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da Cruz TCD, Pavon JAR, de Azevedo FSK, de Souza EC, Ribeiro BM, Slhessarenko RD. Associations between epidemiological and laboratory parameters and disease severity in hospitalized patients with COVID-19 during first and second epidemic waves in middle south Mato Grosso. Braz J Microbiol 2024:10.1007/s42770-024-01379-x. [PMID: 38834861 DOI: 10.1007/s42770-024-01379-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/13/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND COVID-19 is a multisystemic disease characterized by respiratory distress. Disease severity is associated with several factors. Here we characterize virological findings and evaluate the association of laboratorial, epidemiological, virological findings and clinical outcomes of 251 patients during the first and second epidemic waves of COVID-19. METHODS This transversal study used biological samples and data from patients hospitalized with COVID-19 between May 2020 and August 2021 in the metropolitan region of Cuiabá, Mato Grosso Brazil. Biological samples were subjected to RT-qPCR and MinION sequencing. Univariate and multivariate logistic regression and Odds ratio were used to correlate clinical, laboratorial, epidemiological data. FINDINGS Patients were represented by males (61.7%) with mean age of 52.4 years, mild to moderate disease (49,0%), overweight/obese (69.3%), with comorbidities (66.1%) and evolving to death (55.38%). Severe cases showing symptoms for prolonged time, ≥ 25% of ground-glass opacities in the lungs and fatality rate increased significantly in second wave. Fatality was statistically associated to > 61 years of age,>25% ground-glass opacities in the lungs, immune, cardiac, or metabolic comorbidities. Higher viral load (p < 0.01/p = 0.02 in each wave), decreased erythrocyte (p < 0.01), hemoglobin (p < 0.05/p < 0.01), hematocrit (p < 0.01), RDW (p < 0.01), lymphocyte (p < 0.01), increased leucocyte (p < 0.01), neutrophil (p < 0.01) and CRP levels (p < 0.01) showed significant association with fatality in both waves, as did Neutrophil/Platelet (NPR; p < 0.01), Neutrophil/Lymphocyte (NLR; p < 0.01) and Monocyte/Lymphocyte ratio (MLR; p < 0.01). SARS-CoV-2 genomes from lineage B.1.1.33(n = 8) and Gamma/P.1(n = 15) shared 6/7 and 20/23 lineage-defining mutations, respectively. MAIN CONCLUSIONS Severity and mortality of COVID-19 associated with a panel of epidemiological and laboratorial findings, being second wave, caused by Gamma variant, more severe in this in-hospital population.
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Affiliation(s)
- Thais Campos Dias da Cruz
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), B Boa Esperança, 78060-900, Cuiabá, MT, Brasil
| | - Janeth Aracely Ramirez Pavon
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), B Boa Esperança, 78060-900, Cuiabá, MT, Brasil
| | - Francisco Scoffoni Kennedy de Azevedo
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), B Boa Esperança, 78060-900, Cuiabá, MT, Brasil
- Hospital e Pronto Socorro de Várzea Grande, Secretaria Municipal de Saúde, UFMT, Várzea Grande, Mato Grosso, Brasil
| | - Edila Cristina de Souza
- Curso de Graduação em Estatística, Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brasil
| | - Bergman Morais Ribeiro
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), Brasília, Distrito Federal, Brasil
| | - Renata Dezengrini Slhessarenko
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso (UFMT), B Boa Esperança, 78060-900, Cuiabá, MT, Brasil.
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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; 12:e0421823. [PMID: 38651879 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
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3
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Silva T, Oliveira E, Oliveira A, Menezes A, Jeremias WDJ, Grenfell RF, Monte-Neto RLD, Pascoal-Xavier MA, Campos MA, Fernandes G, Alves P. Enhancing the epidemiological surveillance of SARS-CoV-2 using Sanger sequencing to identify circulating variants and recombinants. Braz J Microbiol 2024:10.1007/s42770-024-01387-x. [PMID: 38802687 DOI: 10.1007/s42770-024-01387-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Since the emergence of SARS-CoV-2 in December 2019, more than 12,000 mutations in the virus have been identified. These could cause changes in viral characteristics and directly impact global public health. The emergence of variants is a great concern due to the chance of increased transmissibility and infectivity. Sequencing for surveillance and monitoring circulating strains is extremely necessary as the early identification of new variants allows public health agencies to make faster and more effective decisions to contain the spread of the virus. In the present study, we identified circulating variants in samples collected in Belo Horizonte, Brazil, and detected a recombinant lineage using the Sanger method. The identification of lineages was done through gene amplification of SARS-CoV-2 by Reverse Transcription-Polymerase Chain Reaction (RT-PCR). By using these specific fragments, we were able to differentiate one variant of interest and five circulating variants of concern. We were also able to detect recombinants. Randomly selected samples were sequenced by either Sanger or Next Generation Sequencing (NGS). Our findings validate the effectiveness of Sanger sequencing as a powerful tool for monitoring variants. It is easy to perform and allows the analysis of a larger number of samples in countries that cannot afford NGS.
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Affiliation(s)
- Thaís Silva
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Eneida Oliveira
- Secretaria Municipal de Saúde, 2336, Afonso Pena Avenue, Belo Horizonte, Minas Gerais, 30130-007, Brazil
| | - Alana Oliveira
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - André Menezes
- Secretaria Municipal de Saúde, 2336, Afonso Pena Avenue, Belo Horizonte, Minas Gerais, 30130-007, Brazil
| | - Wander de Jesus Jeremias
- Department of Pharmacy, Federal University of Ouro Preto (UFOP), 27, Nine Street, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | - Rafaella Fq Grenfell
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Drive, Athens, GA, 30602, USA
| | - Rubens Lima do Monte-Neto
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Marcelo A Pascoal-Xavier
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
- Department of Anatomic Pathology, College of Medicine, Federal University of Minas Gerais, 6627, Presidente Antônio Carlos Avenue, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Marco A Campos
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Gabriel Fernandes
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Pedro Alves
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil.
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4
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Abdul Aziz N, Twohig K, Sinnathamby M, Zaidi A, Aliabadi S, Groves N, Nash S, Thelwall S, Dabrera G. Descriptive Epidemiology of Travel and Non-Travel Related SARS-CoV-2 Gamma (P.1/501Y.V3) Variant Cases in England, 2021. Influenza Other Respir Viruses 2024; 18:e13308. [PMID: 38736251 PMCID: PMC11089272 DOI: 10.1111/irv.13308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024] Open
Affiliation(s)
- Nurin Abdul Aziz
- COVID-19 Vaccines and Epidemiology Division, Clinical and Public Health Group, United Kingdom Health Security Agency, London, UK
| | - Katherine Twohig
- Public Health England COVID-19 National Epidemiology Cell, London, UK
| | - Mary Sinnathamby
- COVID-19 Vaccines and Epidemiology Division, Clinical and Public Health Group, United Kingdom Health Security Agency, London, UK
| | - Asad Zaidi
- COVID-19 Vaccines and Epidemiology Division, Clinical and Public Health Group, United Kingdom Health Security Agency, London, UK
| | - Shirin Aliabadi
- Public Health England COVID-19 National Epidemiology Cell, London, UK
| | - Natalie Groves
- TARZET Division, Clinical and Public Health Group, United Kingdom Health Security Agency, London, UK
| | - Sophie Nash
- COVID-19 Vaccines and Epidemiology Division, Clinical and Public Health Group, United Kingdom Health Security Agency, London, UK
| | - Simon Thelwall
- COVID-19 Vaccines and Epidemiology Division, Clinical and Public Health Group, United Kingdom Health Security Agency, London, UK
| | - Gavin Dabrera
- COVID-19 Vaccines and Epidemiology Division, Clinical and Public Health Group, United Kingdom Health Security Agency, London, UK
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5
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Pegg CL, Modhiran N, Parry RH, Liang B, Amarilla AA, Khromykh AA, Burr L, Young PR, Chappell K, Schulz BL, Watterson D. The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 gamma variant. Glycobiology 2024; 34:cwad097. [PMID: 38048640 DOI: 10.1093/glycob/cwad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/10/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity towards the viral spike protein, whether acquired from infection or vaccination. Mutations that impact N-glycosylation of spike may be particularly important in influencing antigenicity, but their consequences are difficult to predict. Here, we compare the glycosylation profiles and antigenicity of recombinant viral spike of ancestral Wu-1 and the Gamma strain, which has two additional N-glycosylation sites due to amino acid substitutions in the N-terminal domain (NTD). We found that a mutation at residue 20 from threonine to asparagine within the NTD caused the loss of NTD-specific antibody COVA2-17 binding. Glycan site-occupancy analyses revealed that the mutation resulted in N-glycosylation switching to the new sequon at N20 from the native N17 site. Site-specific glycosylation profiles demonstrated distinct glycoform differences between Wu-1, Gamma, and selected NTD variant spike proteins, but these did not affect antibody binding. Finally, we evaluated the specificity of spike proteins against convalescent COVID-19 sera and found reduced cross-reactivity against some mutants, but not Gamma spike compared to Wuhan spike. Our results illustrate the impact of viral divergence on spike glycosylation and SARS-CoV-2 antibody binding profiles.
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Affiliation(s)
- Cassandra L Pegg
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, Building 75, Corner College Road and Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Rhys H Parry
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Benjamin Liang
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Alberto A Amarilla
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Alexander A Khromykh
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
- Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence, Brisbane, Queensland 4072 and 4006, Australia
| | - Lucy Burr
- Department of Respiratory Medicine, Mater Health Services, Raymond Terrace, South Brisbane, Queensland 4101, Australia
| | - Paul R Young
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, Building 75, Corner College Road and Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
- Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence, Brisbane, Queensland 4072 and 4006, Australia
| | - Keith Chappell
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, Building 75, Corner College Road and Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
- Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence, Brisbane, Queensland 4072 and 4006, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
- Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence, Brisbane, Queensland 4072 and 4006, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Bioscience, Chemistry Building 68, Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, Building 75, Corner College Road and Cooper Road, University of Queensland, St Lucia, Queensland 4072, Australia
- Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence, Brisbane, Queensland 4072 and 4006, Australia
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6
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Stutz C, Alcantara DMC, dos Santos CM, Torres JM, Rodrigues R, Marcon GEB, Ferreira EDC, Sarti ECFB, de Oliveira TF, Mendes FML, Lemos EF, Demarchi LHF, Lichs GGDC, Zardin MCSU, Gonçalves CCM, Guilhermino JDF, Perdomo RT, Fernandez ZDC. Seroprevalence of antibodies against SARS-CoV-2 in the school community in Campo Grande, state of Mato Grosso do Sul, Brazil, October 2021-November 2022. Front Immunol 2024; 15:1354786. [PMID: 38596680 PMCID: PMC11002276 DOI: 10.3389/fimmu.2024.1354786] [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: 12/12/2023] [Accepted: 02/29/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction With the reopening of schools during the coronavirus disease 2019 (COVID-19) pandemic, it was imperative to understand the role of students and education professionals in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this paper, we determined the seroprevalence of the SARS-CoV-2 anti-nucleocapsid antibodies in the school community in Campo Grande, the capital and most populous city of the state of Mato Grosso do Sul (Brazil) and evaluated its association with sex, school level, and school type. Materials and methods The survey was carried out in 20 public and private schools in the urban region of Campo Grande using the TR DPP® COVID-19 immunoglobulin M/immunoglobulin G (IgM/IgG) kit from the Immunobiological Technology Institute (Bio-Manguinhos, Rio de Janeiro, Brazil). Testing was carried out in three periods: from October to December 2021; from March to July 2022; and from August to November 2022. The participants were students aged 6-17 years enrolled in primary or secondary schools and professionals of different ages and roles. Results During the first testing period, 162 participants were seropositive for the IgM and/or IgG anti-nucleocapsid SARS-CoV-2 antibodies, with an estimated seroprevalence of 19.6% using Bayesian multilevel regression. In the second period, 251 participants were seropositive (estimated seroprevalence, 34.6%), while in the third period, 393 participants were seroconverted (estimated seroprevalence, 56.7%). In 2022, there was an increase in the seroconversion rate compared to that in 2021. The most frequently described acute manifestations in the three periods were fever, headache, sore throat, and runny nose. In terms of the demographic profile, there was no predominance of seropositivity between the sexes, although women represented approximately 70% of the study population. There were also no differences between students and school staff. Discussion The results made it possible to evaluate the extent of SARS-CoV-2 transmission in the school community through immunity developed against the virus, in addition to providing information about COVID-19 symptoms in children, adolescents, and adults.
