is an approach to comprehensively map the circulating SARS-CoV-2 strains from Western Uttar Pradesh using an integrated approach of whole genome sequencing and phylogenetic analysis. These findings will be extremely valuable in developing a structured approach toward pandemic preparedness and evidence-based intervention plans in the future.
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Affiliation(s)
- Gauri Misra
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India.
| | - Ashrat Manzoor
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Meenu Chopra
- National Dairy Research Institute, Karnal, Haryana, India
| | - Archana Upadhyay
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Amit Katiyar
- Bioinformatics Facility, Centralized Core Research Facility, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Brij Bhushan
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Anup Anvikar
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
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8
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Ribeiro AF, Castro MC, Lotta G, Carvalho RDJ, Zamudio M, Barberia LG. Early response to COVID-19 in Brazil: The impact of a targeted approach to suspected cases and on epidemiological surveillance efforts. IJID Reg 2023; 7:242-251. [PMID: 37143704 PMCID: PMC10116149 DOI: 10.1016/j.ijregi.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/06/2023]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entered Brazil before travel restrictions and border closures were imposed. This study reports the characteristics of suspected and confirmed coronavirus disease 2019 (COVID-19) cases among symptomatic international travelers in Brazil and their contacts. Methods The REDCap platform developed by the Brazilian Ministry of Health was analyzed to identify and investigate suspected cases of COVID-19 recorded during the period January 1 to March 20, 2020. The impact of Brazil's targeted approach to suspected cases from specific countries on epidemiological surveillance efforts during the early stages of the COVID-19 pandemic were analyzed. Results Based on molecular RT-PCR tests, there were 217 (4.2%) confirmed, 1030 (20.1%) unconfirmed, 722 (14.1%) suspected, and 3157 (61.6%) non-investigated cases among travelers returning from countries included on the alert list for surveillance, as defined by the Ministry of Health. Among the 3372 travelers who went to countries not included on the alert list, there were 66 (2.0%) confirmed, 845 (25.3%) unconfirmed, 521 (15.6%) suspected, and 1914 (57.2%) non-investigated cases. A comparison of the characteristics of confirmed cases returning from alert and non-alert countries did not reveal a statistically significant difference in symptoms. Almost half of the hospitalized travelers with known travel dates and hospitalization status (53.6%) were inbound from countries not included on the alert list, and RT-PCR tests were reported for only 30.5%. Conclusions Policies adopted at entry points to contain the introduction of SARS-CoV-2 in Brazil were not ideal. An analysis of the early response shows that surveillance of travelers, including testing strategies, data standards, and reporting systems, was insufficient.
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Affiliation(s)
- Ana Freitas Ribeiro
- Institute of Infectious Diseases Emilio Ribas, Health Secretary of the State, Pacaembu, São Paulo, Brazil
- Municipal University of São Caetano do Sul, Centro, São Caetano do Sul, Brazil
| | - Marcia C Castro
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Gabriela Lotta
- Department of Public Administration, Getúlio Vargas Foundation, São Paulo, SP, Brazil
| | - Rebeca de J Carvalho
- Department of Public Administration and Government, FGV EAESP Business Administration School of São Paulo, Bela Vista, São Paulo - SP, Brazil
| | - Marcela Zamudio
- Department of Political Science, University of São Paulo, Cidade Universitária, São Paulo - SP, Brazil
| | - Lorena G Barberia
- Department of Political Science, University of São Paulo, Cidade Universitária, São Paulo - SP, Brazil
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9
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de Menezes MT, Moreira FRR, Whittaker C, Santos FM, Queiroz DC, Geddes V, Fonseca PLC, de Jesus JG, Mendes-Oliveira F, Reis-Souza V, Santos B, Zauli DAG, de Lima AB, de Brito Mendonça C, Alvim LB, do Prado Silva J, Malta FSV, de Souza Ferreira AC, Faria NR, Sabino EC, Aguiar RS. Dynamics of Early Establishment of SARS-CoV-2 VOC Omicron Lineages in Minas Gerais, Brazil. Viruses 2023; 15:585. [PMID: 36851799 PMCID: PMC9962645 DOI: 10.3390/v15020585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 02/22/2023] Open
Abstract
Brazil is one of the nations most affected by Coronavirus disease 2019 (COVID-19). The introduction and establishment of new virus variants can be related to an increase in cases and fatalities. The emergence of Omicron, the most modified SARS-CoV-2 variant, caused alarm for the public health of Brazil. In this study, we examined the effects of the Omicron introduction in Minas Gerais (MG), the second-most populous state of Brazil. A total of 430 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples from November 2021 to June 2022 from Belo Horizonte (BH) city were sequenced. These newly sequenced genomes comprise 72% of all previously available SARS-CoV-2 genomes for the city. Evolutionary analysis of novel viral genomes reveals that a great diversity of Omicron sublineages have circulated in BH, a pattern in-keeping with observations across Brazil more generally. Bayesian phylogeographic reconstructions indicate that this diversity is a product of a large number of international and national importations. As observed previously, São Paulo state is shown as a significant hub for viral spread throughout the country, contributing to around 70% of all viral Omicron introductions detected in MG.
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Affiliation(s)
- Mariane Talon de Menezes
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UK
| | - Franciele Martins Santos
- Laboratory of Integrative Biology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270, Brazil
| | - Daniel Costa Queiroz
- Laboratory of Integrative Biology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270, Brazil
| | - Victor Geddes
- Laboratory of Integrative Biology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270, Brazil
| | - Paula Luize Camargos Fonseca
- Laboratory of Integrative Biology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270, Brazil
| | - Jaqueline Góes de Jesus
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo 04023, Brazil
- Department of Infectious and Parasitic Diseases, Faculty of Medicine, University of São Paulo, São Paulo 04023, Brazil
| | - Franciane Mendes-Oliveira
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo 04023, Brazil
| | - Valquíria Reis-Souza
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo 04023, Brazil
| | | | | | - Aline Brito de Lima
- Pardini Group, Research and Development Department, Belo Horizonte 31270, Brazil
| | | | - Luige Biciati Alvim
- Pardini Group, Research and Development Department, Belo Horizonte 31270, Brazil
| | - Joice do Prado Silva
- Pardini Group, Research and Development Department, Belo Horizonte 31270, Brazil
| | | | | | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UK
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo 04023, Brazil
- Department of Zoology, University of Oxford, Oxford OX3 7BN, UK
| | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo 04023, Brazil
- Department of Infectious and Parasitic Diseases, Faculty of Medicine, University of São Paulo, São Paulo 04023, Brazil
| | - Renato Santana Aguiar
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- Laboratory of Integrative Biology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270, Brazil
- D’OR Institute of Research and Teaching, Rio de Janeiro 21941-901, Brazil
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10
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LaRotta J, Escobar O, Ávila-Aguero ML, Torres JP, Sini de Almeida R, Morales GDC, Srivastava A. COVID-19 in Latin America: A Snapshot in Time and the Road Ahead. Infect Dis Ther 2023; 12:389-410. [PMID: 36633818 PMCID: PMC9835740 DOI: 10.1007/s40121-022-00748-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023] Open
Abstract
Since its initial detection in Brazil in February 2020, SARS-CoV-2 and the associated COVID-19 pandemic have continued to devastate Latin America. Specific comorbidities, as well as sociodemographic and lifestyle factors that may be more prevalent in underserved areas, have been identified as risk factors for COVID-19 infection or associated adverse outcomes. Dynamics of infections and deaths in Latin America have varied by country and temporally, as has SARS-CoV-2 variant prevalence; however, more recently, the Delta and subsequent Omicron variants have become ubiquitous. Successful pandemic responses have involved robust infection mitigation measures, testing, and smart deployment of healthcare resourcing. While in some Latin American countries up to 90% of the population is fully vaccinated (i.e., 2 doses) against COVID-19, other countries have failed to reach the World Health Organization's 70% target. Continued focus on comprehensive surveillance, strategies to maximize vaccine availability and uptake, and mitigation of collateral damage on other aspects of public health and social services are critical for managing the COVID-19 pandemic. This review summarizes the COVID-19 experience in Latin America, including epidemiology and vaccination. Key learnings and future considerations for the ongoing pandemic response are also discussed.
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Affiliation(s)
- Jorge LaRotta
- Vaccines Medical and Scientific Affairs, Pfizer SAS, AV Suba 95-66, Bogotá, Colombia.
| | - Omar Escobar
- Vaccines Medical and Scientific Affairs, Pfizer SAS, AV Suba 95-66, Bogotá, Colombia
| | - María L Ávila-Aguero
- Pediatric Infectious Diseases, Hospital Nacional de Niños, San José, Costa Rica
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, CT, USA
| | - Juan Pablo Torres
- Departamento de Pediatría y Cirugía Infantil Oriente, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | | | - Amit Srivastava
- Vaccines, Medical Development, Scientific and Clinical Affairs, Pfizer Inc, Cambridge, MA, USA
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11
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Elias MC, Slavov SN, Lima ARJ, Martins AJ, Barros CRDS, Moretti DB, Araujo EL, Marqueze EC, Ribeiro G, Ribeiro GMF, Bernardino JST, Koser JR, Clemente LG, Crispin LAC, Alcantara LCJ, Coutinho LL, Giovanetti M, Silva QO, Neto RM, Haddad R, Kashima S, Viala VL, Covas DT, Sampaio SC. A traveling SARS-CoV-2 laboratory as part of a pandemic response among vulnerable Brazilian populations. BMC Public Health 2023; 23:15. [PMID: 36597102 PMCID: PMC9810251 DOI: 10.1186/s12889-022-14867-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/13/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Brazil has been dramatically hit by the SARS-CoV-2 pandemic and is a world leader in COVID-19 morbidity and mortality. Additionally, the largest country of Latin America has been a continuous source of SARS-CoV-2 variants and shows extraordinary variability of the pandemic strains probably related to the country´s outstanding position as a Latin American economical and transportation hub. Not all regions of the country show sufficient infrastructure for SARS-CoV-2 diagnosis and genotyping which can negatively impact the pandemic response. METHODS Due to this reason and to disburden the diagnostic system of the inner São Paulo State, the Butantan Institute established the Mobile Laboratory (in Portuguese: LabMovel) for SARS-CoV-2 testing which started a trip of the most important "hotspots" of the most populous Brazilian region. The LabMovel initiated in two important cities of the State: Aparecida do Norte (an important religious center) and the Baixada Santista region which incorporates the port of Santos, the busiest in Latin America. The LabMovel was fully equipped with an automatized system for SARS-CoV-2 diagnosis and sequencing/genotyping. It also integrated the laboratory systems for patient records and results divulgation including in the Federal Brazilian Healthcare System. RESULTS Currently,16,678 samples were tested, among them 1,217 from Aparecida and 4,564 from Baixada Santista. We tracked the delta introductio in the tested regions with its high diversification. The established mobile SARS-CoV-2 laboratory had a major impact on the Public Health System of the included cities including timely delivery of the results to the healthcare agents and the Federal Healthcare system, evaluation of the vaccination status of the positive individuals in the background of exponential vaccination process in Brazil and scientific and technological divulgation of the fieldwork to the most vulnerable populations. CONCLUSIONS The SARS-CoV-2 pandemic has demonstrated worldwide the importance of science to fight against this viral agent and the LabMovel shows that it is possible to integrate researchers, clinicians, healthcare workers and patients to take rapid actions that can in fact mitigate this and other epidemiological situations.
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Affiliation(s)
- Maria Carolina Elias
- Instituto Butantan, São Paulo, Brazil. .,Center of Toxins, Immune Response and Cell Signaling - CeTICSInstituto Butantan, São Paulo, 05503-900, Brazil.
| | - Svetoslav Nanev Slavov
- grid.11899.380000 0004 1937 0722University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil
| | | | | | | | | | | | | | - Gabriela Ribeiro
- grid.418514.d0000 0001 1702 8585Instituto Butantan, São Paulo, Brazil
| | | | | | | | | | | | - Luiz Carlos Junior Alcantara
- grid.418068.30000 0001 0723 0931Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais Brazil
| | | | - Marta Giovanetti
- grid.418068.30000 0001 0723 0931Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais Brazil
| | | | - Raul Machado Neto
- grid.418514.d0000 0001 1702 8585Instituto Butantan, São Paulo, Brazil
| | - Ricardo Haddad
- grid.418514.d0000 0001 1702 8585Instituto Butantan, São Paulo, Brazil
| | - Simone Kashima
- grid.11899.380000 0004 1937 0722University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil
| | | | - Dimas Tadeu Covas
- grid.418514.d0000 0001 1702 8585Instituto Butantan, São Paulo, Brazil ,grid.11899.380000 0004 1937 0722University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil
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12
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Gustani-Buss EG, Buss CE, Cavalli LR, Panis C, Tuon FF, Telles JP, Follador FAC, Wendt GW, Lucio LC, Ferreto LED, de Oliveira IM, Carraro E, David LE, Simão ANC, Boldt ABW, Luiza Petzl-Erler M, Silva WA, Figueiredo DLA. Cross-sectional study for COVID-19-related mortality predictors in a Brazilian state-wide landscape: the role of demographic factors, symptoms and comorbidities. BMJ Open 2022; 12:e056801. [PMID: 36253047 PMCID: PMC9577275 DOI: 10.1136/bmjopen-2021-056801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE The Brazilian state of Paraná has suffered from COVID-19 effects, understanding predictors of increased mortality in health system interventions prevent hospitalisation of patients. We selected the best models to evaluate the association of death with demographic characteristics, symptoms and comorbidities based on three levels of clinical severity for COVID-19: non-hospitalised, hospitalised non-ICU ward and ICU ward. DESIGN Cross-sectional survey using binomial mixed models. SETTING COVID-19-positive cases diagnosed by reverse transcription-PCR of municipalities located in Paraná State. PATIENTS Cases of anonymous datasets of electronic medical records from 1 April 2020 to 31 December 2020. PRIMARY AND SECONDARY OUTCOME MEASURES The best prediction factors were chosen based on criteria after a stepwise analysis using multicollinearity measure, lower Akaike information criterion and goodness-of-fit χ2 tests from univariate to multivariate contexts. RESULTS Male sex was associated with increased mortality among non-hospitalised patients (OR 1.76, 95% CI 1.47 to 2.11) and non-ICU patients (OR 1.22, 95% CI 1.05 to 1.43) for symptoms and for comorbidities (OR 1.89, 95% CI 1.59 to 2.25, and OR 1.30, 95% CI 1.11 to 1.52, respectively). Higher mortality occurred in patients older than 35 years in non-hospitalised (for symptoms: OR 4.05, 95% CI 1.55 to 10.54; and for comorbidities: OR 3.00, 95% CI 1.24 to 7.27) and in hospitalised over 40 years (for symptoms: OR 2.72, 95% CI 1.08 to 6.87; and for comorbidities: OR 2.66, 95% CI 1.22 to 5.79). Dyspnoea was associated with increased mortality in non-hospitalised (OR 4.14, 95% CI 3.45 to 4.96), non-ICU (OR 2.41, 95% CI 2.04 to 2.84) and ICU (OR 1.38, 95% CI 1.10 to 1.72) patients. Neurological disorders (OR 2.16, 95% CI 1.35 to 3.46), neoplastic (OR 3.22, 95% CI 1.75 to 5.93) and kidney diseases (OR 2.13, 95% CI 1.36 to 3.35) showed the majority of increased mortality for ICU as well in the three levels of severity jointly with heart disease, diabetes and CPOD. CONCLUSIONS These findings highlight the importance of the predictor's assessment for the implementation of public healthcare policy in response to the COVID-19 pandemic, mainly to understand how non-pharmaceutical measures could mitigate the virus impact over the population.
