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Coelho LE, Luz PM, Pires DC, Jalil EM, Perazzo H, Torres TS, Cardoso SW, Peixoto EM, Nazer S, Massad E, Carvalho LM, Réquia WJ, Motta FC, Siqueira MM, Vasconcelos AT, da Fonseca GC, Cavalcante LT, Costa CA, Amancio RT, Villela DA, Pereira T, Goedert GT, Santos CV, Rodrigues NC, Bormann de Souza Filho BA, Csillag D, Grinsztejn B, Veloso VG, Struchiner CJ. SARS-CoV-2 transmission in a highly vulnerable population of Brazil: a household cohort study. LANCET REGIONAL HEALTH. AMERICAS 2024; 36:100824. [PMID: 38993539 PMCID: PMC11237915 DOI: 10.1016/j.lana.2024.100824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 06/01/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024]
Abstract
Background Household transmission studies seek to understand the transmission dynamics of a pathogen by estimating the risk of infection from household contacts and community exposures. We estimated within/extra-household SARS-CoV-2 infection risk and associated factors in a household cohort study in one of the most vulnerable neighbourhoods in Rio de Janeiro city. Methods Individuals ≥1 years-old with suspected or confirmed COVID-19 in the past 30 days (index cases) and household members aged ≥1 year were enrolled and followed at 14 and 28 days (study period November/2020-December/2021). RT-PCR testing, COVID-19 symptoms, and SARS-CoV-2 serologies were ascertained in all visits. Chain binomial household transmission models were fitted using data from 2024 individuals (593 households). Findings Extra-household infection risk was 74.2% (95% credible interval [CrI] 70.3-77.8), while within-household infection risk was 11.4% (95% CrI 5.7-17.2). Participants reporting having received two doses of a COVID-19 vaccine had lower extra-household (68.9%, 95% CrI 57.3-77.6) and within-household (4.1%, 95% CrI 0.4-16.6) infection risk. Within-household infection risk was higher among participants aged 10-19 years, from overcrowded households, and with low family income. Contrastingly, extra-household infection risk was higher among participants aged 20-29 years, unemployed, and public transportation users. Interpretation Our study provides important insights into COVID-19 household/community transmission in a vulnerable population that resided in overcrowded households and who struggled to adhere to lockdown policies and social distancing measures. The high extra-household infection risk highlights the extreme social vulnerability of this population. Prioritising vaccination of the most socially vulnerable could protect these individuals and reduce widespread community transmission. Funding Fundação Oswaldo Cruz, CNPq, FAPERJ, Royal Society, Instituto Serrapilheira, FAPESP.
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Affiliation(s)
- Lara E. Coelho
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Paula M. Luz
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Débora C. Pires
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Emilia M. Jalil
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Hugo Perazzo
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Thiago S. Torres
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Sandra W. Cardoso
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Eduardo M. Peixoto
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Sandro Nazer
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Eduardo Massad
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro, Brazil
| | - Luiz Max Carvalho
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro, Brazil
- Instituto de Ciências Matemáticas e Computação, Universidade de São Paulo, Brazil
| | - Weeberb J. Réquia
- Escola de Políticas Públicas e Governo, Fundação Getulio Vargas, Brasília, Brazil
| | - Fernando Couto Motta
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana T.R. Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Guilherme C. da Fonseca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Liliane T.F. Cavalcante
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Carlos A.M. Costa
- Escola Nacional de Saúde Pública Sérgio Arouca, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Daniel A.M. Villela
- Programa de Computação Científica (PROCC), FIOCRUZ, Rio de Janeiro, Brazil
- Center for Health and Wellbeing, School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - Tiago Pereira
- Instituto de Ciências Matemáticas e Computação, Universidade de São Paulo, Brazil
| | | | - Cleber V.B.D. Santos
- Instituto de Medicina Social Hesio Cordeiro, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nadia C.P. Rodrigues
- Escola Nacional de Saúde Pública Sérgio Arouca, FIOCRUZ, Rio de Janeiro, Brazil
- Instituto de Medicina Social Hesio Cordeiro, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Breno Augusto Bormann de Souza Filho