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Affiliation(s)
- Claudia Stutz
- Fiocruz Ceará, Fundação Oswaldo Cruz (Fiocruz), Eusébio, Ceará, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição (FACFAN), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Camila Maria dos Santos
- Fiocruz Mato Grosso do Sul, Fundação Oswaldo Cruz (Fiocruz), Campo Grande, Mato Grosso do Sul, Brazil
| | - Jaire Marinho Torres
- Fiocruz Mato Grosso do Sul, Fundação Oswaldo Cruz (Fiocruz), Campo Grande, Mato Grosso do Sul, Brazil
| | - Rudielle Rodrigues
- Fiocruz Mato Grosso do Sul, Fundação Oswaldo Cruz (Fiocruz), Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Eduardo de Castro Ferreira
- Fiocruz Mato Grosso do Sul, Fundação Oswaldo Cruz (Fiocruz), Campo Grande, Mato Grosso do Sul, Brazil
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | | | | | - Flavia Maria Lins Mendes
- Fiocruz Mato Grosso do Sul, Fundação Oswaldo Cruz (Fiocruz), Campo Grande, Mato Grosso do Sul, Brazil
| | - Everton Ferreira Lemos
- Universidade Estadual de Mato Grosso do Sul (UEMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Luiz Henrique Ferraz Demarchi
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul (LACEN-MS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Gislene Garcia de Castro Lichs
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul (LACEN-MS), Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Crhistinne Cavalheiro Maymone Gonçalves
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Secretaria Adjunta de Estado, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Renata Trentin Perdomo
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição (FACFAN), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
- Laboratório de Biologia Molecular e Cultura Celular da Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição (FACFAN), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
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7
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Emerick GS, Zandonade E, Prado CBD, Pires LBC, Bezerra OIMDPA, Salaroli LB. Morbimortality profile by COVID-19 in telework and on-site work in an oil and gas company in Brazil. Work 2024:WOR230114. [PMID: 38457165 DOI: 10.3233/wor-230114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND As a reflection of the health emergency caused by COVID-19, many countries adopted guidelines, which included activity restrictions. As a result, some companies maintained their activities with on-site work and telework. OBJECTIVE Analyzing the morbidity and mortality profile due to COVID-19 of workers in telework and on-site work in an oil and gas company. METHODS Cross-sectional, quantitative, and analytical study that included 8,394 workers diagnosed with COVID-19 at an oil and gas company in Brazil, from June 2020 to June 2021. The company's Surveillance Program database was used as an information source. RESULTS The total prevalence of cases was 21.7% . For teleworking and face-to-face workers, they were 20.7% and 23.3%, respectively. There was a predominance of women (19.7%), white ethnicity/colour (64.7%), higher level position (52.6%), age group over 40 years (36.7%), married (53, 8%), working at the company for a period that ranges from 7 to 10 years (17%), administrative activity (68.5%), and a higher number of symptomatic workers and deaths in telework compared to on-site work. CONCLUSIONS The results suggest that testing is important to refrain the virus spread in the company's work environments, as it allowed asymptomatic workers to be diagnosed with COVID-19. The study suggested that on-site work was not a transmission facilitator in the occupational environment, which points out the importance of preventive measures in the workplace and the adoption of remote work for the largest possible number of workers to improve the safety of employees, workers who remained in the on-site work modality.
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Affiliation(s)
- Giselly Storch Emerick
- Graduate Program in Public Health Universidade Federal do Espírito Santo, Vitória - ES, Brazil
| | - Eliana Zandonade
- Graduate Program in Public Health Universidade Federal do Espírito Santo, Vitória - ES, Brazil
| | - Camila Bruneli do Prado
- Research Group on Epidemiology Health and Nutrition, Universidade Federal do Espírito Santo, Vitória - ES, Brazil
| | - Luciana Bicalho Cevolani Pires
- Graduate Program in Nutrition and Health, Health Sciences Center at the Federal University of Espírito Santo (UFES), Vitória, Brazil
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8
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Manaças LRA, de Amorim RLO, Aguila A, Novo PC, Badin RC. Evaluation of hematological changes and immune response biomarkers as a prognostic factor in critical patients with COVID-19. PLoS One 2024; 19:e0297490. [PMID: 38421951 PMCID: PMC10903867 DOI: 10.1371/journal.pone.0297490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/05/2024] [Indexed: 03/02/2024] Open
Abstract
COVID-19 disease has been a challenge for health systems worldwide due to its high transmissibility, morbidity, and mortality. Severe COVID-19 is associated with an imbalance in the immune response, resulting in a cytokine storm and a hyperinflammation state. While hematological parameters correlate with prognosis in COVID patients, their predictive value has not been evaluated specifically among those severely ill. Therefore, we aim to evaluate the role of hematological and immune response biomarkers as a prognostic factor in critically ill patients with COVID-19 admitted to the intensive care unit. From May 2020 to July 2021, a retrospective cohort study was conducted in a reference hospital in Manaus, which belongs to the Brazilian public health system. This study was carried out as single-center research. Clinical and laboratory parameters were analyzed to evaluate the association with mortality. We also evaluated the role of neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), platelet-to-lymphocyte ratio (PLR), and C-reactive protein-to-lymphocyte ratio (CLR). We gathered information from medical records, as well as from prescriptions and forms authorizing the use of antimicrobial medications. During the study period, 177 patients were included, with a mean age of 62.58 ± 14.39 years. The overall mortality rate was 61.6%. Age, mechanical ventilation (MV) requirement, leukocytosis, neutrophilia, high c-reactive protein level, NLR, and CLR showed a statistically significant association with mortality in the univariate analysis. In the multivariate logistic regression analysis, only MV (OR 35.687, 95% CI: 11.084-114.898, p< 0.001) and NLR (OR 1.026, 95% CI: 1.003-1.050, p = 0.028) remained statistically associated with the outcome of death (AUC = 0.8096). While the need for mechanical ventilation is a parameter observed throughout the hospital stay, the initial NLR can be a primary risk stratification tool to establish priorities and timely clinical intervention in patients with severe COVID-19 admitted to the ICU.
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Affiliation(s)
- Liliane Rosa Alves Manaças
- Department of Pharmacology, Brazilian National Cancer Institute (INCA), Hospital II, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Robson Luís Oliveira de Amorim
- Department of Neurosurgery, Getúlio Vargas University Hospital, Manaus, Amazonas, Brazil
- Federal University of Amazonas (UFAM), Manaus, AM, Brazil. Post-graduate Program in Basic and Applied Immunology, Institute of Biological Sciences.
| | - Alian Aguila
- Department of Cardiology, Memorial Hospital System, Florida, United States of America
| | - Paloam Cardoso Novo
- Department of Neurosurgery, Getúlio Vargas University Hospital, Manaus, Amazonas, Brazil
- Federal University of Amazonas (UFAM), Manaus, AM, Brazil. Post-graduate Program in Basic and Applied Immunology, Institute of Biological Sciences.
| | - Rebeka Caribé Badin
- Department of Pharmacology, Brazilian National Cancer Institute (INCA), Hospital II, Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Neurosurgery, Getúlio Vargas University Hospital, Manaus, Amazonas, Brazil
- Federal University of Amazonas (UFAM), Manaus, AM, Brazil. Post-graduate Program in Basic and Applied Immunology, Institute of Biological Sciences.
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9
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Gräf T, Martinez AA, Bello G, Dellicour S, Lemey P, Colizza V, Mazzoli M, Poletto C, Cardoso VLO, da Silva AF, Motta FC, Resende PC, Siqueira MM, Franco L, Gresh L, Gabastou JM, Rodriguez A, Vicari A, Aldighieri S, Mendez-Rico J, Leite JA. Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean. Nat Commun 2024; 15:1837. [PMID: 38418815 PMCID: PMC10902334 DOI: 10.1038/s41467-024-46143-9] [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: 10/11/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.
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Affiliation(s)
- Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Brazil.
| | - Alexander A Martinez
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
- National Research System (SNI), National Secretary of Research, Technology and Innovation (SENACYT), Panama City, Panama
- Department of Microbiology and Immunology, University of Panama, Panama City, Panama
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Mattia Mazzoli
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Chiara Poletto
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Vanessa Leiko Oikawa Cardoso
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, FIOCRUZ-Bahia, Salvador, Brazil
| | | | - Fernando Couto Motta
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marilda M Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leticia Franco
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Lionel Gresh
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Jean-Marc Gabastou
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Angel Rodriguez
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Andrea Vicari
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Sylvain Aldighieri
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Jairo Mendez-Rico
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Juliana Almeida Leite
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA.
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10
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do Amaral CMSSB, da Luz Goulart C, da Silva BM, Valente J, Rezende AG, Fernandes E, Cubas-Vega N, Borba MGS, Sampaio V, Monteiro W, de Melo GC, Lacerda M, Arêas GPT, Almeida-Val F. Low handgrip strength is associated with worse functional outcomes in long COVID. Sci Rep 2024; 14:2049. [PMID: 38267519 PMCID: PMC10808118 DOI: 10.1038/s41598-024-52401-z] [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: 12/02/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024] Open
Abstract
The diagnosis of long COVID is troublesome, even when functional limitations are present. Dynapenia is the loss of muscle strength and power production that is not caused by neurologic or muscular diseases, being mostly associated with changes in neurologic function and/or the intrinsic force-generating properties of skeletal muscle, which altogether, may partially explain the limitations seen in long COVID. This study aimed to identify the distribution and possible associations of dynapenia with functional assessments in patients with long COVID. A total of 113 patients with COVID-19 were evaluated by functional assessment 120 days post-acute severe disease. Body composition, respiratory muscle strength, spirometry, six-minute walk test (6MWT, meters), and hand-grip strength (HGS, Kilogram-force) were assessed. Dynapenia was defined as HGS < 30 Kgf (men), and < 20 Kgf (women). Twenty-five (22%) participants were dynapenic, presenting lower muscle mass (p < 0.001), worse forced expiratory volume in the first second (FEV1) (p = 0.0001), lower forced vital capacity (p < 0.001), and inspiratory (p = 0.007) and expiratory (p = 0.002) peek pressures, as well as worse 6MWT performance (p < 0.001). Dynapenia, independently of age, was associated with worse FEV1, maximal expiratory pressure (MEP), and 6MWT, (p < 0.001) outcomes. Patients with dynapenia had higher intensive care unit (ICU) admission rates (p = 0.01) and need for invasive mechanical ventilation (p = 0.007) during hospitalization. The HGS is a simple, reliable, and low-cost measurement that can be performed in outpatient clinics in low- and middle-income countries. Thus, HGS may be used as a proxy indicator of functional impairment in this population.
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Affiliation(s)
- Camila Miriam Suemi Sato Barros do Amaral
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Av. Pedro Teixeira, -25 - Bairro Dom Pedro, Manaus, AM, Brazil
- Universidade do Estado Do Amazonas, Manaus, AM, Brazil
| | - Cássia da Luz Goulart
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Av. Pedro Teixeira, -25 - Bairro Dom Pedro, Manaus, AM, Brazil
| | - Bernardo Maia da Silva
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Av. Pedro Teixeira, -25 - Bairro Dom Pedro, Manaus, AM, Brazil
| | - Jefferson Valente
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Av. Pedro Teixeira, -25 - Bairro Dom Pedro, Manaus, AM, Brazil
| | | | | | - Nadia Cubas-Vega
- Universidad Nacional Autónoma de Honduras, Tegucigalpa, FM, Honduras
| | - Mayla Gabriela Silva Borba
- Universidade do Estado Do Amazonas, Manaus, AM, Brazil
- Hospital e Pronto-Socorro Delphina Rinaldi Abdel Aziz, Manaus, AM, Brazil
| | | | - Wuelton Monteiro
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Av. Pedro Teixeira, -25 - Bairro Dom Pedro, Manaus, AM, Brazil
- Universidade do Estado Do Amazonas, Manaus, AM, Brazil
| | - Gisely Cardoso de Melo
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Av. Pedro Teixeira, -25 - Bairro Dom Pedro, Manaus, AM, Brazil
- Universidade do Estado Do Amazonas, Manaus, AM, Brazil
| | - Marcus Lacerda
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Av. Pedro Teixeira, -25 - Bairro Dom Pedro, Manaus, AM, Brazil
- Universidade do Estado Do Amazonas, Manaus, AM, Brazil
- Instituto Todos Pela Saúde, São Paulo, SP, Brazil
- Instituto Leônidas & Maria Deane/Fundação Oswaldo Cruz (ILMD/Fiocruz Amazônia), Manaus, Brazil
| | | | - Fernando Almeida-Val
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Av. Pedro Teixeira, -25 - Bairro Dom Pedro, Manaus, AM, Brazil.
- Universidade do Estado Do Amazonas, Manaus, AM, Brazil.
- Universidade Federal do Amazonas, Manaus, AM, Brazil.
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11
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Röltgen K, Boyd SD. Antibody and B Cell Responses to SARS-CoV-2 Infection and Vaccination: The End of the Beginning. ANNUAL REVIEW OF PATHOLOGY 2024; 19:69-97. [PMID: 37738512 DOI: 10.1146/annurev-pathmechdis-031521-042754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
As the COVID-19 pandemic has evolved during the past years, interactions between human immune systems, rapidly mutating and selected SARS-CoV-2 viral variants, and effective vaccines have complicated the landscape of individual immunological histories. Here, we review some key findings for antibody and B cell-mediated immunity, including responses to the highly mutated omicron variants; immunological imprinting and other impacts of successive viral antigenic variant exposures on antibody and B cell memory; responses in secondary lymphoid and mucosal tissues and non-neutralizing antibody-mediated immunity; responses in populations vulnerable to severe disease such as those with cancer, immunodeficiencies, and other comorbidities, as well as populations showing apparent resistance to severe disease such as many African populations; and evidence of antibody involvement in postacute sequelae of infection or long COVID. Despite the initial phase of the pandemic ending, human populations will continue to face challenges presented by this unpredictable virus.
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Affiliation(s)
- Katharina Röltgen
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA;
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
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12
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Jeronimo PMC, Aksenen CF, Duarte IO, Lins RD, Miyajima F. Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation. J Virol 2024; 98:e0140423. [PMID: 38088350 PMCID: PMC10804945 DOI: 10.1128/jvi.01404-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Coronaviruses are large RNA viruses that can infect and spread among humans and animals. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019, has evolved since its first detection in December 2019. Deletions are a common occurrence in SARS-CoV-2 evolution, particularly in specific genomic sites, and may be associated with the emergence of highly competent lineages. While deletions typically have a negative impact on viral fitness, some persist and become fixed in viral populations, indicating that they may confer advantageous benefits for the virus's adaptive evolution. This work presents a literature review and data analysis on structural losses in the SARS-CoV-2 genome and the potential relevance of specific signatures for enhanced viral fitness and spread.