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Affiliation(s)
- Emanuele Gustani Gustani-Buss
- Bioinformatics Laboratory, Institute for Cancer Research, IPEC, Guarapuava, Brazil
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- New Arrangements for Research and Innovation - Genomics-Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Araucária Foundation - FAAP-PR, Curitiba, Parana, Brazil
| | - Carlos E Buss
- Bioinformatics Laboratory, Institute for Cancer Research, IPEC, Guarapuava, Brazil
- New Arrangements for Research and Innovation - Genomics-Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Araucária Foundation - FAAP-PR, Curitiba, Parana, Brazil
- MindFlow Genomics, Guarapuava, Brazil
| | - Luciane R Cavalli
- Postgraduate Program in Biotechnology Applied to Child and Adolescent Health at FPP, Faculdades Pequeno Príncipe, Curitiba, Brazil
| | - Carolina Panis
- Laboratory of Tumor Biology, Western Paraná State University-UNIOESTE, Cascavel, Brazil
| | - Felipe F Tuon
- Laboratory of Emerging Infectious Diseases, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Joao P Telles
- Laboratory of Emerging Infectious Diseases, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Franciele A C Follador
- Department of Life Sciences,Postgraduate Program in Applied Health Sciences, Western Paraná State University-UNIOESTE, Francisco Beltrão, Brazil
| | - Guilherme W Wendt
- Department of Life Sciences,Postgraduate Program in Applied Health Sciences, Western Paraná State University-UNIOESTE, Francisco Beltrão, Brazil
| | - Léia C Lucio
- Department of Life Sciences,Postgraduate Program in Applied Health Sciences, Western Paraná State University-UNIOESTE, Francisco Beltrão, Brazil
| | - Lirane E D Ferreto
- Department of Life Sciences,Postgraduate Program in Applied Health Sciences, Western Paraná State University-UNIOESTE, Francisco Beltrão, Brazil
| | - Isabela M de Oliveira
- New Arrangements for Research and Innovation - Genomics-Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Araucária Foundation - FAAP-PR, Curitiba, Parana, Brazil
- Institute for Cancer Research IPEC, Guarapuava, Brazil
| | - Emerson Carraro
- New Arrangements for Research and Innovation - Genomics-Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Araucária Foundation - FAAP-PR, Curitiba, Parana, Brazil
- Virology Laboratory, Midwestern Parana State University-UNICENTRO, Guarapuava, Brazil
| | - Lualis E David
- Virology Laboratory, Midwestern Parana State University-UNICENTRO, Guarapuava, Brazil
| | - Andréa N C Simão
- Laboratory of Research in Applied Immunology, Department of Pathology, Clinical Analysis and Toxicology, State University of Londrina-UEL, Londrina, Brazil
| | - Angelica B W Boldt
- New Arrangements for Research and Innovation - Genomics-Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Araucária Foundation - FAAP-PR, Curitiba, Parana, Brazil
- Postgraduate Program in Genetics, Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná-UFPR, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- New Arrangements for Research and Innovation - Genomics-Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Araucária Foundation - FAAP-PR, Curitiba, Parana, Brazil
- Postgraduate Program in Genetics, Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná-UFPR, Curitiba, Brazil
| | - Wilson A Silva
- Institute for Cancer Research IPEC, Guarapuava, Brazil
- Ribeirão Preto Medical School and Center for Cell-Based Therapy (CEPID/FAPESP), University of São Paulo (USP), Ribeirão Preto, Brazil
| | - David L A Figueiredo
- New Arrangements for Research and Innovation - Genomics-Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Araucária Foundation - FAAP-PR, Curitiba, Parana, Brazil
- Institute for Cancer Research IPEC, Guarapuava, Brazil
- Department of Medicine, Midwestern Paraná State University-UNICENTRO, Guarapuava, Brazil
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13
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Slavov SN, de La-Roque DGL, da Costa PNM, Rodrigues ES, Santos EV, Borges JS, Evaristo M, de Matos Maçonetto J, Marques AA, Milhomens J, Rós FA, Fonseca V, Lima ARJ, Ribeiro G, Lima LPO, Garibaldi PMM, Ferreira NN, Moraes GR, Marqueze EC, Barros CRDS, Martins AJ, Coutinho LL, Calado RT, Borges M, Elias MC, Sampaio SC, Giovanetti M, Alcantara LCJ, Covas DT, Kashima S. Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil. Viruses 2022; 14. [PMID: 36298703 DOI: 10.3390/v14102148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
From a country with one of the highest SARS-CoV-2 morbidity and mortality rates, Brazil has implemented one of the most successful vaccination programs. Brazil's first model city vaccination program was performed by the CoronaVac vaccine (Sinovac Biotech) in the town of Serrana, São Paulo State. To evaluate the vaccination effect on the SARS-CoV-2 molecular dynamics and clinical outcomes, we performed SARS-CoV-2 molecular surveillance on 4375 complete genomes obtained between June 2020 and April 2022 in this location. This study included the period between the initial SARS-CoV-2 introduction and during the vaccination process. We observed that the SARS-CoV-2 substitution dynamics in Serrana followed the viral molecular epidemiology in Brazil, including the initial identification of the ancestral lineages (B.1.1.28 and B.1.1.33) and epidemic waves of variants of concern (VOC) including the Gamma, Delta, and, more recently, Omicron. Most probably, as a result of the immunization campaign, the mortality during the Gamma and Delta VOC was significantly reduced compared to the rest of Brazil, which was also related to lower morbidity. Our phylogenetic analysis revealed the evolutionary history of the SARS-CoV-2 in this location and showed that multiple introduction events have occurred over time. The evaluation of the COVID-19 clinical outcome revealed that most cases were mild (88.9%, 98.1%, 99.1% to Gamma, Delta, and Omicron, respectively) regardless of the infecting VOC. In conclusion, we observed that vaccination was responsible for reducing the death toll rate and related COVID-19 morbidity, especially during the gamma and Delta VOC; however, it does not prevent the rapid substitution rate and morbidity of the Omicron VOC.
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14
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Silva AVFG, Menezes D, Moreira FRR, Torres OA, Fonseca PLC, Moreira RG, Alves HJ, Alves VR, Amaral TMDR, Coelho AN, Saraiva Duarte JM, da Rocha AV, de Almeida LGP, de Araújo JLF, de Oliveira HS, de Oliveira NJC, Zolini C, de Sousa JH, de Souza EG, de Souza RM, Ferreira LDL, Lehmkuhl Gerber A, Guimarães APDC, Maia PHS, Marim FM, Miguita L, Monteiro CC, Neto TS, Pugêdo FSF, Queiroz DC, Queiroz DNAC, Resende-Moreira LC, Santos FM, Souza EFC, Voloch CM, Vasconcelos AT, de Aguiar RS, de Souza RP. Seroprevalence, Prevalence, and Genomic Surveillance: Monitoring the Initial Phases of the SARS-CoV-2 Pandemic in Betim, Brazil. Front Microbiol 2022; 13:799713. [PMID: 35197952 PMCID: PMC8859412 DOI: 10.3389/fmicb.2022.799713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/07/2022] [Indexed: 11/18/2022] Open
Abstract
The COVID-19 pandemic has created an unprecedented need for epidemiological monitoring using diverse strategies. We conducted a project combining prevalence, seroprevalence, and genomic surveillance approaches to describe the initial pandemic stages in Betim City, Brazil. We collected 3239 subjects in a population-based age-, sex- and neighborhood-stratified, household, prospective; cross-sectional study divided into three surveys 21 days apart sampling the same geographical area. In the first survey, overall prevalence (participants positive in serological or molecular tests) reached 0.46% (90% CI 0.12–0.80%), followed by 2.69% (90% CI 1.88–3.49%) in the second survey and 6.67% (90% CI 5.42–7.92%) in the third. The underreporting reached 11, 19.6, and 20.4 times in each survey. We observed increased odds to test positive in females compared to males (OR 1.88 95% CI 1.25–2.82), while the single best predictor for positivity was ageusia/anosmia (OR 8.12, 95% CI 4.72–13.98). Thirty-five SARS-CoV-2 genomes were sequenced, of which 18 were classified as lineage B.1.1.28, while 17 were B.1.1.33. Multiple independent viral introductions were observed. Integration of multiple epidemiological strategies was able to adequately describe COVID-19 dispersion in the city. Presented results have helped local government authorities to guide pandemic management.
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Affiliation(s)
| | - Diego Menezes
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Paula Luize Camargos Fonseca
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rennan Garcias Moreira
- Centro de Laboratórios Multiusuários, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hugo José Alves
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Júlia Maria Saraiva Duarte
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - João Locke Ferreira de Araújo
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Camila Zolini
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jôsy Hubner de Sousa
- Programa de Pós-graduação em Biologia Celular, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Rafael Marques de Souza
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luciana de Lima Ferreira
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Fernanda Martins Marim
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lucyene Miguita
- Departamento de Patologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Daniel Costa Queiroz
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luciana Cunha Resende-Moreira
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Franciele Martins Santos
- Programa de Pós-graduação em Biologia Celular, Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Carolina Moreira Voloch
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Renato Santana de Aguiar
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Renan Pedra de Souza
- Programa de Pós Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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15
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Aggarwal D, Page AJ, Schaefer U, Savva GM, Myers R, Volz E, Ellaby N, Platt S, Groves N, Gallagher E, Tumelty NM, Le Viet T, Hughes GJ, Chen C, Turner C, Logan S, Harrison A, Peacock SJ, Chand M, Harrison EM. Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nat Commun 2022; 13:1012. [PMID: 35197443 PMCID: PMC8866425 DOI: 10.1038/s41467-022-28371-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/18/2022] [Indexed: 01/16/2023] Open
Abstract
Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16-20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement.
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Affiliation(s)
- Dinesh Aggarwal
- University of Cambridge, Department of Medicine, Cambridge, UK. .,Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. .,Cambridge University Hospital NHS Foundation Trust, Cambridge, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Ulf Schaefer
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Richard Myers
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Erik Volz
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
| | - Nicholas Ellaby
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Steven Platt
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Natalie Groves
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | | | - Niamh M Tumelty
- University of Cambridge, Cambridge University Libraries, Cambridge, UK
| | - Thanh Le Viet
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Gareth J Hughes
- Public Health England National Infections Service, Field Service, Leeds, UK
| | - Cong Chen
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Charlie Turner
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Sophie Logan
- Public Health England, National Infections Service, Field Service, Nottingham, UK
| | - Abbie Harrison
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | | | - Sharon J Peacock
- University of Cambridge, Department of Medicine, Cambridge, UK.,Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK.,Cambridge University Hospital NHS Foundation Trust, Cambridge, UK.,Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Meera Chand
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Ewan M Harrison
- University of Cambridge, Department of Medicine, Cambridge, UK. .,Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,University of Cambridge, Department of Public Health and Primary Care, Cambridge, UK.
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16
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Maia de Souza R, Ruedas Martins RC, Moyses Franco LA, Tuon FF, de Oliveira Junior IG, Maia da Silva CA, Imamura R, Amato VS. Identification of Leishmania species by next generation sequencing of hsp70 gene. Mol Cell Probes 2022; 61:101791. [PMID: 35051596 DOI: 10.1016/j.mcp.2022.101791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/24/2022]
Abstract
Leishmaniasis is a major public health problem worldwide. Although next generation sequencing technology has been widely used in the diagnosis of infectious diseases, it has been scarcely applied in identification of Leishmania species. The aim of this study was to compare the efficiency of MinION™ nanopore sequencing and polymerase chain reaction restriction fragment length polymorphism in identifying Leishmania species. Our results showed that the MinION™ sequencer was able to discriminate reference strains and clinical samples with high sensitivity in a cost and time effective manner without the prior need for culture.