- Escola Nacional de Saúde Pública Sérgio Arouca, FIOCRUZ, Rio de Janeiro, Brazil
- Departamento de Saúde Coletiva, Universidade Federal do Rio Grande do Norte, Rio Grande do Norte, Brazil
| | - Daniel Csillag
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Valdilea G. Veloso
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Claudio J. Struchiner
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro, Brazil
- Instituto de Medicina Social Hesio Cordeiro, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
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Machado LC, Dezordi FZ, de Lima GB, de Lima RE, Silva LCA, Pereira LDM, da Silva AF, da Silva Neto AM, de Oliveira ALS, 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; 12:e0421823. [PMID: 38651879 PMCID: PMC11237429 DOI: 10.1128/spectrum.04218-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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
| | - On behalf of Fiocruz COVID-19 Genomic Network
- 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
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Núcleo de Estatística e Geoprocessamento, Instituto Aggeu Magalhães (IAM)- Fundação Oswaldo Cruz Pernambuco- FIOCRUZ-PE, Recife, Brazil
- Colegiado de Medicina, Universidade Federal do Vale do São Francisco, Petrolina, Brazil
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste, Caruaru, Brazil
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Manaus, Amazonas, Brazil
- Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceará, Fortaleza, Ceará, Brazil
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
- Colegiado de Ciências Farmacêuticas, Universidade Federal do Vale do São Francisco, Petrolina, Brazil
- Departamento de Microbiologia, 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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Arantes I, Gomes M, Ito K, Sarafim S, Gräf T, Miyajima F, Khouri R, de Carvalho FC, de Almeida WAF, Siqueira MM, Resende PC, Naveca FG, Bello G. Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023. Microbiol Spectr 2024; 12:e0383123. [PMID: 38315011 PMCID: PMC10913747 DOI: 10.1128/spectrum.03831-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
The SARS-CoV-2 XBB is a group of highly immune-evasive lineages of the Omicron variant of concern that emerged by recombining BA.2-descendent lineages and spread worldwide during 2023. In this study, we combine SARS-CoV-2 genomic data (n = 11,065 sequences) with epidemiological data of severe acute respiratory infection (SARI) cases collected in Brazil between October 2022 and July 2023 to reconstruct the space-time dynamics and epidemiologic impact of XBB dissemination in the country. Our analyses revealed that the introduction and local emergence of lineages carrying convergent mutations within the Spike protein, especially F486P, F456L, and L455F, propelled the spread of XBB* lineages in Brazil. The average relative instantaneous reproduction numbers of XBB* + F486P, XBB* + F486P + F456L, and XBB* + F486P + F456L + L455F lineages in Brazil were estimated to be 1.24, 1.33, and 1.48 higher than that of other co-circulating lineages (mainly BQ.1*/BE*), respectively. Despite such a growth advantage, the dissemination of these XBB* lineages had a reduced impact on Brazil's epidemiological scenario concerning previous Omicron subvariants. The peak number of SARI cases from SARS-CoV-2 during the XBB wave was approximately 90%, 80%, and 70% lower than that observed during the previous BA.1*, BA.5*, and BQ.1* waves, respectively. These findings revealed the emergence of multiple XBB lineages with progressively increasing growth advantage, yet with relatively limited epidemiological impact in Brazil throughout 2023. The XBB* + F486P + F456L + L455F lineages stand out for their heightened transmissibility, warranting close monitoring in the months ahead. IMPORTANCE Brazil was one the most affected countries by the SARS-CoV-2 pandemic, with more than 700,000 deaths by mid-2023. This study reconstructs the dissemination of the virus in the country in the first half of 2023, a period characterized by the dissemination of descendants of XBB.1, a recombinant of Omicron BA.2 lineages evolved in late 2022. The analysis supports that XBB dissemination was marked by the continuous emergence of indigenous lineages bearing similar mutations in key sites of their Spike protein, a process followed by continuous increments in transmissibility, and without repercussions in the incidence of severe cases. Thus, the results suggest that the epidemiological impact of the spread of a SARS-CoV-2 variant is influenced by an intricate interplay of factors that extend beyond the virus's transmissibility alone. The study also underlines the need for SARS-CoV-2 genomic surveillance that allows the monitoring of its ever-shifting composition.