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Affiliation(s)
| | - Cleber Furtado Aksenen
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Igor Oliveira Duarte
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Roberto D. Lins
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Pernambuco, Recife, Brazil
| | - Fabio Miyajima
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
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13
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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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14
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Vieira DFB, Bandeira DM, da Silva MAN, de Almeida ALT, Araújo M, Machado AB, Tort LFL, Nacife VP, Siqueira MM, Motta FC, Pauvolid-Corrêa A, Barth OM. Comparative analysis of SARS-CoV-2 variants Alpha (B.1.1.7), Gamma (P.1), Zeta (P.2) and Delta (B.1.617.2) in Vero-E6 cells: ultrastructural characterization of cytopathology and replication kinetics. Braz J Infect Dis 2024; 28:103706. [PMID: 38081327 PMCID: PMC10776915 DOI: 10.1016/j.bjid.2023.103706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
This study compares the effects of virus-cell interactions among SARS-CoV-2 variants of concern (VOCs) isolated in Brazil in 2021, hypothesizing a correlation between cellular alterations and mortality and between viral load and transmissibility. For this purpose, reference isolates of Alpha, Gamma, Zeta, and Delta variants were inoculated into monolayers of Vero-E6 cells. Viral RNA was quantified in cell supernatants by RT‒PCR, and infected cells were analyzed by Transmission Electron Microscopy (TEM) for qualitative and quantitative evaluation of cellular changes 24, 48, and 72 hours postinfection (hpi). Ultrastructural analyses showed that all variants of SARS-CoV-2 altered the structure and function of mitochondria, nucleus, and rough endoplasmic reticulum of cells. Monolayers infected with the Delta variant showed the highest number of modified cells and the greatest statistically significant differences compared to those of other variants. Viral particles were observed in the cytosol and the cell membrane in 100 % of the cells at 48 hpi. Alpha showed the highest mean particle diameter (79 nm), and Gamma and Delta were the smallest (75 nm). Alpha and Gamma had the highest particle frequency per field at 48 hpi, while the same was observed for Zeta and Delta at 72 hpi and 24 hpi, respectively. The cycle threshold of viral RNA varied among the target protein, VOC, and time of infection. The findings presented here demonstrate that all four VOCs evaluated caused ultrastructural changes in Vero-E6 cells, which were more prominent when infection occured with the Delta variant.
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Affiliation(s)
- Debora Ferreira Barreto Vieira
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil.
| | - Derick Mendes Bandeira
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil
| | - Marcos Alexandre Nunes da Silva
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil
| | - Ana Luisa Teixeira de Almeida
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil
| | - Mia Araújo
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Ana Beatriz Machado
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Luis Fernando Lopez Tort
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil; Universidad de la República, Centro Universitario Regional - Litoral Norte, Laboratório de Virologia Molecular, Departamento de Ciências Biológicas, Salto, Uruguai
| | - Valéria Pereira Nacife
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Marilda M Siqueira
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Fernando Couto Motta
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Alex Pauvolid-Corrêa
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil; Universidade Federal de Viçosa, Departamento de Veterinária, Laboratório de Virologia Veterinária de Viçosa, Viçosa, MG, Brazil
| | - Ortrud Monika Barth
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil
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15
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Barbosa G, Alberto-Lei F, Chaves APC, Carvalho JMA, Conte DD, Moreira LVL, de Souza Luna LK, Perosa AH, Bellei N. Respiratory virus detection among healthcare professionals in Brazil: work-related contact and episode recurrence during the COVID-19 pandemic. Public Health 2024; 226:159-164. [PMID: 38071948 DOI: 10.1016/j.puhe.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 01/15/2024]
Abstract
OBJECTIVES Since the beginning of the COVID-19 pandemic, changes in the circulation of respiratory viruses have been observed after measures to control the spread of SARS-CoV-2 were implemented. In this sense, we aimed to understand the circulation of the respiratory virus and its impact in a controlled healthy population of healthcare professional (HCP) volunteers in phase III of the clinical trial of the ChadOx nCoV1 conducted in São Paulo, Brazil. STUDY DESIGN This was a nested observational cohort study within a clinical trial. METHODS We performed RT-qPCR to detect SARS-CoV-2, influenza virus A and B (IVA and IVB), respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (hMPV), human coronaviruses (hCoVs: HKU-1, NL63, OC43, and 229-E), parainfluenza virus (PiV) I-IV, and q-PCR for adenovirus in nasopharyngeal and oropharyngeal samples obtained from HCP enrolled in the clinical trial to assess respiratory viruses infection among vaccinated and non-vaccinated. RESULTS From July 2020 to January 2022, 876 samples were included from 737 volunteers (median age: 33 years, 62.9% female). New episodes were registered for 119 individuals. We observed an overall positivity of 37.7% for SARS-CoV-2 and 16.4% for other respiratory viruses; HRV was the second most detected virus (8%), followed by RSV (2.4%). Fully vaccinated individuals accounted for 53.3% of collected samples, and 52.9% presented at least one respiratory virus infection, with SARS-CoV-2 being the most predominant etiologic agent (62.3%). Influenza and hMPV were not detected among the tested samples. Among the subjects that presented more than one episode, SARS-CoV-2 and HRV infections were related to direct contact with patients (P < 0.002). CONCLUSIONS Data show high infection rates among HCPs even under mask policies and contact precautions, highlighting the need for improvement in infection control measures in this population regardless of the vaccination program.
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Affiliation(s)
- G Barbosa
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil.
| | - F Alberto-Lei
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - A P C Chaves
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - J M A Carvalho
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - D D Conte
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - L V L Moreira
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - L K de Souza Luna
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - A H Perosa
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - N Bellei
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
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16
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Castillo AP, Miranda JVO, Fonseca PLC, Silva SDO, Lopes REN, Spanhol VC, Moreira RG, Nicolino RR, Queiroz DC, de Araújo E Santos LCG, Dos Santos APS, Rivetti HAA, Martins-Duarte ES, de Almeida Vitor RW, Dos Reis JKP, Aguiar RS, da Silveira JAG. Evidence of SARS-CoV-2 infection and co-infections in stray cats in Brazil. Acta Trop 2024; 249:107056. [PMID: 37913970 DOI: 10.1016/j.actatropica.2023.107056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/20/2023] [Accepted: 10/29/2023] [Indexed: 11/03/2023]
Abstract
The zoonotic virus SARS-CoV-2, which causes severe acute respiratory syndrome in humans (COVID-19), has been identified in cats. Notably, most positive cases were in cats that had close contact with infected humans, suggesting a role for humans in animal transmission routes. Previous studies have suggested that animals with immune depletion are more susceptible to SARS-CoV-2 infection. To date, there is limited evidence of SARS-CoV-2 infections in stray and free-range cats affected by other pathogens. In this study, we investigated infections caused by SARS-CoV-2, Leishmania spp., Toxoplasma gondii, Mycoplasma spp., Bartonella spp., Feline leukemia virus (FeLV), and Feline immunodeficiency virus (FIV) in stray cats from an urban park in Brazil during the COVID-19 pandemic. From February to September 2021, 78 mixed-breed cats were tested for SARS-CoV-2 and hemopathogens using molecular analysis at Américo Renné Giannetti Municipal Park, Belo Horizonte, Minas Gerais, Brazil. An enzyme-linked immunosorbent assay (ELISA) was used to detect IgG in T. gondii. None of the animals in this study showed any clinical signs of infections. The SARS-CoV-2 virus RNA was detected in 7.7 % of cats, and a whole virus genome sequence analysis revealed the SARS-CoV-2 Delta lineage (B.1.617.2). Phylogenetic analysis showed that SARS-CoV-2 isolated from cats was grouped into the sublineage AY.99.2, which matches the epidemiological scenario of COVID-19 in the urban area of our study. Leishmania infantum was detected and sequenced in 9 % of cats. The seroprevalence of T. gondii was 23.1 %. Hemotropic Mycoplasma spp. was detected in 7.7 % of the cats, with Mycoplasma haemofelis and Candidatus Mycoplasma haemominutum being the most common. Bartonella henselae and Bartonella clarridgeiae were detected in 38.5 % of the cats, FeLV was detected in 17,9 %, and none of the cats studied tested positive for FIV. This study reports, for the first time, the SARS-CoV-2 infection with whole-genome sequencing in stray cats in southeastern Brazil and co-infection with other pathogens, including Bartonella spp. and Feline leukemia virus. Our study observed no correlation between SARS-CoV-2 and the other detected pathogens. Our results emphasize the importance of monitoring SARS-CoV-2 in stray cats to characterize their epidemiological role in SARS-CoV-2 infection and reinforce the importance of zoonotic disease surveillance.
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Affiliation(s)
- Anisleidy Pérez Castillo
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil; Laboratório de PROTOVET, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária da Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Joao Victor Oliveira Miranda
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Paula Luize Camargos Fonseca
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Soraia de Oliveira Silva
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Rosálida Estevam Nazar Lopes
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Viviane Campos Spanhol
- Laboratório de Retroviroses, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rennan Garcias Moreira
- Centro de Laboratórios Multiusuários, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Rafael Romero Nicolino
- Departamento de Epidemiologia e Defesa Sanitária Animal, Escola de Veterinária da Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Daniel Costa Queiroz
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Luiza Campos Guerra de Araújo E Santos
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Anna Pio Soares Dos Santos
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Hugo Adriano Araújo Rivetti
- Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, R. Édna Quintel, 173 - São Bernardo, Belo Horizonte, MG 31270-705, Brazil
| | - Erica S Martins-Duarte
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Ricardo Wagner de Almeida Vitor
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Jenner Karlisson Pimenta Dos Reis
- Laboratório de Retroviroses, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Júlia Angélica Gonçalves da Silveira
- Laboratório de PROTOVET, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária da Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil.
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17
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Penetra SLS, Santos HFP, Resende PC, Bastos LS, da Silva MFB, Pina-Costa A, Lopes RS, Saboia-Vahia L, de Oliveira ACA, Pereira EC, Filho FM, Wakimoto MD, Calvet GA, Fuller TL, Whitworth J, Smith C, Nielsen-Saines K, Carvalho MS, Espíndola OM, Guaraldo L, Siqueira MM, Brasil P. SARS-CoV-2 Reinfection Cases in a Household-Based Prospective Cohort in Rio de Janeiro. J Infect Dis 2023; 228:1680-1689. [PMID: 37571849 PMCID: PMC11032242 DOI: 10.1093/infdis/jiad336] [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: 03/23/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/13/2023] Open
Abstract
This was a household-based prospective cohort study conducted in Rio de Janeiro, in which people with laboratory-confirmed coronavirus disease 2019 (COVID-19) and their household contacts were followed from April 2020 through June 2022. Ninety-eight reinfections were identified, with 71 (72.5%) confirmed by genomic analyses and lineage definition in both infections. During the pre-Omicron period, 1 dose of any COVID-19 vaccine was associated with a reduced risk of reinfection, but during the Omicron period not even booster vaccines had this effect. Most reinfections were asymptomatic or milder in comparison with primary infections, a justification for continuing active surveillance to detect infections in vaccinated individuals. Our findings demonstrated that vaccination may not prevent infection or reinfection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). Therefore we highlight the need to continuously update the antigenic target of SARS CoV-2 vaccines and administer booster doses to the population regularly, a strategy well established in the development of vaccines for influenza immunization programs.
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Affiliation(s)
- Stephanie L S Penetra
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heloisa F P Santos
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Soares Bastos
- Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michele F B da Silva
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anielle Pina-Costa
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata Serrano Lopes
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Saboia-Vahia
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Any Caroline Alves de Oliveira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elisa Cavalcante Pereira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando Medeiros Filho
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mayumi D Wakimoto
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Guilherme A Calvet
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Trevon L Fuller
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- University of California, Los Angeles, Los Angeles, California, USA
| | - Jimmy Whitworth
- International Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher Smith
- International Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | | | - Marilia Sá Carvalho
- Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Otávio M Espíndola
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lusiele Guaraldo
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marilda M Siqueira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia Brasil
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
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18
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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] [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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19
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Domino NR, Lapinscki BA, Zhen F, Yamaguto G, Costa ECS, Moriya VL, Pereira LA, Petterle R, Nogueira MB, Raboni SM. Assessing the impact of the Gamma variant on COVID-19 patient admissions in a southern Brazilian tertiary hospital-A comparison of dual pandemic phases. PLoS One 2023; 18:e0291701. [PMID: 38064470 PMCID: PMC10707562 DOI: 10.1371/journal.pone.0291701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Since the first case of COVID-19, Brazil has undergone infection waves with distinct characteristics. The description of new variants has alerted the emergence of more contagious or virulent viruses. The variant of concern Gamma emerged in Brazil and caused an epidemic wave, but its spread outside the country was limited. We report the clinical-epidemiological profile of hospitalized patients with COVID-19 by comparing two periods. A retrospective cohort study was performed. The primary outcome was to assess individuals with COVID-19 admitted in wards and intensive care units at the academic hospital of the Federal University of Parana (CHC-UFPR) between March 2020 and July 2021, correlating demographic, clinical-epidemiologic, and survival data with the most prevalent viral variant found in each period. We used Kaplan-Meier analysis to estimate the probability of survival and ROC curves to evaluate laboratory tests to find a cutoff point for poor outcomes. Data from 2,887 individuals were analyzed, 1,495 and 1,392 from the first and second periods, respectively. Hospitalization predominated among males in both periods, and the median age was significantly lower in the second one. The frequency of comorbidities was similar. Various demographic factors, clinical assessments, and laboratory tests were examined in relation to greater severity. When comparing the two periods, we observed predominance of the Wild virus during the first wave and the Gamma variant during the second, with no significant difference in outcomes. The findings suggest that despite the association of many factors with increased severity, the temporal variation between the two periods did not result in a notable divergence in the measured outcomes. The COVID-19 pandemic has lasted for a long time, with periods marked by peaks of cases, often caused by the emergence of viral variants, resulting in higher infection rates and rapid dissemination but, for variant Gamma, no apparent greater virulence.