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Affiliation(s)
- Regina Maia de Souza
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical, Laboratório de Parasitologia, São Paulo, Brazil
| | - Roberta Cristina Ruedas Martins
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical, Laboratório de Parasitologia, São Paulo, Brazil
| | - Lucas Augusto Moyses Franco
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical, Laboratório de Parasitologia, São Paulo, Brazil; Universidade de São Paulo, Faculdade de Medicina, Departamento de Doenças e Moléstias Infecciosas, São Paulo, Brazil
| | - Felipe Francisco Tuon
- Pontifícia Universidade Católica do Paraná, Laboratório de Doenças Infecciosas e Emergentes, Curitiba, Paraná, Brazil.
| | - Isael Gomes de Oliveira Junior
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical, Laboratório de Parasitologia, São Paulo, Brazil
| | - Camila Alves Maia da Silva
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical, Laboratório de Parasitologia, São Paulo, Brazil
| | - Rui Imamura
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Otorrinolaringologia, São Paulo, Brazil
| | - Valdir Sabbaga Amato
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical, Laboratório de Parasitologia, São Paulo, Brazil; Universidade de São Paulo, Faculdade de Medicina, Departamento de Doenças e Moléstias Infecciosas, São Paulo, Brazil
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17
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Napolitano F, Xu X, Gao X. Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies. Brief Bioinform 2022; 23:bbab456. [PMID: 34788381 PMCID: PMC8689952 DOI: 10.1093/bib/bbab456] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/08/2021] [Accepted: 10/07/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 caused the first severe pandemic of the digital era. Computational approaches have been ubiquitously used in an attempt to timely and effectively cope with the resulting global health crisis. In order to extensively assess such contribution, we collected, categorized and prioritized over 17 000 COVID-19-related research articles including both peer-reviewed and preprint publications that make a relevant use of computational approaches. Using machine learning methods, we identified six broad application areas i.e. Molecular Pharmacology and Biomarkers, Molecular Virology, Epidemiology, Healthcare, Clinical Medicine and Clinical Imaging. We then used our prioritization model as a guidance through an extensive, systematic review of the most relevant studies. We believe that the remarkable contribution provided by computational applications during the ongoing pandemic motivates additional efforts toward their further development and adoption, with the aim of enhancing preparedness and critical response for current and future emergencies.
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Affiliation(s)
- Francesco Napolitano
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Makkah, Saudi Arabia
| | - Xiaopeng Xu
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Makkah, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Makkah, Saudi Arabia
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18
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Villas-Boas LS, Paula AVD, Silva ARD, Paiao HGO, Tozetto-Mendoza TR, Manuli ER, Leal FE, Ferraz ADBC, Sabino EC, Bierrenbach AL, Witkin SS, Mendes-Correa MC. Absence of neutralizing antibodies against the Omicron SARS-CoV-2 variant in convalescent sera from individuals infected with the ancestral SARS-CoV-2 virus or its Gamma variant. Clinics (Sao Paulo) 2022; 77:100068. [PMID: 35767900 PMCID: PMC9212906 DOI: 10.1016/j.clinsp.2022.100068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/23/2022] [Accepted: 06/06/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES The aim of the present study was to evaluate if neutralizing antibody responses induced by infection with the SARS-CoV-2 strain that was dominant at the beginning of the pandemic or by the Gamma variant was effective against the Omicron variant. METHODS Convalescent sera from 109 individuals, never exposed to a SARS-CoV-2 vaccine, who had mild or moderate symptoms not requiring hospitalization following either a documented SARS-CoV-2 ancestral strain infection or a Gamma variant infection, were assayed for in vitro neutralizing antibody activity against their original strains and the Omicron variant. RESULTS Following an infection with the ancestral strain, 56 (93.3%), 45 (77.6%) and 1 (1.7%) serum sample were positive for neutralizing antibodies against the ancestral, Gamma variant, and Omicron variant, respectively. After infection with the Gamma variant, 43 (87.8%) and 2 (4.1%) sera were positive for neutralizing antibodies against the Gamma and Omicron variants, respectively. CONCLUSIONS Neutralizing antibodies generated following mild or moderate infection with the SARS-CoV-2 ancestral strain or the Gamma variant are not protective against the Omicron variant.
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Affiliation(s)
- Lucy Santos Villas-Boas
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, SP, Brazil; Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Anderson Vicente de Paula
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, SP, Brazil; Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Almir Ribeiro da Silva
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, SP, Brazil; Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Heuder Gustavo Oliveira Paiao
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, SP, Brazil; Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Tania Regina Tozetto-Mendoza
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, SP, Brazil; Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Erika Regina Manuli
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, SP, Brazil; Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Caetano, SP, Brazil
| | - Fábio Eudes Leal
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Caetano, SP, Brazil
| | | | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, SP, Brazil; Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil; Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Caetano, SP, Brazil
| | | | - Steven Sol Witkin
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, SP, Brazil; Weill Cornell Medicine, USA
| | - Maria Cassia Mendes-Correa
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, SP, Brazil; Departamento de Moléstias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil.
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19
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Mee P, Alexander N, Mayaud P, González FDJC, Abbott S, Santos AADS, Acosta AL, Parag KV, Pereira RH, Prete CA, Sabino EC, Faria NR, Brady OJ. Tracking the emergence of disparities in the subnational spread of COVID-19 in Brazil using an online application for real-time data visualisation: A longitudinal analysis. Lancet Reg Health Am 2022; 5:None. [PMID: 35098203 PMCID: PMC8782271 DOI: 10.1016/j.lana.2021.100119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Brazil is one of the countries worst affected by the COVID-19 pandemic with over 20 million cases and 557,000 deaths reported by August 2021. Comparison of real-time local COVID-19 data between areas is essential for understanding transmission, measuring the effects of interventions, and predicting the course of the epidemic, but are often challenging due to different population sizes and structures. METHODS We describe the development of a new app for the real-time visualisation of COVID-19 data in Brazil at the municipality level. In the CLIC-Brazil app, daily updates of case and death data are downloaded, age standardised and used to estimate the effective reproduction number (Rt ). We show how such platforms can perform real-time regression analyses to identify factors associated with the rate of initial spread and early reproduction number. We also use survival methods to predict the likelihood of occurrence of a new peak of COVID-19 incidence. FINDINGS After an initial introduction in São Paulo and Rio de Janeiro states in early March 2020, the epidemic spread to northern states and then to highly populated coastal regions and the Central-West. Municipalities with higher metrics of social development experienced earlier arrival of COVID-19 (decrease of 11·1 days [95% CI:8.9,13.2] in the time to arrival for each 10% increase in the social development index). Differences in the initial epidemic intensity (mean Rt ) were largely driven by geographic location and the date of local onset. INTERPRETATION This study demonstrates that platforms that monitor, standardise and analyse the epidemiological data at a local level can give useful real-time insights into outbreak dynamics that can be used to better adapt responses to the current and future pandemics. FUNDING This project was supported by a Medical Research Council UK (MRC-UK) -São Paulo Research Foundation (FAPESP) CADDE partnership award (MR/S0195/1 and FAPESP 18/14389-0).
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Affiliation(s)
- Paul Mee
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neal Alexander
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Philippe Mayaud
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Felipe de Jesus Colón González
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sam Abbott
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - André Luís Acosta
- Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
| | | | - Carlos A. Prete
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Oliver J Brady
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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20
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Ferreira FB, Barbosa Costa G, Sevá ADP, Albuquerque GR, Mariano APM, Sampaio Lopes AT, Fehlberg HF, Santos de Santana ÍT, dos Santos PR, Santos LC, Silva de Jesus LL, Fontana R, Maciel BM, Silva MDM, Barreto LE, Gadelha SR. Characteristics and Factors Associated with SARS-CoV-2 Infections in Individuals That Attended Referral Hospitals from Southern Region of Bahia State, Brazil: A Surveillance Network Retrospective Study. Viruses 2021; 13:2462. [PMID: 34960731 PMCID: PMC8708485 DOI: 10.3390/v13122462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/25/2021] [Indexed: 01/08/2023] Open
Abstract
In December 2019, a novel coronavirus was detected in Wuhan, China, and rapidly spread worldwide. In Brazil, to date, there have been more than 20,000,000 confirmed cases of COVID-19 and more than 550,000 deaths. The purpose of the current study was to determine the clinical and epidemiological profile of the population affected by COVID-19 that have attended referral hospitals in Southern region of Bahia State, to better understand the disease and its risk factors in order to enable more appropriate conduct for patients. An observational, descriptive, cross-sectional, exploratory study was conducted using secondary data collected from the Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz (LAFEM/UESC). Chi-squared and Fisher's exact tests were applied to determine the association between clinical symptoms and laboratory results, and to identify risk factors associated with SARS-CoV-2 infection. A total of 3135 individuals with suspected severe respiratory illness were analyzed and 41.4% of them tested positive for SARS-CoV-2 infection. Male individuals and having comorbidities were risk factors significantly associated with SARS-CoV-2 infection (OR = 1.17 and OR = 1.37, respectively). Interestingly, being a healthcare professional was a significantly protective factor (OR = 0.81, p < 0.001). Our findings highlight the importance of routinely testing the population for early identification of infected individuals, and also provide important information to health authorities and police makers to improve control measures, management, and screening protocols.
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Affiliation(s)
- Fabrício Barbosa Ferreira
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências da Saúde, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Galileu Barbosa Costa
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências da Saúde, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Anaiá da Paixão Sevá
- Departamento de Ciências Agrárias e AmBientais, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
| | - George Rego Albuquerque
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Agrárias e AmBientais, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
| | - Ana Paula Melo Mariano
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Amanda Teixeira Sampaio Lopes
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Agrárias e AmBientais, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
| | - Hllytchaikra Ferraz Fehlberg
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Agrárias e AmBientais, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
| | - Íris Terezinha Santos de Santana
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Pérola Rodrigues dos Santos
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Luciano Cardoso Santos
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Agrárias e AmBientais, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
| | - Laine Lopes Silva de Jesus
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Renato Fontana
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Bianca Mendes Maciel
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Mylene de Melo Silva
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
| | - Luane Etienne Barreto
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Agrárias e AmBientais, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
| | - Sandra Rocha Gadelha
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.B.F.); (G.R.A.); (A.P.M.M.); (A.T.S.L.); (H.F.F.); (Í.T.S.d.S.); (P.R.d.S.); (L.C.S.); (L.L.S.d.J.); (R.F.); (B.M.M.); (M.d.M.S.); (L.E.B.)
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
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21
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Pepe Razzolini MT, Funada Barbosa MR, Silva de Araújo R, Freitas de Oliveira I, Mendes-Correa MC, Sabino EC, Garcia SC, de Paula AV, Villas-Boas LS, Costa SF, Dropa M, Brandão de Assis D, Levin BS, Pedroso de Lima AC, Levin AS. SARS-CoV-2 in a stream running through an underprivileged, underserved, urban settlement in São Paulo, Brazil: A 7-month follow-up. Environ Pollut 2021; 290:118003. [PMID: 34425371 PMCID: PMC8373523 DOI: 10.1016/j.envpol.2021.118003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 05/11/2023]
Abstract
COVID-19 pandemic has led to concerns on the circulation of SARS-CoV-2 in the environment, its infectivity from the environment and, the relevance of transmission via environmental compartments. During 31 weeks, water samples were collected from a heavily contaminated stream going through an urban, underprivileged community without sewage collection. Our results showed a statistically significant correlation between cases of COVID-19 and SARS in the community, and SARS-CoV-2 concentrations in the water. Based on the model, if the concentrations of SARS-CoV-RNA (N1 and N2 target regions) increase 10 times, there is an expected increase of 104% [95%CI: (62-157%)] and 92% [95%CI: (51-143%)], respectively, in the number of cases of COVID-19 and SARS. We believe that differences in concentration of the virus in the environment reflect the epidemiological status in the community, which may be important information for surveillance and controlling dissemination in areas with vulnerable populations and poor sanitation. None of the samples were found infectious based cultures. Our results may be applicable globally as similar communities exist worldwide.
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Affiliation(s)
- Maria Tereza Pepe Razzolini
- School of Public Health of Universidade de São Paulo, Brazil; NARA - Center for Research in Environmental Risk Assessment, Brazil.
| | - Mikaela Renata Funada Barbosa
- NARA - Center for Research in Environmental Risk Assessment, Brazil; CETESB - Environmental Company of São Paulo State, Brazil
| | | | | | - Maria Cássia Mendes-Correa
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - Ester C Sabino
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | | | - Anderson V de Paula
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - Lucy S Villas-Boas
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - Silvia Figueiredo Costa
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - Milena Dropa
- School of Public Health of Universidade de São Paulo, Brazil
| | | | - Beatriz S Levin
- Guttman Community College, City University of New York, New York, USA
| | | | - Anna S Levin
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
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22
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Cunha MDP, Vilela APP, Molina CV, Acuña SM, Muxel SM, Barroso VDM, Baroni S, Gomes de Oliveira L, Angelo YDS, Peron JPS, Góes LGB, Campos ACDA, Minóprio P. Atypical Prolonged Viral Shedding With Intra-Host SARS-CoV-2 Evolution in a Mildly Affected Symptomatic Patient. Front Med (Lausanne) 2021; 8:760170. [PMID: 34901074 PMCID: PMC8661089 DOI: 10.3389/fmed.2021.760170] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/13/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is caused by a respiratory virus with a wide range of manifestations, varying from asymptomatic to fatal cases, with a generally short outcome. However, some individuals present long-term viral shedding. We monitored 38 individuals who were mildly affected by the SARS-CoV-2 infection. Out of the total studied population, three (7.9%) showed atypical events regarding the duration of positivity for viral RNA detection. In one of these atypical cases, a previously HIV-positive male patient presented a SARS-CoV-2 RNA shedding and subgenomic RNA (sgRNA) detected from the upper respiratory tract, respectively, for 232 and 224 days after the onset of the symptoms. The SARS-CoV-2 B.1.1.28 lineage, one of the most prevalent in Brazil in 2020, was identified in this patient in three serial samples. Interestingly, the genomic analyses performed throughout the infectious process showed an increase in the genetic diversity of the B.1.1.28 lineage within the host itself, with viral clearance occurring naturally, without any intervention measures to control the infection. Contrasting widely spread current knowledge, our results indicate that potentially infectious SARS-CoV-2 virus might be shed by much longer periods by some infected patients. This data call attention to better adapted non-pharmacological measures and clinical discharge of patients aiming at preventing the spread of SARS-CoV-2 to the population.