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Affiliation(s)
- Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Marcelo Gomes
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Fiocruz, Rio de Janeiro, Brazil
| | - Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - Sharbilla Sarafim
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
| | | | | | - Felipe Cotrim de Carvalho
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
| | - Walquiria Aparecida Ferreira de Almeida
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - COVID-19 Fiocruz Genomic Surveillance Network
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Fiocruz, Rio de Janeiro, Brazil
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
- Fiocruz, Fortaleza, Brazil
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Departamento do Programa Nacional de Imunizações, Coordenação-Geral de Vigilância das doenças imunopreveníveis, Secretaria de Vigilância em saúde e ambiente, Brasília, Brazil
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
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Contreras M, Gomes Naveca F, Carvajal-Cortes JJ, Faviero GF, Saavedra J, Ruback dos Santos E, Alves do Nascimento V, Costa de Souza V, Oliveira do Nascimento F, Silva e Silva D, Luz SLB, Romero Vesga KN, Grisales Nieto JC, Avelino-Silva VI, Benzaken AS. Implementing a provisional overarching intervention for COVID-19 monitoring and control in the Brazil-Colombia-Peru frontier. Front Public Health 2024; 11:1330347. [PMID: 38259793 PMCID: PMC10801231 DOI: 10.3389/fpubh.2023.1330347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction he challenge was to provide comprehensive health resources to a remote and underserved population living in the Brazil-Colombia-Peru border, amid the most disruptive global crisis of the century. Methods In August 2021, Fundação Oswaldo Cruz Amazonia (FIOCRUZ Amazônia) and partner collaborators implemented an overarching provisional program for SARS-CoV-2 detection and lineages characterization, training of laboratory personnel and healthcare providers, donation of diagnostic supplies and personal protective equipment, and COVID-19 vaccination. The expedition was conducted at the Port of Tabatinga, a busy terminal with an intense flux of people arriving and departing in boats of all sizes, located in the Amazon River basin. Local government, non-profit organizations, private companies, and other stakeholders supported the intervention. Results The expedition was accomplished in a convergence point, where migrant workers, traders, army personnel, people living in urban areas, and people from small villages living in riversides and indigenous territories are in close and frequent contact, with widespread cross-border movement. Using a boat as a provisional lab and storage facility, the intervention provided clinical and laboratory monitoring for 891 participants; vaccination for 536 individuals; personal protective equipment for 200 healthcare providers; diagnostic supplies for 1,000 COVID-19 rapid tests; training for 42 community health agents on personal protection, rapid test execution, and pulse oximeter management; and hands-on training for four lab technicians on molecular diagnosis. Discussion Our experience demonstrates that multilateral initiatives can counterweigh the scarcity of health resources in underserved regions. Moreover, provisional programs can have a long-lasting effect if investments are also provided for local capacity building.