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Affiliation(s)
- Natalia R. Domino
- Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Bruna A. Lapinscki
- Microorganisms Research and Molecular Biology Laboratory, Universidade Federal do Paraná, Curitiba, Brazil
| | - Felipe Zhen
- Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Guilherme Yamaguto
- Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanueli C. S. Costa
- Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Vitor L. Moriya
- Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Ricardo Petterle
- Department of Integrative Medicine, Universidade Federal do Paraná, Curitiba, Brazil
| | - Meri B. Nogueira
- Virology Laboratory, Universidade Federal do Paraná, Curitiba, Brazil
| | - Sonia M. Raboni
- Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Integrative Medicine, Universidade Federal do Paraná, Curitiba, Brazil
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20
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y Castro TR, Piccoli BC, Vieira AA, Casarin BC, Tessele LF, Salvato RS, Gregianini TS, Martins LG, Resende PC, Pereira EC, Moreira FRR, de Jesus JG, Seerig AP, Lobato MAO, de Campos MMA, Goularte JS, da Silva MS, Demoliner M, Filippi M, Pereira VMAG, Schwarzbold AV, Spilki FR, Trindade PA. Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis. Microorganisms 2023; 11:2938. [PMID: 38138081 PMCID: PMC10745878 DOI: 10.3390/microorganisms11122938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Mutations in the SARS-CoV-2 genome can alter the virus' fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the introduction and dispersal of the Delta variant in the RS state by sequencing 1077 SARS-CoV-2-positive samples from June to October 2021. Of these samples, 34.7% were identified as Gamma and 65.3% as Delta. Notably, 99.2% of Delta sequences were clustered within the 21J lineage, forming a significant Brazilian clade. The estimated clock rate was 5.97 × 10-4 substitutions per site per year. The Delta variant was first reported on 17 June in the Vinhedos Basalto microregion and rapidly spread, accounting for over 70% of cases within nine weeks. Despite this, the number of cases and deaths remained stable, possibly due to vaccination, prior infections, and the continued mandatory mask use. In conclusion, our study provides insights into the Delta variant circulating in the RS state, highlighting the importance of genomic surveillance for monitoring viral evolution, even when the impact of new variants may be less severe in a given region.
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Affiliation(s)
- Thaís Regina y Castro
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Bruna C. Piccoli
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Andressa A. Vieira
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Bruna C. Casarin
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Luíza F. Tessele
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Richard S. Salvato
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil
| | - Tatiana S. Gregianini
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil
| | - Leticia G. Martins
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil
| | - Elisa C. Pereira
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil
| | - Filipe R. R. Moreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-853, Brazil
| | - Jaqueline G. de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05508-220, Brazil
| | - Ana Paula Seerig
- Vigilância em Saúde, Secretaria Municipal da Saúde de Santa Maria, Santa Maria 97060-001, Brazil
| | - Marcos Antonio O. Lobato
- Departamento de Saúde Coletiva, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Marli M. A. de Campos
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Juliana S. Goularte
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Mariana S. da Silva
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | | | - Alexandre V. Schwarzbold
- Departamento de Clínica Médica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Fernando R. Spilki
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil
| | - Priscila A. Trindade
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
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21
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Wei D, Xie Y, Liu X, Chen R, Zhou M, Zhang X, Qu J. Pathogen evolution, prevention/control strategy and clinical features of COVID-19: experiences from China. Front Med 2023; 17:1030-1046. [PMID: 38157194 DOI: 10.1007/s11684-023-1043-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported at the end of 2019 as a worldwide health concern causing a pandemic of unusual viral pneumonia and many other organ damages, which was defined by the World Health Organization as coronavirus disease 2019 (COVID-19). The pandemic is considered a significant threat to global public health till now. In this review, we have summarized the lessons learnt during the emergence and spread of SARS-CoV-2, including its prototype and variants. The overall clinical features of variants of concern (VOC), heterogeneity in the clinical manifestations, radiology and pathology of COVID-19 patients are also discussed, along with advances in therapeutic agents.
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Affiliation(s)
- Dong Wei
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yusang Xie
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Xuefei Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Rong Chen
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Xinxin Zhang
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China.
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22
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Gagnon-Dufresne MC, Gautier L, Beaujoin C, Boivin P, Coulibaly A, Richard Z, Gomes de Medeiros S, Dutra Da Nóbrega RE, de Araujo Oliveira SR, Cloos P, Chabrol F, Ridde V, Zinszer K. Did the design and planning of testing and contact tracing interventions for COVID-19 consider social inequalities in health? A multiple case study from Brazil, Canada, France & Mali. Soc Sci Med 2023; 335:116230. [PMID: 37716184 DOI: 10.1016/j.socscimed.2023.116230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023]
Abstract
The COVID-19 pandemic has led to an unprecedented global crisis. It has exposed and exacerbated weaknesses in public health systems worldwide, particularly with regards to reaching the most vulnerable populations, disproportionately impacted by the pandemic. The objective of our study was to examine whether and how social inequalities in health (SIH) were considered in the design and planning of public health responses to COVID-19 in jurisdictions of Brazil, Canada, France, and Mali. This article reports on a qualitative multiple case study of testing and contact tracing interventions in regions with high COVID-19 incidence in each country, namely: Manaus (Brazil), Montréal (Canada), Île-de-France (France), and Bamako (Mali). We conducted interviews with 108 key informants involved in these interventions in the four jurisdictions, focusing on the first and second waves of the pandemic. We analyzed our data thematically using a theoretical bricolage framework. Our analysis suggests that the lack of a common understanding of SIH among all actors involved and the sense of urgency brought by the pandemic eclipsed the prioritization of SIH in the initial responses. The pandemic increased intersectoral collaboration, but decision-making power was often unequal between Ministries of Health and other actors in each jurisdiction. Various adaptations to COVID-19 interventions were implemented to reach certain population groups, therefore improving the accessibility, availability, and acceptability of testing and contact tracing. Our study contributes to identifying lessons learned from the current pandemic, namely that the ways in which SIH are understood shape how interventions are planned; that having clear guidelines on how to integrate SIH into public health interventions could lead to more inclusive pandemic responses; that for intersectoral collaboration to be fruitful, there needs to be sufficient resources and equitable decision-making power between partners; and that interventions must be flexible to respond to emerging needs while considering long-standing structural inequalities.
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Affiliation(s)
- Marie-Catherine Gagnon-Dufresne
- School of Public Health, University of Montréal, 7101 Avenue Du Parc, Montréal, QC, H3N 1X9, Canada; Centre de Recherche en Santé Publique (CReSP), 1301 Rue Sherbrooke Est, Montréal, QC, H3L 1M3, Canada.
| | - Lara Gautier
- School of Public Health, University of Montréal, 7101 Avenue Du Parc, Montréal, QC, H3N 1X9, Canada; Centre de Recherche en Santé Publique (CReSP), 1301 Rue Sherbrooke Est, Montréal, QC, H3L 1M3, Canada.
| | - Camille Beaujoin
- School of Public Health, University of Montréal, 7101 Avenue Du Parc, Montréal, QC, H3N 1X9, Canada.
| | - Pauline Boivin
- Unité de Recherche en Sciences Sociales Miseli, Ilot N°17, Cité El Farako, P.O. Box E 5448, Bamako, Mali.
| | - Abdourahmane Coulibaly
- Unité de Recherche en Sciences Sociales Miseli, Ilot N°17, Cité El Farako, P.O. Box E 5448, Bamako, Mali.
| | - Zoé Richard
- Université Paris Cité, Institut de Recherche pour le Développement (IRD), Institut National de La Santé et de La Recherche Médicale (INSERM), Centre Population et Développement (CEPED), 45 Rue des Saints-Pères, F-75006, Paris, France.
| | - Stéphanie Gomes de Medeiros
- Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife PE 50670-901, Brazil.
| | - Raylson Emanuel Dutra Da Nóbrega
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Federal University of Pernambuco, Av. Prof. Moraes Rego - Cidade Universitária, Recife PE 50740-465, Brazil.
| | - Sydia Rosana de Araujo Oliveira
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Federal University of Pernambuco, Av. Prof. Moraes Rego - Cidade Universitária, Recife PE 50740-465, Brazil.
| | - Patrick Cloos
- School of Public Health, University of Montréal, 7101 Avenue Du Parc, Montréal, QC, H3N 1X9, Canada; Centre de Recherche en Santé Publique (CReSP), 1301 Rue Sherbrooke Est, Montréal, QC, H3L 1M3, Canada; School of Social Work, University of Montréal, 3150 Rue Jean-Brillant, Montréal, QC, H3T 1N8, Canada.
| | - Fanny Chabrol
- Université Paris Cité, Institut de Recherche pour le Développement (IRD), Institut National de La Santé et de La Recherche Médicale (INSERM), Centre Population et Développement (CEPED), 45 Rue des Saints-Pères, F-75006, Paris, France.
| | - Valéry Ridde
- Université Paris Cité, Institut de Recherche pour le Développement (IRD), Institut National de La Santé et de La Recherche Médicale (INSERM), Centre Population et Développement (CEPED), 45 Rue des Saints-Pères, F-75006, Paris, France.
| | - Kate Zinszer
- School of Public Health, University of Montréal, 7101 Avenue Du Parc, Montréal, QC, H3N 1X9, Canada; Centre de Recherche en Santé Publique (CReSP), 1301 Rue Sherbrooke Est, Montréal, QC, H3L 1M3, Canada.
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23
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da Silva FF, de Abreu LC, Daboin BEG, Morais TC, Cavalcanti MPE, Bezerra IMP, da Silva CG, Figueira FAMDS, de Caldas Guedes VV, Perez Riera AR. Temporal Analysis of COVID-19 Epidemiological Indicators in a Low-Income Brazilian Context: A Retrospective Analysis in Paraiba State. Viruses 2023; 15:2016. [PMID: 37896793 PMCID: PMC10611110 DOI: 10.3390/v15102016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Northeast Brazil is a region with great international tourist potential. Among the states that make up this region, Paraíba stands out due to the presence of vulnerable groups and factors that contribute to adverse outcomes of COVID-19. Therefore, the aim of this study was to analyze the epidemiological data on the incidence, mortality, and case fatality of COVID-19 in Paraíba. An ecological, population-based study was performed, with data extracted from the Brazilian Ministry of Health database. All cases and deaths from COVID-19 from March 2020 to December 2022 were included. The time series was built by applying the Prais-Winsten regression model, and the daily percent change was calculated to analyze the trends. The highest case fatality of the entire period was in April 2020 (7.8%), but in March 2021, the state broke the dismal record of 1248 deaths and the highest mortality rate (30.5 deaths per 100,000 inhabitants). Stationary mortality and case fatality were better in 2022; however, in February 2022, the mortality rate was at levels similar to the same month of the previous year. These results illustrate that COVID-19 is evolving and needs to be constantly monitored.
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Affiliation(s)
- Fabiola Ferreira da Silva
- Laboratory of Studies Design and Scientific Writing, Postgraduate Division, University Center FMABC, Santo André 09060-870, SP, Brazil; (F.F.d.S.); (L.C.d.A.); (B.E.G.D.); (C.G.d.S.); (A.R.P.R.)
| | - Luiz Carlos de Abreu
- Laboratory of Studies Design and Scientific Writing, Postgraduate Division, University Center FMABC, Santo André 09060-870, SP, Brazil; (F.F.d.S.); (L.C.d.A.); (B.E.G.D.); (C.G.d.S.); (A.R.P.R.)
- Department of Integrated Health Education, Federal University of Espirito Santo, Vitoria 29075-910, ES, Brazil
- School of Medicine, University of Limerick, V94 T9PX Limerick, Ireland
- Post-Graduate Program in Medical Sciences, Faculty of Medicine of the University of São Paulo, São Paulo 01246-903, SP, Brazil; (M.P.E.C.); (F.A.M.d.S.F.)
| | - Blanca Elena Guerrero Daboin
- Laboratory of Studies Design and Scientific Writing, Postgraduate Division, University Center FMABC, Santo André 09060-870, SP, Brazil; (F.F.d.S.); (L.C.d.A.); (B.E.G.D.); (C.G.d.S.); (A.R.P.R.)
- School of Medicine, University of Limerick, V94 T9PX Limerick, Ireland
| | - Tassiane Cristina Morais
- Department of Integrated Health Education, Federal University of Espirito Santo, Vitoria 29075-910, ES, Brazil
- School of Sciences of Santa Casa de Misericórdia de Vitória (EMESCAM), Vitoria 29045-402, ES, Brazil;
| | - Matheus Paiva Emidio Cavalcanti
- Post-Graduate Program in Medical Sciences, Faculty of Medicine of the University of São Paulo, São Paulo 01246-903, SP, Brazil; (M.P.E.C.); (F.A.M.d.S.F.)
| | | | - Célia Guarnieri da Silva
- Laboratory of Studies Design and Scientific Writing, Postgraduate Division, University Center FMABC, Santo André 09060-870, SP, Brazil; (F.F.d.S.); (L.C.d.A.); (B.E.G.D.); (C.G.d.S.); (A.R.P.R.)
| | | | | | - Andres Ricardo Perez Riera
- Laboratory of Studies Design and Scientific Writing, Postgraduate Division, University Center FMABC, Santo André 09060-870, SP, Brazil; (F.F.d.S.); (L.C.d.A.); (B.E.G.D.); (C.G.d.S.); (A.R.P.R.)