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Affiliation(s)
| | | | | | | | - Sandra Marcia Muxel
- Scientific Platform Pasteur—USP, São Paulo, Brazil
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vinícius de Morais Barroso
- Scientific Platform Pasteur—USP, São Paulo, Brazil
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | - Jean Pierre Schatzmann Peron
- Scientific Platform Pasteur—USP, São Paulo, Brazil
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Luiz Gustavo Bentim Góes
- Scientific Platform Pasteur—USP, São Paulo, Brazil
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Paola Minóprio
- Scientific Platform Pasteur—USP, São Paulo, Brazil
- Institut Pasteur, Paris, France
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23
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Peçanha-Pietrobom PM, Leite GGF, Hunter J, Ferreira PRA, Burattini MN, Bellei N, Ota-Arakaki JS, Salomao R. The clinical course of hospitalized moderately ill COVID-19 patients is mirrored by routine hematologic tests and influenced by renal transplantation. PLoS One 2021; 16:e0258987. [PMID: 34793468 PMCID: PMC8601535 DOI: 10.1371/journal.pone.0258987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/10/2021] [Indexed: 01/08/2023] Open
Abstract
Several studies of patients with COVID-19 have evaluated biological markers for predicting outcomes, most of them retrospectively and with a wide scope of clinical severity. We followed a prospective cohort of patients admitted in hospital wards with moderate COVID-19 disease, including those with a history of kidney transplantation, and examined the ability of changes in routine hematologic laboratory parameters to predict and mirror the patients' clinical course regarding the severity of their condition (classified as critical vs. non-critical) and in-hospital mortality or hospital discharge. Among the 68 patients, 20 (29%) were kidney transplanted patients (KT), and they had much higher mortality than non-kidney transplanted patients in this cohort (40% X 8.3%). Lymphocytes, neutrophils and neutrophils/lymphocytes ratio (NLR) at admission and platelets as well as the red blood cells parameters hemoglobin, hematocrit, and RDW by the time of hospital discharge or death clearly differentiated patients progressing to critical disease and those with clinical recovery. Patients with deteriorating clinical courses presented elevated and similar NLRs during the first week of hospitalization. However, they were dramatically different at hospital discharge, with a decrease in the survivors (NLR around 5.5) and sustained elevation in non-survivors (NLR around 21). Platelets also could distinguish survivors from non-survivors among the critical patients. In conclusion, routine hematologic tests are useful to monitor the clinical course of COVID-19 patients admitted with moderate disease. Unexpectedly, changes in hematologic tests, including lymphopenia, were not predictive of complicated outcomes among KT recipients.
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Affiliation(s)
- Paula M. Peçanha-Pietrobom
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | | | - James Hunter
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Paulo R. Abrão Ferreira
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Marcelo N. Burattini
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Nancy Bellei
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Jaquelina Sonoe Ota-Arakaki
- Division of Respiratory Diseases, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Reinaldo Salomao
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
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24
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Moreira FRR, D'arc M, Mariani D, Herlinger AL, Schiffler FB, Rossi ÁD, Leitão IDC, Miranda TDS, Cosentino MAC, Tôrres MCDP, da Costa RMDSC, Gonçalves CCA, Faffe DS, Galliez RM, Junior ODCF, Aguiar RS, Dos Santos AFA, Voloch CM, Castiñeiras TMPP, Tanuri A. Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil. Virus Evol 2021; 7:veab087. [PMID: 34725568 PMCID: PMC8522364 DOI: 10.1093/ve/veab087] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70 per cent, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates that VOC Gamma spread throughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95 per cent confidence interval = ± 0.7). This analysis corroborates the previously proposed mechanistic basis for this variant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.
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Affiliation(s)
- Filipe Romero Rebello Moreira
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Mirela D'arc
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | | | - Alice Laschuk Herlinger
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Francine Bittencourt Schiffler
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Átila Duque Rossi
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Isabela de Carvalho Leitão
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Cincias da Saúde, Bloco C, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Thamiris Dos Santos Miranda
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Matheus Augusto Calvano Cosentino
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Marcelo Calado de Paula Tôrres
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Raíssa Mirella Dos Santos Cunha da Costa
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Cássia Cristina Alves Gonçalves
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Débora Souza Faffe
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Cincias da Saúde, Bloco C, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Rafael Mello Galliez
- Departamento de Doenças Infecciosase Parasitárias, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco K, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Orlando da Costa Ferreira Junior
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Renato Santana Aguiar
- Departamento de Genética, Ecologia e Evolução, Laboratório de Biologia Integrativa, Universidade Federal de Minas Gerais, Belo Horizonte, Av. Antônio Carlos, 6627, Instituto de Ciências Biológicas, G3-60, Pampulha, Belo Horizonte 31270901, Brazil
| | - André Felipe Andrade Dos Santos
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Carolina Moreira Voloch
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Terezinha Marta Pereira Pinto Castiñeiras
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco K, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
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25
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Grosche VR, Santos IA, Ferreira GM, Dutra JVR, Costa LC, Nicolau-Junior N, Queiroz ATL, José DP, Jardim ACG. Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Microb Genom 2021; 7:000656. [PMID: 34730486 PMCID: PMC8743548 DOI: 10.1099/mgen.0.000656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
Since the beginning of the SARS-CoV-2 spread in Brazil, few studies have been published analysing the variability of viral genome. Herein, we described the dynamic of SARS-CoV-2 strains circulating in Brazil from May to September 2020, to better understand viral changes that may affect the ongoing pandemic. Our data demonstrate that some of the mutations identified are currently observed in variants of interest and variants of concern, and emphasize the importance of studying previous periods in order to comprehend the emergence of new variants. From 720 SARS-CoV-2 genome sequences, we found few sites under positive selection pressure, such as the D614G (98.5 %) in the spike, that has replaced the old variant; the V1167F in the spike (41 %), identified in the P.2 variant that emerged from Brazil during the period of analysis; and I292T (39 %) in the N protein. There were a few alterations in the UTRs, which was expected, however, our data suggest that the emergence of new variants was not influenced by mutations in UTR regions, since it maintained its conformational structure in most analysed sequences. In phylogenetic analysis, the spread of SARS-CoV-2 from the large urban centres to the countryside during these months could be explained by the flexibilization of social isolation measures and also could be associated with possible new waves of infection. These results allow a better understanding of SARS-CoV-2 strains that have circulated in Brazil, and thus, with relevant infomation, provide the potential viral changes that may have affected and/or contributed to the current and future scenario of the COVID-19 pandemic.
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Affiliation(s)
- Victória Riquena Grosche
- São Paulo State University, São José do Rio Preto, São Paulo, Brazil
- Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | | | | | | | - Larissa Catharina Costa
- Center of Data and Knowledge Integration for Health (CIDACS), Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil
| | | | - Artur Trancoso Lopo Queiroz
- Center of Data and Knowledge Integration for Health (CIDACS), Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil
| | - Diego Pandeló José
- Federal University of Triângulo Mineiro, Campus Universitário Iturama, Iturama, Minas Gerais, Brazil
| | - Ana Carolina Gomes Jardim
- São Paulo State University, São José do Rio Preto, São Paulo, Brazil
- Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
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Beltrão FEDL, Beltrão DCDA, Carvalhal G, Beltrão FEDL, Brito ADS, Capistrano KHRD, Bastos IHDA, Hecht F, Daltro CHDC, Bianco AC, Gonçalves MDCR, Ramos HE. Thyroid Hormone Levels During Hospital Admission Inform Disease Severity and Mortality in COVID-19 Patients. Thyroid 2021; 31:1639-1649. [PMID: 34314259 DOI: 10.1089/thy.2021.0225] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Illness severity in patients infected with COVID-19 is variable. Methods: Here, we conducted an observational, longitudinal, and prospective cohort study to investigate serum thyroid hormone (TH) levels in adult COVID-19 patients, admitted between June and August 2020, and to determine whether they reflect the severity or mortality associated with the disease. Results: Two hundred forty-five patients [median age: 62 (49-75) years] were stratified into non-critical (181) and critically ill (64) groups. Fifty-eight patients (23.6%) were admitted to the intensive care unit, and 41 (16.7%) died. Sixteen (6.5%) exhibited isolated low levels of free triiodothyronine (fT3). fT3 levels were lower in critically ill compared with non-critical patients [fT3: 2.82 (2.46-3.29) pg/mL vs. 3.09 (2.67-3.63) pg/mL, p = 0.007]. Serum reverse triiodothyronine (rT3) was mostly elevated but less so in critically ill compared with non-critical patients [rT3: 0.36 (0.28-0.56) ng/mL vs. 0.51 (0.31-0.67) ng/mL, p = 0.001]. The univariate logistic regression revealed correlation between in-hospital mortality and serum fT3 levels (odds ratio [OR]: 0.47; 95% confidence interval [CI 0.29-0.74]; p = 0.0019), rT3 levels (OR: 0.09; [CI 0.01-0.49]; p = 0.006) and the product fT3 × rT3 (OR: 0.47; [CI 0.28-0.74]; p = 0.0026). Serum thyrotropin, free thyroxine, and fT3/rT3 values were not significantly associated with mortality and severity of the disease. A serum cutoff level of fT3 (≤2.6 pg/mL) and rT3 (≤0.38 ng/mL) was associated with 3.46 and 5.94 OR of mortality, respectively. We found three COVID-19 mortality predictors using the area under the receiver operating characteristic (ROC) curve (AUC score): serum fT3 (AUC = 0.66), rT3 (AUC = 0.64), and the product of serum fT3 × rT3 (AUC = 0.70). Non-thyroidal illness syndrome (fT3 < 2.0 pg/mL) was associated with a 7.05 OR of mortality ([CI 1.78-28.3], p = 0.005) and the product rT3 × fT3 ≤ 1.29 with an 8.08 OR of mortality ([CI 3.14-24.2], p < 0.0001). Conclusions: This prospective study reports data on the largest number of hospitalized moderate-to-severe COVID-19 patients and correlates serum TH levels with illness severity, mortality, and other biomarkers to critical illness. The data revealed the importance of early assessment of thyroid function in hospitalized patients with COVID-19, given the good prognostic value of serum fT3, rT3, and fT3 × rT3 product. Further studies are necessary to confirm these observations.
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Affiliation(s)
- Fabyan Esberard de Lima Beltrão
- Department of Endocrinology, Lauro Wanderley University Hospital, Federal University of Paraíba, João Pessoa, Brazil
- Post-Graduation Program in Nutritional Sciences, Department of Nutrition, Center for Health Sciences, Federal University of Paraíba, João Pessoa, Brazil
- Department of Medicine, Faculty of Medical Sciences, João Pessoa, Brazil
| | | | - Giulia Carvalhal
- Center for Biological and Health Sciences, Federal University of Campina Grande, Campina Grande, Brazil
| | | | - Amanda da Silva Brito
- Department of Endocrinology, Lauro Wanderley University Hospital, Federal University of Paraíba, João Pessoa, Brazil
| | - Kamilla Helen Rodrigues da Capistrano
- Post-Graduation Program in Nutritional Sciences, Department of Nutrition, Center for Health Sciences, Federal University of Paraíba, João Pessoa, Brazil
| | - Isis Henriques de Almeida Bastos
- Post-Graduate Program in Medicine and Health, Medical School of Medicine; Health and Science Institute; Federal University of Bahia, Salvador, Brazil
| | - Fabio Hecht
- The Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carla Hilário da Cunha Daltro
- Post-Graduate Program in Medicine and Health, Medical School of Medicine; Health and Science Institute; Federal University of Bahia, Salvador, Brazil
- Department of Nutrition Sciences; Health and Science Institute; Federal University of Bahia, Salvador, Brazil
| | - Antonio Carlos Bianco
- Section of Endocrinology and Metabolism, Division of the Biological Sciences, University of Chicago, Chicago, Illinois, USA
| | - Maria da Conceição Rodrigues Gonçalves
- Post-Graduation Program in Nutritional Sciences, Department of Nutrition, Center for Health Sciences, Federal University of Paraíba, João Pessoa, Brazil
| | - Helton Estrela Ramos
- Post-Graduate Program in Medicine and Health, Medical School of Medicine; Health and Science Institute; Federal University of Bahia, Salvador, Brazil
- Postgraduate Program in Interactive Processes of Organs and Systems, Health & Science Institute; Health and Science Institute; Federal University of Bahia, Salvador, Brazil
- Bioregulation Department, Health and Science Institute; Federal University of Bahia, Salvador, Brazil
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Wolf JM, Kipper D, Borges GR, Streck AF, Lunge VR. Temporal spread and evolution of SARS-CoV-2 in the second pandemic wave in Brazil. J Med Virol 2021; 94:926-936. [PMID: 34596904 PMCID: PMC8661965 DOI: 10.1002/jmv.27371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil that presented more than 21 million coronavirus disease 2019 cases and 590 000 deaths. The recent emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide. The present study describes the temporal spreading and evolution of SARS‐CoV2 in the beginning of the second pandemic wave in Brazil, highlighting the fast dissemination of the two major concerning variants (P.1 and P.2). A total of 2507 SARS‐CoV‐2 whole‐genome sequences (WGSs) with available information from the country (Brazil) and sampling date (July 2020–February 2021), were obtained and the frequencies of the lineages were evaluated in the period of the growing second pandemic wave. The results demonstrated the increasing prevalence of P.1 and P.2 lineages in the period evaluated. P.2 lineage was first detected in the middle of 2020, but a high increase occurred only in the last trimester of this same year and the spreading to all Brazilian regions. P.1 lineage emerged even later, first in the North region in December 2020 and really fast dissemination to all other Brazilian regions in January and February 2021. All SARS‐CoV‐2 WGSs of P.1 and P.2 were further separately evaluated with a Bayesian approach. The rates of nucleotide and amino acid substitutions were statistically higher in P.1 than P.2 (p < 0.01). The phylodynamic analysis demonstrated that P.2 gradually spread in all the country from September 2020 to January 2021, while P.1 disseminated even faster from December 2020 to February 2021. Skyline plots of both lineages demonstrated a slight rise in the spreading for P.2 and exponential growth for P.1. In conclusion, these data demonstrated that the P.1 (recently renamed as Gamma) and P.2 lineages have predominated in the second pandemic wave due to the very high spreading across all geographic regions in Brazil at the end of 2020 and beginning of 2021. In Brazil, P.1 (Gamma) and P.2 lineages have predominated in the second pandemic wave. The Bayesian approach showed very high spreading for both lineages across all geographic regions at the end of 2020 and the beginning of 2021. P.2 increased only in the last trimester of 2020 and the spreading to all Brazilian regions. P.1 (Gamma) emerged even later with fast dissemination to all Brazilian regions in January and February 2021.