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Affiliation(s)
- Matilde Contreras
- Instituto Leônidas and Maria Deane, Fundação Oswaldo Cruz, Manaus, Brazil
| | | | | | - Guilherme F. Faviero
- AHF Global Public Health Institute at the University of Miami, Miami, FL, United States
| | - Jorge Saavedra
- AHF Global Public Health Institute, Fort Lauderdale, FL, United States
| | | | | | | | | | | | | | | | | | - Vivian I. Avelino-Silva
- Department of Infectious and Parasitic Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- AIDS Healthcare Foundation, Los Angeles, CA, United States
| | - Adele Schwartz Benzaken
- Instituto Leônidas and Maria Deane, Fundação Oswaldo Cruz, Manaus, Brazil
- AIDS Healthcare Foundation, Los Angeles, CA, United States
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de Sousa LAF, Ferreira LSDS, Lobato LFL, Ferreira HLDS, Sousa LHDS, Santos VFD, Nunes PRS, Maramaldo CEC, Neto SS, Sampaio HL, Silva FVD, Brito MDC, Lima WKR, Lima CZGPA, Neto LGL. Molecular epidemiology of SARS-CoV-2 variants in circulation in the state of Maranhão, Brazil. J Med Virol 2023; 95:e29092. [PMID: 37724346 DOI: 10.1002/jmv.29092] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a coronavirus belonging to the beta CoV genus, responsible for SARS in humans, which became known as COVID-19. The emergence of variants of this virus is related to the presence of cases of reinfection, reduced vaccine effectiveness and greater transmission of the virus. Objective: In this study, we evaluated the molecular epidemiology of SARS-CoV-2 lineages circulating in the state of Maranhão. This is a cross-sectional and retrospective epidemiological study of genomic surveillance of SARS-CoV-2. The study comprised of 338 genomes sequenced by the Next Generation Sequencing technique on Illumina's Miseq equipment, submitted to Global Initiative on Sharing Avian Influenza Data, 190 (56.2%) are from samples of female and 148 (43.8%) from male patients. Sequencing performed covered samples of patients aged between 1 and 108 years, with emphasis on the age groups from 30 to 39 years with 15.0% of sequenced genomes and 20 to 29 years with 12.4%. As for the distribution of sequenced genomes by health macro-regions, 285 (84.3%) are from cities in the northern macro-region. We evidenced the circulation of 29 lineages and sub-lineages, four of which belonging to the Delta variant (AY.43, AY.99.1, AY.99.2 and AY.101 responsible for 4.5% of the genomes) and the others belonging to the Omicron variant, with emphasis on: BA.1 and sub-lineages (42.8%); BA.4, BA.5 and sub-lineages (5.3% and 41.1%); the sub-lineages DL.1 and BQ.1 (5% and 2%). A strong genomic surveillance system allows the study of the natural history of the disease, when there is a resurgence of SARS-CoV-2 cases.
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Affiliation(s)
- Luis Artur Ferreira de Sousa
- Virology Laboratory, Postgraduation Program in Microbial Biology, CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
| | | | - Luis Felipe Lima Lobato
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
- Postgraduation Program in Tropical Medicine-IOC/FIOCRUZ-RJ, Rio de Janeiro, Brazil
| | | | | | - Valdenice Ferreira Dos Santos
- Post-graduate Programme in Biodiversity and Biotechnology (BIONORTE), CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
| | - Paulo Ricardo Silva Nunes
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
| | | | - Sebastião Silveira Neto
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
| | - Hellen Lobato Sampaio
- Virology Laboratory, Postgraduation Program in Microbial Biology, CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
| | - Fabiano Vieira da Silva
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
- Postgraduation Program in Tropical Medicine-IOC/FIOCRUZ-RJ, Rio de Janeiro, Brazil
| | - Marcelo da Costa Brito
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
| | - Washington Kleber Rodrigues Lima
- Post-graduate Programme in Biodiversity and Biotechnology (BIONORTE), CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
- UniCEUMA, CEUMA University, São Luís, Maranhão, Brazil
| | | | - Lidio Gonçalves Lima Neto
- Virology Laboratory, Postgraduation Program in Microbial Biology, CEUMA University, UniCEUMA, São Luís, Maranhão, Brazil
- Oswaldo Cruz Institute/Central Public Health Laboratory of Maranhão-IOC/LACEN-MA, São Luís, Maranhão, Brazil
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