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24
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Hojo-Souza NS, Jassat W, Guidoni DL, de Souza FSH. Risks of Adverse Outcomes for Hospitalized COVID-19 Patients during the Four Waves in Brazil According to SARS-CoV-2 Variants, Age Group, and Vaccine Status. Viruses 2023; 15:1997. [PMID: 37896773 PMCID: PMC10610718 DOI: 10.3390/v15101997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 10/29/2023] Open
Abstract
Brazil was hit with four consecutive waves of COVID-19 until 2022 due to the ancestral SARS-CoV-2 (B.1 lineage), followed by the emergence of variants/subvariants. Relative risks of adverse outcomes for COVID-19 patients hospitalized during the four waves were evaluated. Data were extracted from the largest Brazilian database (SIVEP-Gripe), and COVID-19 patients who were hospitalized during the peak of each of the four waves (15-week intervals) were included in this study. The outcomes of in-hospital death, invasive (IMV) and non-invasive (NIV) ventilation requirements, and intensive care unit (ICU) admission were analyzed to estimate the relative risks. A higher risk of in-hospital death was found during the second wave for all age groups, but a significant reduction was observed in the risk of death for the elderly during the third and fourth waves compared to patients in the first wave. There was an increased risk of IMV requirement and ICU admissions during the second wave for patients aged 18-59 years old compared to the first wave. Relative risk analysis showed that booster-vaccinated individuals have lower risks of in-hospital death and IMV requirement in all age groups compared to unvaccinated/partially vaccinated patients, demonstrating the relevance of full/booster vaccination in reducing adverse outcomes for patients who were hospitalized during the variant prevalence.
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Affiliation(s)
- Natália Satchiko Hojo-Souza
- Laboratory of Immunopathology, Oswaldo Cruz Foundation—Minas, Av. Augusto de Lima, 1715, Belo Horizonte 30190-002, MG, Brazil
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Daniel Ludovico Guidoni
- Department of Computing, Federal University of Ouro Preto, Morro do Cruzeiro Campus, Ouro Preto 35400-000, MG, Brazil
| | - Fernanda Sumika Hojo de Souza
- Department of Computing, Federal University of Ouro Preto, Morro do Cruzeiro Campus, Ouro Preto 35400-000, MG, Brazil
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25
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Salgado BB, Barbosa ARC, Arcanjo AR, de Castro DB, Ramos TCA, Naveca F, Altmann DM, Boyton RJ, Lalwani JDB, Lalwani P. Hybrid Immunity Results in Enhanced and More Sustained Antibody Responses after the Second Sinovac-CoronaVac Dose in a Brazilian Cohort: DETECTCoV-19 Cohort. Viruses 2023; 15:1987. [PMID: 37896766 PMCID: PMC10610994 DOI: 10.3390/v15101987] [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: 08/12/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 10/29/2023] Open
Abstract
We measured anti-SARS-CoV-2 antibody responses before and after CoronaVac (inactivated) vaccination in a case-control study performed in CoronaVac-immunized individuals participating in a longitudinal prospective study of adults in Manaus (DETECTCoV-19). Antibody responses were measured by standard serological immunoassays. Peak anti-S-RBD and neutralizing RBD-ACE2 blocking antibody responses after two doses of CoronaVac vaccine were similar in vaccine breakthrough cases (n = 9) and matched controls (n = 45). Individuals with hybrid immunity resulting from prior SARS-CoV-2 infection followed by vaccination (n = 22) had elevated levels of anti-N, anti-S-RBD and RBD-ACE2 blocking antibodies after the second vaccine dose compared to infection-naïve individuals (n = 48). Post-vaccination SARS-CoV-2-specific antibody responses rapidly waned in infection-naïve individuals. Antibody responses wane after vaccination, making individuals susceptible to infection by SARS-CoV-2 variants. These findings support the need for booster doses after primary vaccination. Population antibody serosurveys provide critical information toward implementing optimal timing of booster doses.
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Affiliation(s)
- Bárbara Batista Salgado
- Instituto Leônidas e Maria Deane (ILMD), Fiocruz Amazônia, Rua Terezina, 476 Adrianópolis, Manaus 69057-070, AM, Brazil; (B.B.S.); (A.R.C.B.); (F.N.)
- Laboratory of Infectious Diseases and Immunology, ILMD/Fiocruz Amazônia and PPGIBA/ICB-UFAM, Manaus 69080-900, AM, Brazil;
| | - Aguyda Rayany Cavalcante Barbosa
- Instituto Leônidas e Maria Deane (ILMD), Fiocruz Amazônia, Rua Terezina, 476 Adrianópolis, Manaus 69057-070, AM, Brazil; (B.B.S.); (A.R.C.B.); (F.N.)
- Laboratory of Infectious Diseases and Immunology, ILMD/Fiocruz Amazônia and PPGIBA/ICB-UFAM, Manaus 69080-900, AM, Brazil;
| | - Ana Ruth Arcanjo
- Fundação de Vigilância em Saúde do Amazonas (FVS/AM), Manaus 69093-018, AM, Brazil; (A.R.A.); (D.B.d.C.); (T.C.A.R.)
| | - Daniel Barros de Castro
- Fundação de Vigilância em Saúde do Amazonas (FVS/AM), Manaus 69093-018, AM, Brazil; (A.R.A.); (D.B.d.C.); (T.C.A.R.)
| | - Tatyana Costa Amorim Ramos
- Fundação de Vigilância em Saúde do Amazonas (FVS/AM), Manaus 69093-018, AM, Brazil; (A.R.A.); (D.B.d.C.); (T.C.A.R.)
| | - Felipe Naveca
- Instituto Leônidas e Maria Deane (ILMD), Fiocruz Amazônia, Rua Terezina, 476 Adrianópolis, Manaus 69057-070, AM, Brazil; (B.B.S.); (A.R.C.B.); (F.N.)
| | - Daniel M. Altmann
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK;
| | - Rosemary J. Boyton
- Lung Division, Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ NHS Foundation Trust, London SW3 6LY, UK;
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Jaila Dias Borges Lalwani
- Laboratory of Infectious Diseases and Immunology, ILMD/Fiocruz Amazônia and PPGIBA/ICB-UFAM, Manaus 69080-900, AM, Brazil;
- Faculdade de Ciências Farmacêuticas (FCF), Universidade Federal do Amazonas (UFAM), Manaus 69080-900, AM, Brazil
| | - Pritesh Lalwani
- Instituto Leônidas e Maria Deane (ILMD), Fiocruz Amazônia, Rua Terezina, 476 Adrianópolis, Manaus 69057-070, AM, Brazil; (B.B.S.); (A.R.C.B.); (F.N.)
- Laboratory of Infectious Diseases and Immunology, ILMD/Fiocruz Amazônia and PPGIBA/ICB-UFAM, Manaus 69080-900, AM, Brazil;
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26
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de Araújo Rolo C, Machado BAS, Dos Santos MC, Dos Santos RF, Fonseca MS, Hodel KVS, Silva JR, Nunes DDG, Dos Santos Almeida E, de Andrade JB. Long-term monitoring of COVID-19 prevalence in raw and treated wastewater in Salvador, the largest capital of the Brazilian Northeast. Sci Rep 2023; 13:15238. [PMID: 37709804 PMCID: PMC10502096 DOI: 10.1038/s41598-023-41060-1] [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: 02/08/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023] Open
Abstract
Wastewater-based epidemiology (WBE) becomes an interesting epidemiological approach to monitoring the prevalence of SARS-CoV-2 broadly and non-invasively. Herein, we employ for the first time WBE, associated or not with the PEG 8000 precipitation method, for the detection of SARS-CoV-2 in samples of raw or treated wastewater from 22 municipal wastewater treatment stations (WWTPs) located in Salvador, the fourth most populous city in Brazil. Our results demonstrate the success of the application of WBE for detecting SARS-CoV-2 in both types of evaluated samples, regardless of the usage of PEG 8000 concentration procedure. Further, an increase in SARS-CoV-2 positivity rate was observed in samples collected in months that presented the highest number of confirmed COVID-19 cases (May/2021, June/2021 and January/2022). While PEG 8000 concentration step was found to significantly increase the positivity rate in treated wastewater samples (p < 0.005), a strong positive correlation (r: 0.84; p < 0.002) between non-concentrated raw wastewater samples with the number of new cases of COVID-19 (April/2021-February/2022) was observed. In general, the present results reinforce the efficiency of WBE approach to monitoring the presence of SARS-CoV-2 in either low- or high-capacity WWTPs. The successful usage of WBE even in raw wastewater samples makes it an interesting low-cost tool for epidemiological surveillance.
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Affiliation(s)
- Carolina de Araújo Rolo
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Bruna Aparecida Souza Machado
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, 41650-010, Brazil
| | - Matheus Carmo Dos Santos
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Rosângela Fernandes Dos Santos
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Maísa Santos Fonseca
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Katharine Valéria Saraiva Hodel
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Jéssica Rebouças Silva
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Danielle Devequi Gomes Nunes
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Edna Dos Santos Almeida
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, 41650-010, Brazil
| | - Jailson Bittencourt de Andrade
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil.
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, 41650-010, Brazil.
- Centro Interdisciplinar de Energia e Ambiente - CIEnAm, Federal University of Bahia, Salvador, 40170-115, Brazil.
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27
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Charles CM, Souza Neto LA, Soares CF, Souza Araújo T, Torezzan C, Lima EEC, Munezero A, Bahamondes L, Souza RT, Costa ML, Cecatti JG, Pacagnella RC. Preterm births prevalence during the COVID-19 pandemic in Brazil: results from the national database. Sci Rep 2023; 13:14580. [PMID: 37666901 PMCID: PMC10477268 DOI: 10.1038/s41598-023-37871-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/28/2023] [Indexed: 09/06/2023] Open
Abstract
The SARS-CoV-2 (COVID-19) pandemic impacted the health systems between and within countries, and in the course of the pandemic sexual and reproductive health services were the most disrupted. Findings from high-income settings have reported significant changes in preterm birth prevalence during the pandemic period. To understand the possible effects of the COVID-19 pandemic on preterm birth numbers at the Brazilian national level. We compare the number of preterm deliveries during the COVID-19 pandemic period (2020 and 2021) with previous years. We conducted a population-based cross-sectional study taking the period from January 2017 to December 2021 to account. We use individual-level live births data from the Brazilian Live Birth Information System (SINASC), and we estimate the odds ratio (OR) of preterm deliveries using propensity score weighting analysis in Brazil and its regions. During the study period (from 2017 to 2021), about 2.7 million live births were recorded per year, and the missing value for gestational age at delivery was less than 1.5%. The preterm birth prevalence slightly increased during the COVID-19 pandemic compared to the pre-pandemic period (11.32% in 2021 vs 11.09% in 2019, p-value < 0.0001). After adjusting for sociodemographic variables, the OR of preterm births in Brazil has significantly increased, 4% in 2020 (OR: 1.04 [1.03-1.05] 95% CI, p-value < 0.001), and 2% in 2021(OR: 1.02 [1.01-1.03] 95% CI, p-value < 0.001), compared to 2019. At the regional level, the preterm birth pattern in the South, Southeast and Northeast regions show a similar pattern. The highest odds ratio was observed in the South region (2020 vs 2019, OR: 1.07 [1.05-1.10] 95% CI; 2021 vs 2019, OR: 1.03 [1.01-1.06] 95% CI). However, we also observed a significant reduction in the ORs of preterm births in the northern region during the COVID-19 pandemic (2020 vs 2019, OR: 0.96 [0.94-0.98] 95% CI) and (2021 vs 2019, OR: 0.97 [0.95-0.99] 95% CI). Our analysis shows that the pandemic has increased regional variation in the number of preterm births in Brazil in 2020 and 2021 compared to the pre-pandemic years.