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Affiliation(s)
- Jonas M Wolf
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - Diéssy Kipper
- Laboratório de Diagnóstico em Medicina Veterinária, Universidade de Caxias do Sul, UCS, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Gabriela R Borges
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - André F Streck
- Laboratório de Diagnóstico em Medicina Veterinária, Universidade de Caxias do Sul, UCS, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Vagner R Lunge
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil.,Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
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Jacob Machado D, Scott R, Guirales S, Janies DA. Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV and SARS-CoV-2. Cladistics 2021; 37:461-488. [PMID: 34570933 PMCID: PMC8239696 DOI: 10.1111/cla.12454] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 also involves Chiroptera-hosted lineages. However, factors such as the lack of comprehensive phylogenies hamper our understanding of host shifts once MERS-CoV emerged in humans and Artiodactyla. Since 2019, the origin of SARS-CoV-2, causative agent of coronavirus disease 2019 (COVID-19), added to this episodic history of zoonotic transmission events. Here we introduce a phylogenetic analysis of 2006 unique and complete genomes of different lineages of Orthocoronavirinae. We used gene annotations to align orthologous sequences for total evidence analysis under the parsimony optimality criterion. Deltacoronavirus and Gammacoronavirus were set as outgroups to understand spillovers of Alphacoronavirus and Betacoronavirus among ten orders of animals. We corroborated that Chiroptera-hosted viruses are the sister group of SARS-CoV, SARS-CoV-2 and MERS-related viruses. Other zoonotic events were qualified and quantified to provide a comprehensive picture of the risk of coronavirus emergence among humans. Finally, we used a 250 SARS-CoV-2 genomes dataset to elucidate the phylogenetic relationship between SARS-CoV-2 and Chiroptera-hosted coronaviruses.
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Affiliation(s)
- Denis Jacob Machado
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Rachel Scott
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Sayal Guirales
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Daniel A. Janies
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
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Oliveira EA, Oliveira MCL, Martelli DB, Colosimo EA, Silva LR, Lanza K, Martelli-Júnior H, Simões E Silva AC. COVID-19 pandemic and the answer of science: a year in review. AN ACAD BRAS CIENC 2021; 93:e20210543. [PMID: 34495206 DOI: 10.1590/0001-3765202120210543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/05/2021] [Indexed: 01/16/2023] Open
Abstract
The world is looking forward to a prompt response by the scientific community in order to overcome the first pandemic of the 21st century. This study aimed to provide an overview of scientific output on COVID-19 during its first year. We assembled information regarding 60,830 articles related to COVID-19 indexed in the WoS database from January 24 to December 13, 2020. Only 4 countries accounted for about 60% of the articles (USA, China, Italy, and England) and 12 countries accounted for about 95% of the world scientific output on COVID-19 (USA, China, Italy, England, India, Canada, Germany, Spain, Australia, Brazil, Iran, and Turkey). 25 research centers around the world contributed with more than 500 papers on COVID-19. Papers were scattered throughout 6,133 journals, with 12 journals with > 250 articles. 20 articles (0.03%) have already received more than the 1,000 citations. The response of the scientific endeavor to this acute global public health emergency has been fast and robust. The overview provided by the analysis of the scientific response to the pandemic may contribute to further studies aiming to evaluate the impact and changes in the scientific endeavor for the next years in light of the forthcoming new world framework.
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Affiliation(s)
- Eduardo A Oliveira
- Federal University of Minas Gerais (UFMG), Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Alfredo Balena, 190, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Maria Christina L Oliveira
- Federal University of Minas Gerais (UFMG), Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Alfredo Balena, 190, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Daniella B Martelli
- State University of Montes Claros (Unimontes), Health Science/Primary Care Postgraduate Program, Prof. Rui Braga, s/n, 39401-089 Montes Claros, MG, Brazil
| | - Enrico Antônio Colosimo
- Federal University of Minas Gerais, Department of Statistics, Pres. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - Ludmila R Silva
- Federal University of Minas Gerais, Health Science/Postgraduate Program in Nursing. School of Nursing, Alfredo Balena 190, 30130-100 Belo Horizonte, MG, Brazil
| | - Katharina Lanza
- Federal University of Minas Gerais (UFMG), Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Alfredo Balena, 190, 30130-100 Belo Horizonte, Minas Gerais, Brazil
| | - Hercílio Martelli-Júnior
- State University of Montes Claros (Unimontes), Health Science/Primary Care Postgraduate Program, Prof. Rui Braga, s/n, 39401-089 Montes Claros, MG, Brazil
| | - Ana Cristina Simões E Silva
- Federal University of Minas Gerais (UFMG), Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Alfredo Balena, 190, 30130-100 Belo Horizonte, Minas Gerais, Brazil
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Tess BH, Granato CFH, Alves MCGP, Pintão MCT, Nunes MC, Rizzatti EG, Reinach FDC. Assessment of initial SARS-CoV-2 seroprevalence in the most affected districts in the municipality of São Paulo, Brazil. Braz J Infect Dis 2021; 25:101604. [PMID: 34416142 PMCID: PMC8352673 DOI: 10.1016/j.bjid.2021.101604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/20/2021] [Accepted: 07/07/2021] [Indexed: 12/23/2022] Open
Abstract
Background São Paulo city has been one of the regions most affected by the COVID-19 pandemic in Brazil. Frequent asymptomatic and oligosymptomatic infections and poor access to diagnostic tests make serosurveys crucial to monitor the magnitude of the epidemic and to inform public health policies, such as vaccination plans. Objectives To estimate, early in the epidemic, the seroprevalence of antibodies to SARS-CoV-2 in adults living in the six most affected districts in São Paulo city, and to assess potential associated risk factors. Methods This was a cross-sectional population-based survey of 1,152 households randomly selected from 72 census tracts. During the period May 4–12, 2020, 463 participants completed a questionnaire on sociodemographic characteristics and history of symptoms in the past two weeks, and provided a blood sample. Prevalence of SARS-CoV-2 antibodies was the outcome of interest and was estimated based on results of two immunoassays, Maglumi SARS-CoV-2 chemiluminescence assay Immunoglobulin (Ig) M (IgM) and IgG, and Roche electrochemiluminescence assay total Ig. Serum samples reactive to either assay were considered positive. Results Weighted overall seroprevalence was 6% (95%CI 3.9–8.3%). No association was observed between seropositivity and sex, age group or education level. Participants who reported black and brown skin color showed a 2.7 fold higher prevalence than people with white skin (p = 0.007). Among the 30 seropositive individuals, 14 (46.6%) reported no COVID-19 compatible symptoms in the past two weeks. Conclusion This study represents the first assessment of SARS-CoV-2 seroprevalence in the city of São Paulo and 6% is the baseline estimate of a series of population-based seroprevalence surveys. Serological screening using sound serological assays is the key tool to monitoring temporal and geographic changes in the spread of the virus through an important epicenter of the COVID-19 pandemic in Brazil. Ultimately, it may inform prevention and control efforts.
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Affiliation(s)
- Beatriz Helena Tess
- Universidade de São Paulo, Faculdade de Medicina FMUSP, Departamento de Medicina Preventiva, São Paulo, SP, Brazil.
| | | | | | | | | | - Edgar Gil Rizzatti
- Grupo Fleury, Divisão de Pesquisa e Desenvolvimento, São Paulo, SP, Brazil
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Abstract
OBJECTIVE This narrative, non-systematic review provides an update on the genetic aspects of the SARS-CoV-2 virus and its interactions with the human genome within the context of COVID-19. Although the main focus is on the etiology of this new disease, the genetics of SARS-CoV-2 impacts prevention, diagnosis, prognosis, and the development of therapies. DATA SOURCE A literature search was conducted on MEDLINE, BioRxiv, and SciELO, as well as a manual search on the internet (mainly in 2019 and 2020) using the keywords "COVID-19," "SARS-CoV-2," "coronavirus," "genetics," "molecular," "mutation," "vaccine," "Brazil," "Brasil," and combinations of these terms. The keywords "Brazil" and "Brasil" were used to find publications that were specific to the Brazilian population's molecular epidemiology data. Articles most relevant to the scope were selected non-systematically. DATA SYNTHESIS A number of publications illustrate an expanding knowledge on the genetics and genomics of SARS-CoV-2 and its implications for understanding COVID-19. CONCLUSIONS Knowledge of the SARS-CoV-2 genome sequence permits an in-depth investigation of the role its proteins play in the pathophysiology of COVID-19, which in turn will be enormously valuable for understanding the evolutionary, clinical, and epidemiological aspects of this disease and focusing on prevention and treatment.
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Affiliation(s)
- Salmo Raskin
- Laboratório Genetika, Curitiba, PR, Brazil; Comitê Científico de Genética, Sociedade Brasileira de Pediatria, Brazil.
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Assunção AÁ, Maia EG, Jardim R, de Araújo TM. Incidence of Reported Flu-Like Syndrome Cases in Brazilian Health Care Workers in 2020 (March to June). Int J Environ Res Public Health 2021; 18:ijerph18115952. [PMID: 34206062 PMCID: PMC8198595 DOI: 10.3390/ijerph18115952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 01/10/2023]
Abstract
Health care workers (HCWs) are at an increased risk of being exposed to COVID-19. This study aimed to characterize flu-like syndrome cases (FS) in HCWs notified in Brazil and compare them with FS cases in the general community (GC). In the Brazilian protocol, FS corresponds to a suspected case of COVID-19. The manuscript analyzed cases of FS in five Brazilian states, estimating the incidence rates of cases of FS and clinical and epidemiological characteristics. Registered cases (March to June 2020) totaled about 1,100,000 cases of FS. HCWs represented 17% of the registers, whose incidence was 20.41/100 vs. 2.15/100 in the GC. FS cases in HCWs concentrated the highest percentages in the age group of 30 to 49 years (65.15%) and among the nursing staff (46.86%). This study was the first interstate evaluation in Brazil to estimate suspected cases of FS by COVID-19 in HCWs. In order to control the spread of viral respiratory infections in HCWs, including COVID-19, it is necessary to review the management of health information to identify who they are, how many they are, and to what situations these workers are most frequently exposed, as well as in what professions they have. This information can guide specific, practical, and far-reaching actions.
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Affiliation(s)
- Ada Ávila Assunção
- Departamento de Medicina Preventiva e Social, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Brazil
- Correspondence:
| | - Emanuella Gomes Maia
- Departamento de Ciências da Saúde, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil;
| | - Renata Jardim
- Departamento de Educação e Saúde, Universidade Federal de Sergipe, Lagarto 49100-000, Brazil;
| | - Tânia Maria de Araújo
- Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, Brazil;
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Jorge DCP, Rodrigues MS, Silva MS, Cardim LL, da Silva NB, Silveira IH, Silva VAF, Pereira FAC, de Azevedo AR, Amad AAS, Pinho STR, Andrade RFS, Ramos PIP, Oliveira JF. Assessing the nationwide impact of COVID-19 mitigation policies on the transmission rate of SARS-CoV-2 in Brazil. Epidemics 2021; 35:100465. [PMID: 33984687 DOI: 10.1101/2020.06.26.20140780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 03/13/2021] [Accepted: 04/30/2021] [Indexed: 05/25/2023] Open
Abstract
COVID-19 is now identified in almost all countries in the world, with poorer regions being particularly more disadvantaged to efficiently mitigate the impacts of the pandemic. In the absence of efficient therapeutics or large-scale vaccination, control strategies are currently based on non-pharmaceutical interventions, comprising changes in population behavior and governmental interventions, among which the prohibition of mass gatherings, closure of non-essential establishments, quarantine and movement restrictions. In this work we analyzed the effects of 707 governmental interventions published up to May 22, 2020, and population adherence thereof, on the dynamics of COVID-19 cases across all 27 Brazilian states, with emphasis on state capitals and remaining inland cities. A generalized SEIR (Susceptible, Exposed, Infected and Removed) model with a time-varying transmission rate (TR), that considers transmission by asymptomatic individuals, is presented. We analyze the effect of both the extent of enforced measures across Brazilian states and population movement on the changes in the TR and effective reproduction number. The social mobility reduction index, a measure of population movement, together with the stringency index, adapted to incorporate the degree of restrictions imposed by governmental regulations, were used in conjunction to quantify and compare the effects of varying degrees of policy strictness across Brazilian states. Our results show that population adherence to social distance recommendations plays an important role for the effectiveness of interventions and represents a major challenge to the control of COVID-19 in low- and middle-income countries.
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Affiliation(s)
- Daniel C P Jorge
- Instituto de Fısica, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | | | - Mateus S Silva
- Instituto de Fısica, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Luciana L Cardim
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Bahia, Brazil
| | - Nívea B da Silva
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Bahia, Brazil; Instituto de Matemática e Estatística, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Ismael H Silveira
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Vivian A F Silva
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Bahia, Brazil
| | | | - Arthur R de Azevedo
- Instituto de Matemática e Estatística, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Alan A S Amad
- College of Engineering, Swansea University, Swansea, Wales, United Kingdom
| | - Suani T R Pinho
- Instituto de Fısica, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Roberto F S Andrade
- Instituto de Fısica, Universidade Federal da Bahia, Salvador, Bahia, Brazil; Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Bahia, Brazil
| | - Pablo I P Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Bahia, Brazil
| | - Juliane F Oliveira
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Bahia, Brazil; Centre of Mathematics of the University of Porto (CMUP), Department of Mathematics, Porto, Portugal.
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Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FCS, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MUG, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, Ferreira ACDS, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, Dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, Dos Santos HM, Aguiar RS, Proença-Modena JL, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Prete CA, Nascimento VH, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science 2021; 372:815-821. [PMID: 33853970 PMCID: PMC8139423 DOI: 10.1126/science.abh2644] [Citation(s) in RCA: 881] [Impact Index Per Article: 293.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/11/2021] [Indexed: 12/17/2022]
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.
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Affiliation(s)
- Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Thomas A Mellan
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Ingra M Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Darlan da S Candido
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Myuki A E Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
| | - Flavia C S Sales
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ruben J G Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lucas A M Franco
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana S Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline G de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pamela S Andrade
- Departamento de Epidemiologia, Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, Brazil
| | - Thais M Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia M Ferreira
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Camila A M Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Pedro S Peixoto
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - William M Souza
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Esmenia C Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leandro M de Souza
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana C de Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo J T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | | | | | | | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José L Proença-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Bruce Nelson
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - James A Hay
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, UK
| | | | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Raphael Sonabend
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Michaela Vollmer
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Axel Gandy
- Department of Mathematics, Imperial College London, London, UK
| | - Carlos A Prete
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - Vitor H Nascimento
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - Marc A Suchard
- Department of Biomathematics, Department of Biostatistics, and Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sergei L K Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | - Nick J Loman
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nelson A Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Maria do P S S Carvalho
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Wolf JM, Streck AF, Fonseca A, Ikuta N, Simon D, Lunge VR. Dissemination and evolution of SARS-CoV-2 in the early pandemic phase in South America. J Med Virol 2021; 93:4496-4507. [PMID: 33764553 PMCID: PMC8250755 DOI: 10.1002/jmv.26967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil with more than seven million cases of infection. Three major pandemic lineages/clades could be identified along with SARS-CoV-2 dissemination (G, GR, and GH) in the Americas. These clades differ according to their genomic characteristics, virulence, and spreading times. The present study describes the main clades and the respective temporal spreading analyses based on SARS-CoV-2 whole-genome sequences (WGS) from South America, obtained in the early pandemic phase (from March 1 to May 31 in 2020). SARS-CoV-2 WGSs with available information from country and year of sampling were obtained from different countries and the main clades were identified and analyzed independently with a Bayesian approach. The results demonstrated the prevalence of clades GR (n = 842; 54.6%), G (n = 529; 34.3%), and GH (n = 171; 11.1%). The frequencies of the clades were significantly different between South American countries. Clade G was the most prevalent in Ecuador, Suriname, and Uruguay, clade GR in Argentina, Brazil, and Peru, and clade GH in Colombia. The phylodynamic analysis indicated that all these main lineages increased viral spreading from February to early March and after an evolutionary stationary phase was observed. The decrease observed in the virus dissemination was directly associated to the reduction of social movement after March. In conclusion, these data demonstrated the current predominance of clades G, GR, and GH in South America because of the early dissemination of them in the first pandemic phase in South America.
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Affiliation(s)
- Jonas Michel Wolf
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - André Felipe Streck
- Universidade de Caxias do Sul, UCS, Caxias do Sul, Rio Grande do Sul, Brazil
| | - André Fonseca
- Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
| | - Nilo Ikuta
- Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
| | - Daniel Simon
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil
| | - Vagner Ricardo Lunge
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil.,Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
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36
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Braz LMA, Tahmasebi R, da Costa AC, Witkin SS. Disparity between scientific accomplishment and biotechnology availability in Brazil. Sci Prog 2021; 104:368504211028373. [PMID: 34191659 PMCID: PMC10454951 DOI: 10.1177/00368504211028373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Despite being among the world's leaders in scientific output, Brazil ranks 66th among countries in the production of reagents and supplies needed for state-of-the-art scientific analyses. The production of needed reagents and equipment for experimental analyses and patient diagnostics is sorely lacking within Brazil and explicit in this pandemic period caused by SARS-CoV-2. A significant fraction of resources from Brazilian funding agencies is now being transferred to companies in other countries for the purchase of essential scientific-related products. Is this sustainable? Therefore it is necessary to draw the attention of all the world and Brazilian society about this situation.
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Affiliation(s)
- Lucia Maria Almeida Braz
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Roozbeh Tahmasebi
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Steven S Witkin
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
- Weill Cornell Medicine, New York, NY, USA
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Li SL, Pereira RHM, Prete CA, Zarebski AE, Emanuel L, Alves PJH, Peixoto PS, Braga CKV, de Souza Santos AA, de Souza WM, Barbosa RJ, Buss LF, Mendrone A, de Almeida-Neto C, Ferreira SC, Salles NA, Marcilio I, Wu CH, Gouveia N, Nascimento VH, Sabino EC, Faria NR, Messina JP. Higher risk of death from COVID-19 in low-income and non-White populations of São Paulo, Brazil. BMJ Glob Health 2021; 6:e004959. [PMID: 33926892 PMCID: PMC8094342 DOI: 10.1136/bmjgh-2021-004959] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/08/2021] [Accepted: 04/06/2021] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Little evidence exists on the differential health effects of COVID-19 on disadvantaged population groups. Here we characterise the differential risk of hospitalisation and death in São Paulo state, Brazil, and show how vulnerability to COVID-19 is shaped by socioeconomic inequalities. METHODS We conducted a cross-sectional study using hospitalised severe acute respiratory infections notified from March to August 2020 in the Sistema de Monitoramento Inteligente de São Paulo database. We examined the risk of hospitalisation and death by race and socioeconomic status using multiple data sets for individual-level and spatiotemporal analyses. We explained these inequalities according to differences in daily mobility from mobile phone data, teleworking behaviour and comorbidities. RESULTS Throughout the study period, patients living in the 40% poorest areas were more likely to die when compared with patients living in the 5% wealthiest areas (OR: 1.60, 95% CI 1.48 to 1.74) and were more likely to be hospitalised between April and July 2020 (OR: 1.08, 95% CI 1.04 to 1.12). Black and Pardo individuals were more likely to be hospitalised when compared with White individuals (OR: 1.41, 95% CI 1.37 to 1.46; OR: 1.26, 95% CI 1.23 to 1.28, respectively), and were more likely to die (OR: 1.13, 95% CI 1.07 to 1.19; 1.07, 95% CI 1.04 to 1.10, respectively) between April and July 2020. Once hospitalised, patients treated in public hospitals were more likely to die than patients in private hospitals (OR: 1.40%, 95% CI 1.34% to 1.46%). Black individuals and those with low education attainment were more likely to have one or more comorbidities, respectively (OR: 1.29, 95% CI 1.19 to 1.39; 1.36, 95% CI 1.27 to 1.45). CONCLUSIONS Low-income and Black and Pardo communities are more likely to die with COVID-19. This is associated with differential access to quality healthcare, ability to self-isolate and the higher prevalence of comorbidities.
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Affiliation(s)
- Sabrina L Li
- School of Geography and the Environment, University of Oxford, Oxford, UK
| | | | - Carlos A Prete
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil
| | | | - Lucas Emanuel
- Institute of Applied Economic Research, Brasília, Brazil
| | | | - Pedro S Peixoto
- Department of Applied Mathematics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | | | - William M de Souza
- Department of Zoology, University of Oxford, Oxford, UK
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Rogerio J Barbosa
- Institute of Social and Political Studies (IESP), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Lewis F Buss
- Departamento de Molestias Infecciosas e Parasitarias andInstituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Cesar de Almeida-Neto
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
- Disciplina de Ciências Médicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Suzete C Ferreira
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco - Immuno - Hematology (LIM-31) HCFMUSP, University of São Paulo Medical School, São Paulo, Brazil
| | - Nanci A Salles
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco - Immuno - Hematology (LIM-31) HCFMUSP, University of São Paulo Medical School, São Paulo, Brazil
| | - Izabel Marcilio
- Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, University of São Paulo, São Paulo, Brazil
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, UK
| | - Nelson Gouveia
- Department of Preventive Medicine, University of São Paulo Medical School, São Paulo, Brazil
| | - Vitor H Nascimento
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil
| | - Ester C Sabino
- Departamento de Molestias Infecciosas e Parasitarias andInstituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Departamento de Molestias Infecciosas e Parasitarias andInstituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Jane P Messina
- School of Geography and the Environment, University of Oxford, Oxford, UK
- Oxford School of Global and Area Studies, University of Oxford, Oxford, UK
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Umair M, Ikram A, Salman M, Khurshid A, Alam M, Badar N, Suleman R, Tahir F, Sharif S, Montgomery J, Whitmer S, Klena J. Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. PLoS One 2021; 16:e0248371. [PMID: 33755704 PMCID: PMC7987156 DOI: 10.1371/journal.pone.0248371] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/25/2021] [Indexed: 12/22/2022] Open
Abstract
Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed positive for SARS-CoV-2 through real-time RT-PCR at National Institute of Health, Pakistan, were selected for whole-genome sequencing. Sequencing was performed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEW ENGLAND BioLabs Inc., MA, US) and Illumina iSeq 100 instrument (Illumina, San Diego, US). Based on whole-genome analysis, three Pakistani SARS-CoV-2 strains clustered into the 20A (GH) clade along with the strains from Oman, Slovakia, United States, and Pakistani strain EPI_ISL_513925. The two 19B (S)-clade strains were closely related to viruses from India and Oman. Overall, twenty-nine amino acid mutations were detected in the current study genome sequences, including fifteen missense and four novel mutations. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. This report highlights the detection of GH and S clade strains and G614 variant from Pakistan warranting large-scale whole-genome sequencing of strains prevalent in different regions to understand virus evolution and to explore their genetic diversity.
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Affiliation(s)
- Massab Umair
- National Institute of Health, Islamabad, Pakistan
- * E-mail:
| | - Aamer Ikram
- National Institute of Health, Islamabad, Pakistan
| | | | | | - Masroor Alam
- National Institute of Health, Islamabad, Pakistan
| | - Nazish Badar
- National Institute of Health, Islamabad, Pakistan
| | - Rana Suleman
- National Institute of Health, Islamabad, Pakistan
| | - Faheem Tahir
- National Institute of Health, Islamabad, Pakistan
| | | | - Joel Montgomery
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Shannon Whitmer
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John Klena
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, de S. Ferreira AC, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, dos Santos HM, Aguiar RS, Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. medRxiv 2021:2021.02.26.21252554. [PMID: 33688664 PMCID: PMC7941639 DOI: 10.1101/2021.02.26.21252554] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early 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 1.4-2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with 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.