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Affiliation(s)
- Charles M'poca Charles
- Department of Obstetrics and Gynecology, University of Campinas, Campinas, SP, Brazil
- Provincial Health Administration, DPS Manica, Chimoio, Mozambique
| | - Luiz Alves Souza Neto
- Institute of Mathematics, Statistics and Scientific Computing (IMEEC), University of Campinas, Campinas, SP, Brazil
- School of Applied Sciences (FCA), University of Campinas, Campinas, SP, Brazil
| | - Camila Ferreira Soares
- College of Philosophy and Human Sciences (IFCH), University of Campinas, Campinas, SP, Brazil
| | - Tacildo Souza Araújo
- Institute of Mathematics, Statistics and Scientific Computing (IMEEC), University of Campinas, Campinas, SP, Brazil
| | - Cristiano Torezzan
- Center for Population Studies (NEPO), University of Campinas, Campinas, SP, Brazil
| | - Everton Emanuel Campos Lima
- College of Philosophy and Human Sciences (IFCH), University of Campinas, Campinas, SP, Brazil
- Center for Population Studies (NEPO), University of Campinas, Campinas, SP, Brazil
| | - Aline Munezero
- Department of Obstetrics and Gynecology, University of Campinas, Campinas, SP, Brazil
| | - Luis Bahamondes
- Department of Obstetrics and Gynecology, University of Campinas, Campinas, SP, Brazil
- Campinas Reproductive Health Research Center (CEMICAMP), Campinas, Brasil
| | - Renato Teixeira Souza
- Department of Obstetrics and Gynecology, University of Campinas, Campinas, SP, Brazil
| | - Maria Laura Costa
- Department of Obstetrics and Gynecology, University of Campinas, Campinas, SP, Brazil
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Hojo-Souza NS, Freitas VLDS, Guidoni DL, de Souza FSH. Clinical symptom profile of hospitalized COVID-19 Brazilian patients according to SARS-CoV-2 variants. Epidemiol Health 2023; 45:e2023079. [PMID: 37654165 PMCID: PMC10867512 DOI: 10.4178/epih.e2023079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/08/2023] [Indexed: 09/02/2023] Open
Abstract
OBJECTIVES The aim of this study was to investigate the prevalence of the main symptoms in Brazilian coronavirus disease 2019 (COVID-19) patients hospitalized during 4 distinct waves, based on their infection with different severe acute respiratory disease coronavirus 2 (SARS-CoV-2) variants. METHODS This study included hospitalized patients who tested positive for SARS-CoV-2 during 15 weeks around the peak of each of 4 waves: W1, ancestral strain/B.1 lineage (May 31 to September 12, 2020); W2, Gamma/P.1 variant (January 31 to May 15, 2021); W3, Omicron variant (December 5, 2021 to March 19, 2022); and W4, BA.4/BA.5 subvariants (May 22 to September 3, 2022). Symptom data were extracted from the Brazilian Severe Acute Respiratory Syndrome Database. Relative risks were calculated, and an analysis of symptom networks was performed. RESULTS Patients who were hospitalized during the prevalence of the Gamma/P.1 variant demonstrated a higher risk, primarily for symptoms such as fatigue, abdominal pain, low oxygen saturation, and sore throat, than patients hospitalized during the first wave. Conversely, patients who were hospitalized during the predominance of the Omicron variant exhibited a lower relative risk, particularly for symptoms such as loss of smell, loss of taste, diarrhea, fever, respiratory distress, and dyspnea. Similar results were observed in COVID-19 patients who were hospitalized during the wave of the Omicron subvariants BA.4/BA.5. A symptom network analysis, conducted to explore co-occurrence patterns among different variants, revealed significant differential profiles across the 4 waves, with the most notable difference observed between the W2 and W4 networks. CONCLUSIONS Overall, the relative risks and patterns of symptom co-occurrence associated with different SARS-CoV-2 variants may reflect disease severity.
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Ramakrishnan J, Chinnamadhu A, Suresh S, Poomani K. Probing the binding nature and stability of highly transmissible mutated variant alpha to omicron of SARS-CoV-2 RBD with ACE2 via molecular dynamics simulation. J Cell Biochem 2023; 124:1115-1134. [PMID: 37435893 DOI: 10.1002/jcb.30432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 07/13/2023]
Abstract
Currently, no approved drug is available as a causative agent of coronavirus disease 2019 (COVID-19) except for some repurposed drugs. The first structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in late 2019, based on that some vaccines and repurposed drugs were approved to prevent people from COVID-19 during the pandemic situation. Since then, new types of variants emerged and notably, the receptor binding domain (RBD) adopted different binding modes with angiotensin-converting enzyme 2 (ACE2); this made significant changes in the progression of COVID-19. Some of the new variants are highly infectious spreading fast and dangerous. The present study is focused on understanding the binding mode of the RBD of different mutated SARS-CoV-2 variants of concern (alpha to omicron) with the human ACE2 using molecular dynamics simulation. Notably, some variants adopted a new binding mode of RBD with ACE2 and formed different interactions, which is unlike the wild type; this was confirmed from the comparison of interaction between RBD-ACE2 of all variants with its wild-type structure. Binding energy values confirm that some mutated variants exhibit high binding affinity. These findings demonstrate that the variations in the sequence of SARS-CoV-2 S-protein altered the binding mode of RBD; this may be the reason that the virus has high transmissibility and causes new infections. This in-silico study on mutated variants of SARS-CoV-2 RBD with ACE2 insights into their binding mode, binding affinity, and stability. This information may help to understand the RBD-ACE2 binding domains, which allows for designing newer drugs and vaccines.
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Affiliation(s)
- Jaganathan Ramakrishnan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Archana Chinnamadhu
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Suganya Suresh
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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de Mello Almeida Maziero L, Giovanetti M, Fonseca V, Zardin MCSU, de Castro Lichs GG, de Rezende Romera GR, Tsuha DH, Frias DFR, Escandolhero VC, Demarchi LH, Domingues Castilho L, Barbosa KF, Tebet DGM, Xavier J, Fritsch H, Lima M, de Oliveira C, Santos EV, Kashima S, Said RFDC, Rosewell A, Croda J, Alcantara LCJ, Cavalheiro Maymone Gonçalves C. Unveiling the Impact of the Omicron Variant: Insights from Genomic Surveillance in Mato Grosso do Sul, Midwest Brazil. Viruses 2023; 15:1604. [PMID: 37515290 PMCID: PMC10386548 DOI: 10.3390/v15071604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Genomic surveillance has emerged as a crucial tool in monitoring and understanding the dynamics of viral variants during the COVID-19 pandemic. In the Midwest region of Brazil, Mato Grosso do Sul has faced a significant burden from the SARS-CoV-2 epidemic, with a total of 613,000 confirmed cases as of June 2023. In collaboration with the Central Public Health Laboratory in the capital city of Campo Grande, we conducted a portable whole-genome sequencing and phylodynamic analysis to investigate the circulation of the Omicron variant in the region. The study aimed to uncover the genomic landscape and provide valuable insights into the prevalence and transmission patterns of this highly transmissible variant. Our findings revealed an increase in the number of cases within the region during 2022, followed by a gradual decline as a result of the successful impact of the vaccination program together with the capacity of this unpredictable and very transmissible variant to quickly affect the proportion of susceptible population. Genomic data indicated multiple introduction events, suggesting that human mobility played a differential role in the variant's dispersion dynamics throughout the state. These findings emphasize the significance of implementing public health interventions to mitigate further spread and highlight the powerful role of genomic monitoring in promptly tracking and uncovering the circulation of viral strains. Together those results underscore the importance of proactive surveillance, rapid genomic sequencing, and data sharing to facilitate timely public health responses.
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Affiliation(s)
- Lívia de Mello Almeida Maziero
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Preto 30190-009, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Vagner Fonseca
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde/Organização Mundial da Saúde (OPAS/OMS), Brasília 25045-002, Brazil
| | | | | | | | | | | | | | - Luiz Henrique Demarchi
- SES-MS-Laboratório Central de Saúde Pública de Mato Grosso do Sul, Campo Grande 79080-320, Brazil
| | - Larissa Domingues Castilho
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Karine Ferreira Barbosa
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Danielle Galindo Martins Tebet
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Joilson Xavier
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Preto 30190-009, Brazil
| | - Hegger Fritsch
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Preto 30190-009, Brazil
| | - Mauricio Lima
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Preto 30190-009, Brazil
| | - Carla de Oliveira
- lnstituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | | | - Simone Kashima
- Fundação Hemocentro de Ribeirão Preto, Rio de Janeiro 14015-160, Brazil
| | | | - Alexander Rosewell
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde (OPAS/OMS), Brasilia 25045-002, Brazil
| | - Julio Croda
- Fundação Oswaldo Cruz, Universidade Federal de Mato Grosso do Sul-UFMS, Campo Grande 79081-746, Brazil
| | | | - Crhistinne Cavalheiro Maymone Gonçalves
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
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Corrêa TD, Midega TD, Cordioli RL, Barbas CSV, Rabello Filho R, Silva BCD, Silva Júnior M, Nawa RK, Carvalho FRTD, Matos GFJD, Lucinio NM, Rodrigues RD, Eid RAC, Bravim BDA, Pereira AJ, Santos BFCD, Pinho JRR, Pardini A, Teich VD, Laselva CR, Cendoroglo Neto M, Klajner S, Ferraz LJR. Clinical characteristics and outcomes of patients with COVID-19 admitted to the intensive care unit during the first and second waves of the pandemic in Brazil: a single-center retrospective cohort study. EINSTEIN-SAO PAULO 2023; 21:eAO0233. [PMID: 37493832 PMCID: PMC10356126 DOI: 10.31744/einstein_journal/2023ao0233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/07/2023] [Indexed: 07/27/2023] Open
Abstract
OBJECTIVE To describe and compare the clinical characteristics and outcomes of patients admitted to intensive care units during the first and second waves of the COVID-19 pandemic. METHODS In this retrospective single-center cohort study, data were retrieved from the Epimed Monitor System; all adult patients admitted to the intensive care unit between March 4, 2020, and October 1, 2021, were included in the study. We compared the clinical characteristics and outcomes of patients admitted to the intensive care unit of a quaternary private hospital in São Paulo, Brazil, during the first (May 1, 2020, to August 31, 2020) and second (March 1, 2021, to June 30, 2021) waves of the COVID-19 pandemic. RESULTS In total, 1,427 patients with COVID-19 were admitted to the intensive care unit during the first (421 patients) and second (1,006 patients) waves. Compared with the first wave group [median (IQR)], the second wave group was younger [57 (46-70) versus 67 (52-80) years; p<0.001], had a lower SAPS 3 Score [45 (42-52) versus 49 (43-57); p<0.001], lower SOFA Score on intensive care unit admission [3 (1-6) versus 4 (2-6); p=0.018], lower Charlson Comorbidity Index [0 (0-1) versus 1 (0-2); p<0.001], and were less frequently frail (10.4% versus 18.1%; p<0.001). The second wave group used more noninvasive ventilation (81.3% versus 53.4%; p<0.001) and high-flow nasal cannula (63.2% versus 23.0%; p<0.001) during their intensive care unit stay. The intensive care unit (11.3% versus 10.5%; p=0.696) and in-hospital mortality (12.3% versus 12.1%; p=0.998) rates did not differ between both waves. CONCLUSION In the first and second waves, patients with severe COVID-19 exhibited similar mortality rates and need for invasive organ support, despite the second wave group being younger and less severely ill at the time of intensive care unit admission.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sidney Klajner
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
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Golden A, Oliveira-Silva M, Slater H, Vieira AM, Bansil P, Gerth-Guyette E, Leader BT, Zobrist S, Braga Ferreira AK, Santos de Araujo EC, de Lucena Cruz CD, Garbin E, Bizilj GT, Carlson SJ, Sagalovsky M, Pal S, Gupta V, Wolansky L, Boyle DS, Vieira Dall'Acqua DS, Naveca FG, do Nascimento VA, Villalobos Salcedo JM, Drain PK, Costa ADT, Pereira D, Domingo GJ. Antigen concentration, viral load, and test performance for SARS-CoV-2 in multiple specimen types. PLoS One 2023; 18:e0287814. [PMID: 37467188 DOI: 10.1371/journal.pone.0287814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/13/2023] [Indexed: 07/21/2023] Open
Abstract
The relationship between N-antigen concentration and viral load within and across different specimens guides the clinical performance of rapid diagnostic tests (RDT) in different uses. A prospective study was conducted in Porto Velho, Brazil, to investigate RDT performance in different specimen types as a function of the correlation between antigen concentration and viral load. The study included 214 close contacts with recent exposures to confirmed cases, aged 12 years and older and with various levels of vaccination. Antigen concentration was measured in nasopharyngeal swab (NPS), anterior nares swab (ANS), and saliva specimens. Reverse transcriptase (RT)-PCR was conducted on the NPS and saliva specimens, and two RDTs were conducted on ANS and one RDT on saliva. Antigen concentration correlated well with viral load when measured in the same specimen type but not across specimen types. Antigen levels were higher in symptomatic cases compared to asymptomatic/oligosymptomatic cases and lower in saliva compared to NPS and ANS samples. Discordant results between the RDTs conducted on ANS and the RT-PCR on NPS were resolved by antigen concentration values. The analytical limit-of-detection of RDTs can be used to predict the performance of the tests in populations for which the antigen concentration is known. The antigen dynamics across different sample types observed in SARS-CoV-2 disease progression support use of RDTs with nasal samples. Given lower antigen concentrations in saliva, rapid testing using saliva is expected to require improved RDT analytical sensitivity to achieve clinical sensitivity similar to rapid testing of nasal samples.