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Affiliation(s)
- Nuno R. Faria
- Department of Infectious Disease Epidemiology, Imperial College London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, UK
| | - Thomas A. Mellan
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Charles Whittaker
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Ingra M. Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Darlan da S. Candido
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, UK
| | - Swapnil Mishra
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Myuki A. E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
| | - Flavia C. Sales
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Iwona Hawryluk
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ruben J. G. Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lucas A. M. Franco
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana S. Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline G. de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pamela S. Andrade
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Thais M. Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia M. Ferreira
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Camila A. M. Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R. Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Pedro S. Peixoto
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - William M. Souza
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Esmenia C. Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leandro M. de Souza
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana C. de Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo J. T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | | | | | | | - Daniel J. Laydon
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | | | | | | | | | | | | | | | - Renato S. Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José L. P. Modena
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Bruce Nelson
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - James A. Hay
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Melodie Monod
- Department of Mathematics, Imperial College London, UK
| | | | - Helen Coupland
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Raphael Sonabend
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Michaela Vollmer
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Axel Gandy
- Department of Mathematics, Imperial College London, UK
| | - Marc A. Suchard
- Department of Biomathematics, Department of Biostatistics and Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sergei L. K. Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, USA
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, UK
| | | | - Neil M. Ferguson
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | | | - Nick J. Loman
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nelson A. Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Maria do P. S. S. Carvalho
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Seth Flaxman
- Department of Infectious Disease Epidemiology, Imperial College London, UK
| | - Samir Bhatt
- Department of Infectious Disease Epidemiology, Imperial College London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Denmark
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Castro RR, Santos RSC, Sousa GJB, Pinheiro YT, Martins RRIM, Pereira MLD, Silva RAR. Spatial dynamics of the COVID-19 pandemic in Brazil. Epidemiol Infect 2021; 149:e60. [PMID: 33629938 PMCID: PMC7985898 DOI: 10.1017/s0950268821000479] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 11/06/2022] Open
Abstract
The objective of this study was to analyse the dynamics of spatial dispersion of the coronavirus disease 2019 (COVID-19) in Brazil by correlating them to socioeconomic indicators. This is an ecological study of COVID-19 cases and deaths between 26 February and 31 July 2020. All Brazilian counties were used as units of analysis. The incidence, mortality, Bayesian incidence and mortality rates, global and local Moran indices were calculated. A geographic weighted regression analysis was conducted to assess the relationship between incidence and mortality due to COVID-19 and socioeconomic indicators (independent variables). There were confirmed 2 662 485 cases of COVID-19 reported in Brazil from February to July 2020 with higher rates of incidence in the north and northeast. The Moran global index of incidence rate (0.50, P = 0.01) and mortality (0.45 with P = 0.01) indicate a positive spatial autocorrelation with high standards in the north, northeast and in the largest urban centres between cities in the southeast region. In the same period, there were 92 475 deaths from COVID-19, with higher mortality rates in the northern states of Brazil, mainly Amazonas, Pará and Amapá. The results show that there is a geospatial correlation of COVID-19 in large urban centres and regions with the lowest human development index in the country. In the geographic weighted regression, it was possible to identify that the percentage of people living in residences with density higher than 2 per dormitory, the municipality human development index (MHDI) and the social vulnerability index were the indicators that most contributed to explaining incidence, social development index and the municipality human development index contributed the most to the mortality model. We hope that the findings will contribute to reorienting public health responses to combat COVID-19 in Brazil, the new epicentre of the disease in South America, as well as in other countries that have similar epidemiological and health characteristics to those in Brazil.
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Affiliation(s)
- R. R. Castro
- Postgraduate program in Clinical Nursing Care and Health, Universidade Estadual do Ceará, Fortaleza, Ceará, Brasil
| | - R. S. C. Santos
- Postgraduate program in Nursing, Faculdade Metropolitana de Ciências e Tecnologia, Parnamirim, Rio Grande do Norte, Brasil
| | - G. J. B. Sousa
- Postgraduate program in Clinical Nursing Care and Health, Universidade Estadual do Ceará, Fortaleza, Ceará, Brasil
| | - Y. T. Pinheiro
- Faculdade Maurício de Nassau, João Pessoa, Paraíba, Brasil
| | | | - M. L. D. Pereira
- Postgraduate program in Clinical Care in Nursing and Health, Universidade Estadual do Ceará, Fortaleza, Ceará, Brasil
| | - R. A. R. Silva
- Postgraduate program in Nursing, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brasil
- Postgraduate program in Collective Health, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brasil
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41
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Sena GR, Lima TPF, Vidal SA, Duarte MDCMB, Bezerra PGM, Fonseca Lima EJ, Braga C, Andrade LBD, Lins MM, Torres LC, Lima JTO, Mello MJG. Clinical Characteristics and Mortality Profile of COVID-19 Patients Aged less than 20 years Old in Pernambuco - Brazil. Am J Trop Med Hyg 2021; 104:1507-1512. [PMID: 33606669 PMCID: PMC8045659 DOI: 10.4269/ajtmh.20-1368] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/01/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 in children and adolescents has low frequency, severity, and fatality rate all over the world. A cross-sectional study was conducted to assess the epidemiological and clinical aspects of COVID-19 in patients younger than 20 years in Pernambuco (Brazil), with cases confirmed by reverse-transcriptase–PCR SARS-CoV-2 between 13 February and June 19, 2020, reported on information systems. Data regarding age (< 30 days, 1–11 months, 1–4 years, 5–9 years, 10–14 years, and 15–19 years), gender, color/race, symptoms, pregnancy or puerperium, comorbidities, hospitalization, and death were investigated. Fatality rate and mortality coefficient were calculated, and a multiple logistic regression analysis was performed to determine if gender, age, and comorbidities were factors associated with death. Of 682 pediatric cases, 52.8% were female, with a mean age of 9 ± 7.2 years. The most frequent symptoms were fever (64.4%), cough (52.4%), and respiratory distress (32.4%). Hospitalization was reported in 46.2% of cases, mainly among neonates (80.3%) and infants (73.8%). Thirty-eight deaths were notified, and a fatality rate of 5.6% (95% CI: 3.9–7.3) was found, with higher fatality rates among neonates 11.5% (7 of 61) and 9.5% (8 of 84) infants. The mortality coefficient was 10.9 per 100,000 inhabitants < 1 year of age, whereas comorbidities (Odds ratio [OR] = 14.13, 95% CI: 6.35–31.44), age < 30 days (OR = 5.17, 95% CI: 1.81–14.77), and age 1–11 months (OR = 3.28, 95% CI: 1.21–8.91) were independent factors associated with death. The results demonstrate the vulnerability of neonates and infants with severe conditions, need hospitalization, and high fatality rate, indicating the necessity to adapt public health policies for these age-groups.
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Affiliation(s)
- Gabrielle R Sena
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil.,2Faculdade Pernambucana de Saúde, Recife, Brazil.,3Universidade de Pernambuco, Recife, Brazil
| | - Tiago P F Lima
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil.,4Instituto Federal de Pernambuco, Garanhuns, Brazil
| | - Suely A Vidal
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil
| | | | - Patrícia G M Bezerra
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil.,2Faculdade Pernambucana de Saúde, Recife, Brazil
| | - Eduardo J Fonseca Lima
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil.,2Faculdade Pernambucana de Saúde, Recife, Brazil
| | - Cynthia Braga
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil.,5Instituto Ageu Magalhães - Fiocruz PE, Recife, Brazil
| | - Lívia B de Andrade
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil.,2Faculdade Pernambucana de Saúde, Recife, Brazil
| | - Mecneide M Lins
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil
| | - Leuridan C Torres
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil
| | - Jurema T O Lima
- 1Instituto de Medicina Integral Prof. Fernando Figueira, Recife, Brazil.,2Faculdade Pernambucana de Saúde, Recife, Brazil
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42
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Resende PC, Delatorre E, Gräf T, Mir D, Motta FC, Appolinario LR, da Paixão ACD, Mendonça ACDF, Ogrzewalska M, Caetano B, Wallau GL, Docena C, dos Santos MC, de Almeida Ferreira J, Sousa Junior EC, da Silva SP, Fernandes SB, Vianna LA, Souza LDC, Ferro JFG, Nardy VB, Santos CA, Riediger I, do Carmo Debur M, Croda J, Oliveira WK, Abreu A, Bello G, Siqueira MM. Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil. Front Microbiol 2021; 11:615280. [PMID: 33679622 PMCID: PMC7925893 DOI: 10.3389/fmicb.2020.615280] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
A previous study demonstrates that most of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Brazilian strains fell in three local clades that were introduced from Europe around late February 2020. Here we investigated in more detail the origin of the major and most widely disseminated SARS-CoV-2 Brazilian lineage B.1.1.33. We recovered 190 whole viral genomes collected from 13 Brazilian states from February 29 to April 31, 2020 and combined them with other B.1.1 genomes collected globally. Our genomic survey confirms that lineage B.1.1.33 is responsible for a variable fraction of the community viral transmissions in Brazilian states, ranging from 2% of all SARS-CoV-2 genomes from Pernambuco to 80% of those from Rio de Janeiro. We detected a moderate prevalence (5-18%) of lineage B.1.1.33 in some South American countries and a very low prevalence (<1%) in North America, Europe, and Oceania. Our study reveals that lineage B.1.1.33 evolved from an ancestral clade, here designated B.1.1.33-like, that carries one of the two B.1.1.33 synapomorphic mutations. The B.1.1.33-like lineage may have been introduced from Europe or arose in Brazil in early February 2020 and a few weeks later gave origin to the lineage B.1.1.33. These SARS-CoV-2 lineages probably circulated during February 2020 and reached all Brazilian regions and multiple countries around the world by mid-March, before the implementation of air travel restrictions in Brazil. Our phylodynamic analysis also indicates that public health interventions were partially effective to control the expansion of lineage B.1.1.33 in Rio de Janeiro because its median effective reproductive number (R e ) was drastically reduced by about 66% during March 2020, but failed to bring it to below one. Continuous genomic surveillance of lineage B.1.1.33 might provide valuable information about epidemic dynamics and the effectiveness of public health interventions in some Brazilian states.
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Affiliation(s)
- Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Daiana Mir
- Unidad de Genomica y Bioinformatica, Centro Universitario Regional del Litoral Norte, Universidad de la Republica, Salto, Uruguay
| | - Fernando Couto Motta
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Luciana Reis Appolinario
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Anna Carolina Dias da Paixão
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Ana Carolina da Fonseca Mendonça
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Maria Ogrzewalska
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Braulia Caetano
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | | | - Cássia Docena
- Instituto Aggeu Magalhaes, Fundação Oswaldo Cruz, Recife, Brazil
| | | | | | | | | | | | - Lucas Alves Vianna
- Laboratorio Central de Saude Publica do Estado Espirito Santo (LACEN-ES), Vitoria, Brazil
| | | | - Jean F. G. Ferro
- Laboratorio Central de Saude Publica de Alagoas (LACEN-AL), Maceio, Brazil
| | - Vanessa B. Nardy
- Laboratorio Central de Saude Publica da Bahia (LACEN-BA), Salvador, Brazil
| | - Cliomar A. Santos
- Laboratorio Central de Saude Publica de Sergipe (LACEN-SE), Aracaju, Brazil
| | - Irina Riediger
- Laboratorio Central de Saude Publica de Parana (LACEN-PR), Curitiba, Brazil
| | | | - Júlio Croda
- Fiocruz Mato Grosso do Sul, Campo Grande, Brazil
- Universidade Federal de Mato Grosso do Sul – UFMS, Campo Grande, Brazil
| | | | - André Abreu
- Coordenadoria Geral de Laboratorios – Ministério da Saude, Brazilia, Brazil
| | - Gonzalo Bello
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Marilda M. Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
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43
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Franco D, Gonzalez C, Abrego LE, Carrera JP, Diaz Y, Caicedo Y, Moreno A, Chavarria O, Gondola J, Castillo M, Valdespino E, Gaitán M, Martínez-Mandiche J, Hayer L, Gonzalez P, Lange C, Molto Y, Mojica D, Ramos R, Mastelari M, Cerezo L, Moreno L, Donnelly CA, Pascale JM, Faria NR, Lopez-Verges S, Martinez AA. Early Transmission Dynamics, Spread, and Genomic Characterization of SARS-CoV-2 in Panama. Emerg Infect Dis 2021; 27:612-615. [PMID: 33496228 PMCID: PMC7853578 DOI: 10.3201/eid2702.203767] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We report an epidemiologic analysis of 4,210 cases of infection with severe acute respiratory syndrome coronavirus 2 and genetic analysis of 313 new near-complete virus genomes in Panama during March 9-April 16, 2020. Although containment measures reduced R0 and Rt, they did not interrupt virus spread in the country.
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44
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Loney T, Khansaheb H, Ramaswamy S, Harilal D, Deesi ZO, Varghese RM, Belal Al Ali A, Khadeeja A, Al Suwaidi H, Alkhajeh A, Mohamed AlDabal L, Uddin M, Al Faresi M, Joshi M, Senok A, Nowotny N, Alsheikh-Ali A, Abou Tayoun A. Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. Transbound Emerg Dis 2021; 69:465-476. [PMID: 33506644 PMCID: PMC8013505 DOI: 10.1111/tbed.14004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/22/2022]
Abstract
The geographic location and heterogeneous multi‐ethnic population of Dubai (United Arab Emirates; UAE) provide a unique setting to explore the global molecular epidemiology of SARS‐CoV‐2 and relationship between different viral strains and disease severity. We systematically selected (i.e. every 100th individual in the central Dubai COVID‐19 database) 256 patients by age, sex, disease severity and month to provide a representative sample of laboratory‐confirmed COVID‐19 patients (nasopharyngeal swab PCR positive) during the first wave of the UAE outbreak (January to June 2020). Sociodemographic and clinical data were extracted from medical records and full SARS‐CoV‐2 genome sequences extracted from nasopharyngeal swabs were analysed. Older age was significantly associated with COVID‐19‐associated hospital admission and mortality. Overweight/obese or diabetic patients were 3–4 times more likely to be admitted to hospital and intensive care unit (ICU). Sequencing data showed multiple independent viral introductions into the UAE from Europe, Iran and Asia (29 January–18 March), and these early strains seeded significant clustering consistent with almost exclusive community‐based transmission between April and June 2020. Majority of sequenced strains (N = 60, 52%) were from the European cluster consistent with the higher infectivity rates associated with the D614G mutation carried by most strains in this cluster. A total of 986 mutations were identified in 115 genomes, 272 were unique (majority were missense, n = 134) and 20/272 mutations were novel. A missense (Q271R) and synonymous (R41R) mutation in the S and N proteins, respectively, were identified in 2/27 patients with severe COVID‐19 but not in patients with mild or moderate disease (0/86; p = .05, Fisher's Exact Test). Both patients were women (51–64 years) with no significant underlying health conditions. The same two mutations were identified in a healthy 37‐year‐old Indian man who was hospitalized in India due to COVID‐19. Our findings provide evidence for continued community‐based transmission of the European strains in the Dubai population and highlight new mutations that might be associated with severe disease in otherwise healthy adults.
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Affiliation(s)
- Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Hamda Khansaheb
- Medical Education & Research Department, Dubai Health Authority, Dubai, United Arab Emirates
| | | | - Divinlal Harilal
- Al Jalila Genomics Center, Al Jalila Children's Hospital, Dubai, United Arab Emirates
| | - Zulfa Omar Deesi
- Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Rupa Murthy Varghese
- Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Aydah Belal Al Ali
- Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Anees Khadeeja
- Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Hanan Al Suwaidi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Abdulmajeed Alkhajeh
- Medical Education & Research Department, Dubai Health Authority, Dubai, United Arab Emirates
| | - Laila Mohamed AlDabal
- Medical Affairs Department, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mubarak Al Faresi
- Microbiology Department, Sheikh Khalifa General Hospital, Umm Al Quwain, United Arab Emirates
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, India
| | - Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Norbert Nowotny
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ahmad Abou Tayoun
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Al Jalila Genomics Center, Al Jalila Children's Hospital, Dubai, United Arab Emirates
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Buss LF, Prete CA, Abrahim CMM, Mendrone A, Salomon T, de Almeida-Neto C, França RFO, Belotti MC, Carvalho MPSS, Costa AG, Crispim MAE, Ferreira SC, Fraiji NA, Gurzenda S, Whittaker C, Kamaura LT, Takecian PL, da Silva Peixoto P, Oikawa MK, Nishiya AS, Rocha V, Salles NA, de Souza Santos AA, da Silva MA, Custer B, Parag KV, Barral-Netto M, Kraemer MUG, Pereira RHM, Pybus OG, Busch MP, Castro MC, Dye C, Nascimento VH, Faria NR, Sabino EC. Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic. Science 2021; 371:288-292. [PMID: 33293339 PMCID: PMC7857406 DOI: 10.1126/science.abe9728] [Citation(s) in RCA: 294] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/02/2020] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread rapidly in Manaus, the capital of Amazonas state in northern Brazil. The attack rate there is an estimate of the final size of the largely unmitigated epidemic that occurred in Manaus. We use a convenience sample of blood donors to show that by June 2020, 1 month after the epidemic peak in Manaus, 44% of the population had detectable immunoglobulin G (IgG) antibodies. Correcting for cases without a detectable antibody response and for antibody waning, we estimate a 66% attack rate in June, rising to 76% in October. This is higher than in São Paulo, in southeastern Brazil, where the estimated attack rate in October was 29%. These results confirm that when poorly controlled, COVID-19 can infect a large proportion of the population, causing high mortality.
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Affiliation(s)
- Lewis F Buss
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Carlos A Prete
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - Claudia M M Abrahim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Alfredo Mendrone
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
- Laboratório de Investigação Médica em Patogênese e Terapia dirigida em Onco-Imuno-Hematologia (LIM-31), Departamento de Hematologia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Tassila Salomon
- Fundação Hemominas-Fundação Centro de Hematologia e Hemoterapia de Minas Gerais, Belo Horizonte, Brazil
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil
| | - Cesar de Almeida-Neto
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
- Laboratório de Investigação Médica em Patogênese e Terapia dirigida em Onco-Imuno-Hematologia (LIM-31), Departamento de Hematologia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Rafael F O França
- Department of Virology and Experimental Therapy, Institute Aggeu Magalhaes, Oswaldo Cruz Foundation, Recife, Brazil
| | - Maria C Belotti
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | | | - Allyson G Costa
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Myuki A E Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Suzete C Ferreira
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
- Laboratório de Investigação Médica em Patogênese e Terapia dirigida em Onco-Imuno-Hematologia (LIM-31), Departamento de Hematologia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Nelson A Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Susie Gurzenda
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Charles Whittaker
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Leonardo T Kamaura
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - Pedro L Takecian
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | - Marcio K Oikawa
- Center of Mathematics, Computing and Cognition-Universidade Federal do ABC, São Paulo, Brazil
| | - Anna S Nishiya
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
- Laboratório de Investigação Médica em Patogênese e Terapia dirigida em Onco-Imuno-Hematologia (LIM-31), Departamento de Hematologia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Vanderson Rocha
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
- Laboratório de Investigação Médica em Patogênese e Terapia dirigida em Onco-Imuno-Hematologia (LIM-31), Departamento de Hematologia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Nanci A Salles
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
| | | | | | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | | | | | | | | | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Márcia C Castro
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Vítor H Nascimento
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - Nuno R Faria
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ester C Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
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46
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Amaku M, Covas DT, Coutinho FAB, Azevedo RS, Massad E. Modelling the impact of contact tracing of symptomatic individuals on the COVID-19 epidemic. Clinics (Sao Paulo) 2021; 76:e2639. [PMID: 33787657 PMCID: PMC7978843 DOI: 10.6061/clinics/2021/e2639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/28/2021] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES With the declining numbers of coronavirus disease 2019 (COVID-19) cases in the state of São Paulo, Brazil, social distancing measures have gradually been lifted. However, the risk of a surge in the number of cases cannot be overlooked. Even with the adoption of nonpharmaceutical interventions, such as restrictions on mass gatherings, wearing of masks, and complete or partial closure of schools, other public health measures may help control the epidemic. We aimed to evaluate the impact of the contact tracing of symptomatic individuals on the COVID-19 epidemic regardless of the use of diagnostic testing. METHODS We developed a mathematical model that includes isolation of symptomatic individuals and tracing of contacts to assess the effects of the contact tracing of symptomatic individuals on the COVID-19 epidemic in the state of São Paulo. RESULTS For a selection efficacy (proportion of isolated contacts who are infected) of 80%, cases and deaths may be reduced by 80% after 60 days when 5000 symptomatic individuals are isolated per day, each of them together with 10 contacts. On the other hand, for a selection efficacy of 20%, the number of cases and deaths may be reduced by approximately 40% and 50%, respectively, compared with the scenario in which no contact-tracing strategy is implemented. CONCLUSION Contact tracing of symptomatic individuals may potentially be an alternative strategy when the number of diagnostic tests available is not sufficient for massive testing.
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Affiliation(s)
- Marcos Amaku
- Laboratorio de Investigacao Medica (LIM01), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
- Faculdade de Medicina Veterinaria e Zootecnia, Universidade de Sao Paulo, Sao Paulo, SP, BR
- *Corresponding author. E-mail:
| | | | | | - Raymundo Soares Azevedo
- Laboratorio de Investigacao Medica (LIM01), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Eduardo Massad
- Laboratorio de Investigacao Medica (LIM01), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
- Escola de Matematica Aplicada, Fundacao Getulio Vargas, Rio de Janeiro, RJ, BR
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47
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Romano CM, Felix AC, Paula AVD, Jesus JGD, Andrade PS, Cândido D, Oliveira FMD, Ribeiro AC, Silva FCD, Inemami M, Costa AA, Leal COD, Figueiredo WM, Pannuti CS, Souza WMD, Faria NR, Sabino EC. SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil. Rev Inst Med Trop Sao Paulo 2021; 63:e36. [PMID: 33909850 PMCID: PMC8075619 DOI: 10.1590/s1678-9946202163036] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 11/21/2022] Open
Abstract
Reinfection by the severe acute respiratory syndrome coronavirus type 2 (SARS-COV-2) has been reported in many countries, suggesting that the virus may continue to circulate among humans despite the possibility of local herd immunity due to massive previous infections. The emergence of variants of concern (VOC) that are more transmissible than the previous circulating ones has raised particular concerns on the vaccines effectiveness and reinfection rates. The P.1 lineage was first identified in December 2020 in Manaus city and is now globally spread. We report the first case of reinfection of SARS-CoV-2 caused by the P.1 variant outside of Manaus. The potential of these new variants to escape naturally and vaccine- induced immunity highlights the need for a global vigilance.
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Affiliation(s)
- Camila Malta Romano
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Alvina Clara Felix
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Anderson Vicente de Paula
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Jaqueline Góes de Jesus
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Pamela S Andrade
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Darlan Cândido
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil.,University of Oxford, Department of Zoology, Oxford, United Kingdom
| | - Franciane M de Oliveira
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Andreia C Ribeiro
- Universidade de São Paulo, Serviço Especial de Saúde de Araraquara, Araraquara, São Paulo, Brazil
| | - Francini C da Silva
- Universidade de São Paulo, Serviço Especial de Saúde de Araraquara, Araraquara, São Paulo, Brazil
| | - Marta Inemami
- Universidade de São Paulo, Serviço Especial de Saúde de Araraquara, Araraquara, São Paulo, Brazil
| | - Angela Aparecida Costa
- Universidade de São Paulo, Serviço Especial de Saúde de Araraquara, Araraquara, São Paulo, Brazil
| | - Cibele O D Leal
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Walter Manso Figueiredo
- Universidade de São Paulo, Serviço Especial de Saúde de Araraquara, Araraquara, São Paulo, Brazil
| | - Claudio Sergio Pannuti
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - William M de Souza
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Pesquisa em Virologia, Ribeirão Preto, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil.,Imperial College of London, MRC Centre for Global Infectious Disease Analysis, London, United Kingdom
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
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48
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Abstract
Using a stochastic model, we assess the risk of importation-induced local transmission chains in locations seeing few or no local transmissions and evaluate the role of quarantine in the mitigation of this risk. We find that the rate of importations plays a critical role in determining the risk that case importations lead to local transmission chains, more so than local transmission characteristics, i.e. strength of social distancing measures (NPI). The latter influences the severity of the outbreaks when they do take place. Quarantine after arrival in a location is an efficacious way to reduce the rate of importations. Locations that see no or low-level local transmission should ensure that the rate of importations remains low. A high level of compliance with post-arrival quarantine followed by testing achieves this objective with less of an impact than travel restrictions or bans.
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49
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Xavier J, Giovanetti M, Adelino T, Fonseca V, Barbosa da Costa AV, Ribeiro AA, Felicio KN, Duarte CG, Ferreira Silva MV, Salgado Á, Lima MT, de Jesus R, Fabri A, Soares Zoboli CF, Souza Santos TG, Iani F, Ciccozzi M, Bispo de Filippis AM, Teixeira de Siqueira MAM, de Abreu AL, de Azevedo V, Ramalho DB, Campelo de Albuquerque CF, de Oliveira T, Holmes EC, Lourenço J, Junior Alcantara LC, Assunção Oliveira MA. The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing. Emerg Microbes Infect 2020; 9:1824-1834. [PMID: 32726185 PMCID: PMC7473129 DOI: 10.1080/22221751.2020.1803146] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/06/2020] [Accepted: 07/26/2020] [Indexed: 12/30/2022]
Abstract
The recent emergence of a coronavirus (SARS-CoV-2), first identified in the Chinese city of Wuhan in December 2019, has had major public health and economic consequences. Although 61,888 confirmed cases were reported in Brazil by 28 April 2020, little is known about the SARS-CoV-2 epidemic in this country. To better understand the recent epidemic in the second most populous state in southeast Brazil - Minas Gerais (MG) - we sequenced 40 complete SARS-CoV-2 genomes from MG cases and examined epidemiological data from three Brazilian states. Both the genome analyses and the geographical distribution of reported cases indicate for multiple independent introductions into MG. Epidemiological estimates of the reproductive number (R) using different data sources and theoretical assumptions suggest the potential for sustained virus transmission despite a reduction in R from the first reported case to the end of April 2020. The estimated date of SARS-CoV-2 introduction into Brazil was consistent with epidemiological data from the first case of a returned traveller from Lombardy, Italy. These findings highlight the nature of the COVID-19 epidemic in MG and reinforce the need for real-time and continued genomic surveillance strategies to better understand and prepare for the epidemic spread of emerging viral pathogens..
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Affiliation(s)
- Joilson Xavier
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Talita Adelino
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Brazil
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZuluNatal, Durban4001, South Africa
| | | | | | | | - Clara Guerra Duarte
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Brazil
| | | | - Álvaro Salgado
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mauricio Teixeira Lima
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ronaldo de Jesus
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Allison Fabri
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | - Felipe Iani
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Brazil
| | | | | | | | - André Luiz de Abreu
- Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Vasco de Azevedo
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZuluNatal, Durban4001, South Africa
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - José Lourenço
- Department of Zoology, University of Oxford, OxfordOX1 3PS, UK
| | - Luiz Carlos Junior Alcantara
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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50
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Amaku M, Covas DT, Bezerra Coutinho FA, Azevedo Neto RS, Struchiner C, Wilder-Smith A, Massad E. Modelling the test, trace and quarantine strategy to control the COVID-19 epidemic in the state of São Paulo, Brazil. Infect Dis Model 2021; 6:46-55. [PMID: 33235942 DOI: 10.1016/j.idm.2020.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/11/2020] [Accepted: 11/14/2020] [Indexed: 02/06/2023] Open
Abstract
Testing for detecting the infection by SARS-CoV-2 is the bridge between the lockdown and the opening of society. In this paper we modelled and simulated a test-trace-and-quarantine strategy to control the COVID-19 outbreak in the State of São Paulo, Brasil. The State of São Paulo failed to adopt an effective social distancing strategy, reaching at most 59% in late March and started to relax the measures in late June, dropping to 41% in 08 August. Therefore, São Paulo relies heavily on a massive testing strategy in the attempt to control the epidemic. Two alternative strategies combined with economic evaluations were simulated. One strategy included indiscriminately testing the entire population of the State, reaching more than 40 million people at a maximum cost of 2.25 billion USD, that would reduce the total number of cases by the end of 2020 by 90%. The second strategy investigated testing only symptomatic cases and their immediate contacts – this strategy reached a maximum cost of 150 million USD but also reduced the number of cases by 90%. The conclusion is that if the State of São Paulo had decided to adopt the simulated strategy on April the 1st, it would have been possible to reduce the total number of cases by 90% at a cost of 2.25 billion US dollars for the indiscriminate strategy but at a much smaller cost of 125 million US dollars for the selective testing of symptomatic cases and their contacts.
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