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Affiliation(s)
- Allison Golden
- Diagnostics, PATH, Seattle, Washington, United States of America
| | | | - Hannah Slater
- Diagnostics, PATH, Seattle, Washington, United States of America
| | | | - Pooja Bansil
- Diagnostics, PATH, Seattle, Washington, United States of America
| | | | - Brandon T Leader
- Diagnostics, PATH, Seattle, Washington, United States of America
| | | | | | | | | | - Eduardo Garbin
- Centro de Pesquisa em Medicina Tropical (CEPEM), Porto Velho, Rondônia, Brazil
| | - Greg T Bizilj
- Diagnostics, PATH, Seattle, Washington, United States of America
| | - Sean J Carlson
- Diagnostics, PATH, Seattle, Washington, United States of America
| | | | - Sampa Pal
- Diagnostics, PATH, Seattle, Washington, United States of America
| | - Vin Gupta
- Amazon.com, Seattle, Washington, United States of America
| | - Leo Wolansky
- Pandemic Prevention Institute, The Rockefeller Foundation, New York City, New York, United States of America
| | - David S Boyle
- Diagnostics, PATH, Seattle, Washington, United States of America
| | | | - Felipe Gomes Naveca
- Instituto Leônidas e Maria Deane (ILMD), Fundação Oswaldo Cruz (FIOCRUZ), Manaus, Amazonas, Brazil
| | | | | | - Paul K Drain
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | | | - Dhélio Pereira
- Centro de Pesquisa em Medicina Tropical (CEPEM), Porto Velho, Rondônia, Brazil
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Sgorlon G, Roca TP, Passos-Silva AM, Custódio MGF, Queiroz JADS, da Silva ALF, Teixeira KS, Batista FS, Salcedo JMV, Rampazzo RDCP, Naveca FG, Vieira D. SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia. Bioinform Biol Insights 2023; 17:11779322231186477. [PMID: 37461740 PMCID: PMC10350575 DOI: 10.1177/11779322231186477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/18/2023] [Indexed: 07/20/2023] Open
Abstract
The increased transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated variants of concern (VOCs) throughout the pandemic, responsible for waves of cases worldwide. To monitor mutations in the S gene of SARS-CoV-2 in different variants, we evaluated 1497 individuals with COVID-19 in western Amazonia in the period April 2021 to July 2022. The epidemiological and clinical data of the individuals were collected; subsequently, the samples were extracted using a commercial kit, the viral load was assessed, and viral genomes were sequenced. We analyzed the quality and mutations of the genomes and maximum likelihood phylogenetic inference. However, 3 main clusters were observed, referring to Gamma (52.91%), Delta (24.38%), and Omicron (20.38%) VOCs with wide distribution in all health regions of the Rondônia state. Regarding the vaccination profile, there was a higher percentage of unvaccinated and partially vaccinated individuals, with more representatives by the Gamma variant. A total of 1412 sequences were suitable for mutation analysis in the S gene region. The Omicron VOC showed 38 mutations, with the Delta and Gamma variants with 16 and 17, respectively. The VOC Omicron and Gamma shared 4 mutations E484K, H655Y, N501Y, and N679K with high frequency, and Delta and Omicron 2 mutations (T478K and T95I). Regarding the comparison between the frequency of mutations for each variant concerning the vaccination groups, there were no changes in mutations for each group. In conclusion, the study showed a temporal increase in mutations and subvariants for characterized strains. Furthermore, the vaccination profile did not impact significant changes in the mutational profile yet remains a determining factor for severe disease.
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Affiliation(s)
- Gabriella Sgorlon
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | - Tárcio Peixoto Roca
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz (IOC), FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Maisa Passos-Silva
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | | | - Jackson Alves da Silva Queiroz
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | - André Luiz Ferreira da Silva
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | - Karolaine Santos Teixeira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | | | - Juan Miguel Villalobos Salcedo
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | | | - Felipe Gomes Naveca
- Laboratório de Virologia do Instituto Leônidas e Maria Deane, FIOCRUZ/AM, Manaus, Brazil
| | - Deusilene Vieira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
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Jimenez-Silva C, Rivero R, Douglas J, Bouckaert R, Villabona-Arenas CJ, Atkins KE, Gastelbondo B, Calderon A, Guzman C, Echeverri-De la Hoz D, Muñoz M, Ballesteros N, Castañeda S, Patiño LH, Ramirez A, Luna N, Paniz-Mondolfi A, Serrano-Coll H, Ramirez JD, Mattar S, Drummond AJ. Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia. COMMUNICATIONS MEDICINE 2023; 3:97. [PMID: 37443390 DOI: 10.1038/s43856-023-00328-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere. METHODS To better understand the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia. We performed Bayesian phylodynamic analyses to estimate the time of variants' introduction, their respective effective reproductive number, and effective population size, and the impact of disease control measures. RESULTS Here, we detect a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the pandemic's start. We show that the effective reproduction number oscillated drastically throughout the first two years of the pandemic, with Mu showing the highest transmissibility (Re and growth rate estimation). CONCLUSIONS Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions toward the emergence and circulation of novel SARS-CoV-2 variants.
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Affiliation(s)
- Cinthy Jimenez-Silva
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Ricardo Rivero
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia.
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA.
| | - Jordan Douglas
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- Department of Physics, University of Auckland, Auckland, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Ch Julian Villabona-Arenas
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Katherine E Atkins
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Bertha Gastelbondo
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia
- Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba-GIMBIC, Universidad de Córdoba, Monteria, Colombia
- Grupo de Salud Pública y Auditoría en Salud, Corporación Universitaria del Caribe- CECAR, Sincelejo, Colombia
| | - Alfonso Calderon
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia
| | - Camilo Guzman
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia
- Grupo de Investigación, Evaluación y Desarrollo de Farmacos y Afines - IDEFARMA, Universidad de Córdoba, Montería, Colombia
| | - Daniel Echeverri-De la Hoz
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz H Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Angie Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Alberto Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Hector Serrano-Coll
- Instituto Colombiano de Medicina Tropical-Universidad CES, Medellín, Colombia
| | - Juan David Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA.
| | - Salim Mattar
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia.
| | - Alexei J Drummond
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- School of Computer Science, University of Auckland, Auckland, New Zealand
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Pinho CT, Vidal AF, Negri Rocha TC, Oliveira RRM, da Costa Barros MC, Closset L, Azevedo-Pinheiro J, Braga-da-Silva C, Silva CS, Magalhães LL, do Carmo Pinto PD, Souza GBS, dos Santos Vieira JR, Burbano RMR, de Sousa MS, de Souza JES, Nunes G, da Silva MB, da Costa PF, Salgado CG, Sousa RCM, Degrave WMS, Ribeiro-dos-Santos Â, Oliveira G. Transmission dynamics of SARS-CoV-2 variants in the Brazilian state of Pará. Front Public Health 2023; 11:1186463. [PMID: 37790714 PMCID: PMC10543262 DOI: 10.3389/fpubh.2023.1186463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/30/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction After three years since the beginning of the pandemic, the new coronavirus continues to raise several questions regarding its infectious process and host response. Several mutations occurred in different regions of the SARS-CoV-2 genome, such as in the spike gene, causing the emergence of variants of concern and interest (VOCs and VOIs), of which some present higher transmissibility and virulence, especially among patients with previous comorbidities. It is essential to understand its spread dynamics to prevent and control new biological threats that may occur in the future. In this population_based retrospective observational study, we generated data and used public databases to understand SARS-CoV-2 dynamics. Methods We sequenced 1,003 SARS-CoV-2 genomes from naso-oropharyngeal swabs and saliva samples from Pará from May 2020 to October 2022. To gather epidemiological data from Brazil and the world, we used FIOCRUZ and GISAID databases. Results Regarding our samples, 496 (49.45%) were derived from female participants and 507 (50.55%) from male participants, and the average age was 43 years old. The Gamma variant presented the highest number of cases, with 290 (28.91%) cases, followed by delta with 53 (5.28%). Moreover, we found seven (0.69%) Omicron cases and 651 (64.9%) non-VOC cases. A significant association was observed between sex and the clinical condition (female, p = 8.65e-08; male, p = 0.008961) and age (p = 3.6e-10). Discussion Although gamma had been officially identified only in December 2020/January 2021, we identified a gamma case from Belém (capital of Pará State) dated May 2020 and three other cases in October 2020. This indicates that this variant was circulating in the North region of Brazil several months before its formal identification and that Gamma demonstrated its actual transmission capacity only at the end of 2020. Furthermore, the public data analysis showed that SARS-CoV-2 dispersion dynamics differed in Brazil as Gamma played an important role here, while most other countries reported a new infection caused by the Delta variant. The genetic and epidemiological information of this study reinforces the relevance of having a robust genomic surveillance service that allows better management of the pandemic and that provides efficient solutions to possible new disease-causing agents.
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Affiliation(s)
- Catarina T. Pinho
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | | | - Maria Clara da Costa Barros
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Laura Closset
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Jhully Azevedo-Pinheiro
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cíntia Braga-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Caio Santos Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Leandro L. Magalhães
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Pablo Diego do Carmo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Giordano Bruno Soares Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - José Ricardo dos Santos Vieira
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | - Jorge Estefano Santana de Souza
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Bioinformatics Núcleo Multidisciplinar de Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Moises Batista da Silva
- Laboratório de Dermatologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, Pará, Brazil
| | - Patrícia Fagundes da Costa
- Laboratório de Dermatologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, Pará, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermatologia e Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, Pará, Brazil
| | | | - Wim Maurits Sylvain Degrave
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
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Solanky D, McGovern OL, Edwards JR, Mahon G, Patel TS, Lessa FC, Hicks LA, Patel PK. Prescribing of Outpatient Antibiotics Commonly Used for Respiratory Infections Among Adults Before and During the Coronavirus Disease 2019 Pandemic in Brazil. Clin Infect Dis 2023; 77:S12-S19. [PMID: 37406052 DOI: 10.1093/cid/ciad183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic may have impacted outpatient antibiotic prescribing in low- and middle-income countries such as Brazil. However, outpatient antibiotic prescribing in Brazil, particularly at the prescription level, is not well-described. METHODS We used the IQVIA MIDAS database to characterize changes in prescribing rates of antibiotics commonly prescribed for respiratory infections (azithromycin, amoxicillin-clavulanate, levofloxacin/moxifloxacin, cephalexin, and ceftriaxone) among adults in Brazil overall and stratified by age and sex, comparing prepandemic (January 2019-March 2020) and pandemic periods (April 2020-December 2021) using uni- and multivariate Poisson regression models. The most common prescribing provider specialties for these antibiotics were also identified. RESULTS In the pandemic period compared to the prepandemic period, outpatient azithromycin prescribing rates increased across all age-sex groups (incidence rate ratio [IRR] range, 1.474-3.619), with the greatest increase observed in males aged 65-74 years; meanwhile, prescribing rates for amoxicillin-clavulanate and respiratory fluoroquinolones mostly decreased, and changes in cephalosporin prescribing rates varied across age-sex groups (IRR range, 0.134-1.910). For all antibiotics, the interaction of age and sex with the pandemic in multivariable models was an independent predictor of prescribing changes comparing the pandemic versus prepandemic periods. General practitioners and gynecologists accounted for the majority of increases in azithromycin and ceftriaxone prescribing during the pandemic period. CONCLUSIONS Substantial increases in outpatient prescribing rates for azithromycin and ceftriaxone were observed in Brazil during the pandemic with prescribing rates being disproportionally different by age and sex. General practitioners and gynecologists were the most common prescribers of azithromycin and ceftriaxone during the pandemic, identifying them as potential specialties for antimicrobial stewardship interventions.
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Affiliation(s)
- Dipesh Solanky
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Olivia L McGovern
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonathan R Edwards
- Surveillance Branch, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Garrett Mahon
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- CACI International Inc., Reston, Virginia, USA
| | - Twisha S Patel
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Chenega Enterprise Systems and Solutions, Chesapeake, Virginia, USA
| | - Fernanda C Lessa
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauri A Hicks
- Prevention and Response Branch, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Payal K Patel
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Division of Clinical Epidemiology and Infectious Diseases, Intermountain Healthcare, Salt Lake City, Utah, USA
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de Souza Araújo AA, Quintans-Júnior LJ, Heimfarth L, Schimieguel DM, Corrêa CB, de Moura TR, Cavalcante RCM, Grespan R, de Souza Siqueira Quintans J, dos Santos DM, da Silva DN, de Oliveira YLM, de Franca MNF, da Conceição Silva M, de Sá DLF, de Carvalho FO, de Souza MF, de Oliveira Góes MA, Santos VS, Martins-Filho PR. Dynamics of SARS-CoV-2 seroprevalence during the first year of the COVID-19 pandemic in the Northeast region of Brazil. Pathog Glob Health 2023; 117:505-512. [PMID: 36094065 PMCID: PMC10262788 DOI: 10.1080/20477724.2022.2121366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
In this household-based seroepidemiological survey, we analyzed the dynamics of SARS-CoV-2 seroprevalence during the first year of the COVID-19 pandemic in Sergipe State, Northeast Brazil, the poorest region of the country. A total of 16,547 individuals were tested using a rapid IgM-IgG antibody test and fluorescence immunoassay (FIA). Seroprevalence rates were presented according to age, sex, and geographic region. A comparative analysis was performed between the results obtained in July 2020 (peak of the first wave), August - November 2020 (end of the first wave), and February - March 2021 (beginning of the second wave). Seroprevalence rates in the three phases were estimated at 9.3% (95% CI 8.5-10.1), 12.0% (95% CI 11.2-12.9) and 15.4% (95% CI 14.5-16.4). At the end of the first wave, there was a rise in seroprevalence in the countryside (p < 0.001). At the beginning of the second wave, we found an increase in seroprevalence among women (p < 0.001), adults aged 20 to 59 years (p < 0.001), and the elderly (p < 0.001). In this phase, we found an increase in estimates both in metropolitan areas and in the countryside (p < 0.001). This study showed an increase in SARS-CoV-2 seroprevalence over the first year of the pandemic, with approximately one in six people having anti-SARS-CoV-2 antibodies at the beginning of the second wave of COVID-19. Furthermore, our results suggest a rapid spread of COVID-19 from metropolitan areas to the countryside during the first months of the pandemic.
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Affiliation(s)
- Adriano Antunes de Souza Araújo
- Department of Pharmacy, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Graduate Program in Pharmaceutical Sciences, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | - Lucindo José Quintans-Júnior
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Graduate Program in Pharmaceutical Sciences, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Department of Physiology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | - Luana Heimfarth
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
| | - Dulce Marta Schimieguel
- Department of Pharmacy, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Graduate Program in Pharmaceutical Sciences, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | - Cristiane Bani Corrêa
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Department of Morphology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | - Tatiana Rodrigues de Moura
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Department of Morphology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | | | - Renata Grespan
- Department of Physiology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Graduate Program in Physiological Sciences, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | - Jullyana de Souza Siqueira Quintans
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Department of Physiology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | | | - Danilo Nobre da Silva
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
| | | | | | | | - Darla Lorena Freitas de Sá
- Graduate Program in Pharmaceutical Sciences, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
| | | | | | - Marco Aurélio de Oliveira Góes
- Government of Sergipe State, State Health Department, Aracaju, Sergipe, Brazil
- Department of Medicine, Federal University of Sergipe, Lagarto, Sergipe, Brazil
| | - Victor Santana Santos
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Department of Medicine, Federal University of Sergipe, Lagarto, Sergipe, Brazil
| | - Paulo Ricardo Martins-Filho
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Sergipe, Brazil
- Investigative Pathology Laboratory, Federal University of Sergipe, Aracaju, Sergipe, Brazil
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Orf GS, Pérez LJ, Ciuoderis K, Cardona A, Villegas S, Hernández-Ortiz JP, Baele G, Mohaimani A, Osorio JE, Berg MG, Cloherty GA. The Principles of SARS-CoV-2 Intervariant Competition Are Exemplified in the Pre-Omicron Era of the Colombian Epidemic. Microbiol Spectr 2023; 11:e0534622. [PMID: 37191534 PMCID: PMC10269686 DOI: 10.1128/spectrum.05346-22] [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: 12/28/2022] [Accepted: 04/25/2023] [Indexed: 05/17/2023] Open
Abstract
The first 18 months of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Colombia were characterized by three epidemic waves. During the third wave, from March through August 2021, intervariant competition resulted in Mu replacing Alpha and Gamma. We employed Bayesian phylodynamic inference and epidemiological modeling to characterize the variants in the country during this period of competition. Phylogeographic analysis indicated that Mu did not emerge in Colombia but acquired increased fitness there through local transmission and diversification, contributing to its export to North America and Europe. Despite not having the highest transmissibility, Mu's genetic composition and ability to evade preexisting immunity facilitated its domination of the Colombian epidemic landscape. Our results support previous modeling studies demonstrating that both intrinsic factors (transmissibility and genetic diversity) and extrinsic factors (time of introduction and acquired immunity) influence the outcome of intervariant competition. This analysis will help set practical expectations about the inevitable emergences of new variants and their trajectories. IMPORTANCE Before the appearance of the Omicron variant in late 2021, numerous SARS-CoV-2 variants emerged, were established, and declined, often with different outcomes in different geographic areas. In this study, we considered the trajectory of the Mu variant, which only successfully dominated the epidemic landscape of a single country: Colombia. We demonstrate that Mu competed successfully there due to its early and opportune introduction time in late 2020, combined with its ability to evade immunity granted by prior infection or the first generation of vaccines. Mu likely did not effectively spread outside of Colombia because other immune-evading variants, such as Delta, had arrived in those locales and established themselves first. On the other hand, Mu's early spread within Colombia may have prevented the successful establishment of Delta there. Our analysis highlights the geographic heterogeneity of early SARS-CoV-2 variant spread and helps to reframe the expectations for the competition behaviors of future variants.
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Affiliation(s)
- Gregory S. Orf
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Lester J. Pérez
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Karl Ciuoderis
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Andrés Cardona
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Simón Villegas
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Juan P. Hernández-Ortiz
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Evolutionary Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Aurash Mohaimani
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Jorge E. Osorio
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
- UW-GHI One Health Colombia, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Michael G. Berg
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Gavin A. Cloherty
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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Pandit R, Matthews QL. A SARS-CoV-2: Companion Animal Transmission and Variants Classification. Pathogens 2023; 12:775. [PMID: 37375465 DOI: 10.3390/pathogens12060775] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The continuous emergence of novel viruses and their diseases are a threat to global public health as there have been three outbreaks of coronaviruses that are highly pathogenic to humans in the span of the last two decades, severe acute respiratory syndrome (SARS)-CoV in 2002, Middle East respiratory syndrome (MERS)-CoV in 2012, and novel SARS-CoV-2 which emerged in 2019. The unprecedented spread of SARS-CoV-2 worldwide has given rise to multiple SARS-CoV-2 variants that have either altered transmissibility, infectivity, or immune escaping ability, causing diseases in a broad range of animals including human and non-human hosts such as companion, farm, zoo, or wild animals. In this review, we have discussed the recent SARS-CoV-2 outbreak, potential animal reservoirs, and natural infections in companion and farm animals, with a particular focus on SARS-CoV-2 variants. The expeditious development of COVID-19 vaccines and the advancements in antiviral therapeutics have contained the COVID-19 pandemic to some extent; however, extensive research and surveillance concerning viral epidemiology, animal transmission, variants, or seroprevalence in diverse hosts are essential for the future eradication of COVID-19.
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Affiliation(s)
- Rachana Pandit
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Qiana L Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
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41
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Ribeiro IP, Nascimento LGD, Tort LFL, Pereira EC, Menezes LSR, Malta FC, Oliveira BCEPDD, Rodrigues JP, Manso PPDA, Pelajo M, Bonaldo MC, Silva PCR, Siqueira MM, Brasil P, Fumian TM. Infectious SARS-CoV-2 Particles from Rectal Swab Samples from COVID-19 Patients in Brazil. Viruses 2023; 15:v15051152. [PMID: 37243238 DOI: 10.3390/v15051152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The main objective of this study was to investigate the dynamic of SARS-CoV-2 viral excretion in rectal swab (RS), saliva, and nasopharyngeal swab (NS) samples from symptomatic patients and asymptomatic contacts. In addition, in order to evaluate the replication potential of SARS-CoV-2 in the gastrointestinal (GI) tract and the excretion of infectious SARS-CoV-2 from feces, we investigated the presence of subgenomic nucleoprotein gene (N) mRNA (sgN) in RS samples and cytopathic effects in Vero cell culture. A prospective cohort study was performed to collect samples from symptomatic patients and contacts in Rio de Janeiro, Brazil, from May to October 2020. One hundred and seventy-six patients had samples collected at home visits and/or during the follow up, resulting in a total of 1633 RS, saliva, or NS samples. SARS-CoV-2 RNA was detected in 130 (73.9%) patients who had at least one sample that tested positive for SARS-CoV-2. The presence of replicating SARS-CoV-2 in RS samples, measured by the detection of sgN mRNA, was successfully achieved in 19.4% (6/31) of samples, whilst infectious SARS-CoV-2, measured by the generation of cytopathic effects in cell culture, was identified in only one RS sample. Although rare, our results demonstrated the replication capacity of SARS-CoV-2 in the GI tract, and infectious viruses in one RS sample. There is still a gap in the knowledge regarding SARS-CoV-2 fecal-oral transmission. Additional studies are warranted to investigate fecal or wastewater exposure as a risk factor for transmission in human populations.
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Affiliation(s)
- Ieda Pereira Ribeiro
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Lilian Gonçalves do Nascimento
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Luis Fernando Lopez Tort
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
- Laboratório de Virologia Molecular, Universidad de la República, Centro Universitario Regional Litoral Norte, Salto 50000, Uruguay
| | - Elisa Cavalcante Pereira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Lidiane Souza Raphael Menezes
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Fabio Correia Malta
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | | | - João Paulo Rodrigues
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Pedro Paulo de Abreu Manso
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Marcelo Pelajo
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Myrna Cristina Bonaldo
- Laboratório de Medicina Experimental e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Paola Cristina Resende Silva
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Patricia Brasil
- Laboratório de Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
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42
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Naveca FG, Nascimento VA, Nascimento F, Ogrzewalska M, Pauvolid-Corrêa A, Araújo MF, Arantes I, Batista ÉR, Magalhães AÁ, Vinhal F, Mattos TP, Riediger I, Debur MDC, Grinsztejn B, Veloso VG, Brasil P, Rodrigues RR, Rovaris DB, Fernandes SB, Fernandes C, Santos JHA, Abdalla LF, Costa-Filho R, Silva M, Souza V, Costa ÁA, Mejía M, Brandão MJ, Gonçalves LF, Silva GA, de Jesus MS, Pessoa K, Corado ADLG, Duarte DCG, Machado AB, Zukeram KDA, Valente N, Lopes RS, Pereira EC, Appolinario LR, Rocha AS, Tort LFL, Sekizuka T, Itokawa K, Hashino M, Kuroda M, Dezordi FZ, Wallau GL, Delatorre E, Gräf T, Siqueira MM, Bello G, Resende PC. SARS-CoV-2 intra-host diversity, antibody response, and disease severity after reinfection by the variant of concern Gamma in Brazil. Sci Rep 2023; 13:7306. [PMID: 37147348 PMCID: PMC10160723 DOI: 10.1038/s41598-023-33443-1] [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: 07/01/2022] [Accepted: 04/12/2023] [Indexed: 05/07/2023] Open
Abstract
The rapid spread of the SARS-CoV-2 Variant of Concern (VOC) Gamma in Amazonas during early 2021 fueled a second large COVID-19 epidemic wave and raised concern about the potential role of reinfections. Very few cases of reinfection associated with the VOC Gamma have been reported to date, and their potential impact on clinical, immunological, and virological parameters remains largely unexplored. Here we describe 25 cases of SARS-CoV-2 reinfection in Brazil. SARS-CoV-2 genomic analysis confirmed that individuals were primo-infected with distinct viral lineages between March and December 2020 (B.1.1, B.1.1.28, B.1.1.33, B.1.195, and P.2) and reinfected with the VOC Gamma between 3 to 12 months after primo-infection. We found a similar mean cycle threshold (Ct) value and limited intra-host viral diversity in both primo-infection and reinfection samples. Sera of 14 patients tested 10-75 days after reinfection displayed detectable neutralizing antibodies (NAb) titers against SARS-CoV-2 variants that circulated before (B.1.*), during (Gamma), and after (Delta and Omicron) the second epidemic wave in Brazil. All individuals had milder or no symptoms after reinfection, and none required hospitalization. These findings demonstrate that individuals reinfected with the VOC Gamma may display relatively high RNA viral loads at the upper respiratory tract after reinfection, thus contributing to onward viral transmissions. Despite this, our study points to a low overall risk of severe Gamma reinfections, supporting that the abrupt increase in hospital admissions and deaths observed in Amazonas and other Brazilian states during the Gamma wave was mostly driven by primary infections. Our findings also indicate that most individuals analyzed developed a high anti-SARS-CoV-2 NAb response after reinfection that may provide some protection against reinfection or disease by different SARS-CoV-2 variants.
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Affiliation(s)
- Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil.
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Valdinete Alves Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Maria Ogrzewalska
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Alex Pauvolid-Corrêa
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Mia Ferreira Araújo
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Ighor Arantes
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | | | - Tirza Peixoto Mattos
- Laboratório Central de Saúde Pública do Amazonas (LACEN-AM, Manaus, Amazonas, Brazil
| | - Irina Riediger
- Laboratório Central de Saúde Pública do Paraná (LACEN-PR) Curitiba, Paraná, Brazil
| | - Maria do Carmo Debur
- Laboratório Central de Saúde Pública do Paraná (LACEN-PR) Curitiba, Paraná, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas (INI), Fiocruz, Rio de Janeiro, Brazil
| | - Valdiléa G Veloso
- Instituto Nacional de Infectologia Evandro Chagas (INI), Fiocruz, Rio de Janeiro, Brazil
| | - Patrícia Brasil
- Instituto Nacional de Infectologia Evandro Chagas (INI), Fiocruz, Rio de Janeiro, Brazil
| | | | - Darcita Buerger Rovaris
- Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC), Florianópolis, Santa Catarina, Brazil
| | - Sandra Bianchini Fernandes
- Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC), Florianópolis, Santa Catarina, Brazil
| | - Cristiano Fernandes
- Fundação de Vigilância em Saúde do Amazonas-Dra Rosemary Costa Pinto, Manaus, Amazonas, Brazil
| | | | | | | | - Marineide Silva
- Laboratório Central de Saúde Pública do Amazonas (LACEN-AM, Manaus, Amazonas, Brazil
| | - Victor Souza
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Ágatha Araújo Costa
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Matilde Mejía
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Maria Júlia Brandão
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Luciana Fé Gonçalves
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- Fundação de Vigilância em Saúde do Amazonas-Dra Rosemary Costa Pinto, Manaus, Amazonas, Brazil
| | - George Allan Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Michele Silva de Jesus
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Karina Pessoa
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - André de Lima Guerra Corado
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Debora Camila Gomes Duarte
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Ana Beatriz Machado
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Ketiuce de Azevedo Zukeram
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Natalia Valente
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Renata Serrano Lopes
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Elisa Cavalcante Pereira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Luciana Reis Appolinario
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Alice Sampaio Rocha
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Luis Fernando Lopez Tort
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
- CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-Ku, Tokyo, 162-8640, Japan
| | - Kentaro Itokawa
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-Ku, Tokyo, 162-8640, Japan
| | - Masanori Hashino
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-Ku, Tokyo, 162-8640, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-Ku, Tokyo, 162-8640, Japan
| | | | - Gabriel Luz Wallau
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
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43
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Lanzarini NM, Mannarino CF, Ribeiro AVC, Prado T, Vahia LS, Siqueira MM, Resende PC, Quintaes BR, Miagostovich MP. SARS-CoV-2 surveillance-based on municipal solid waste leachate in Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:67368-67377. [PMID: 37101215 PMCID: PMC10132925 DOI: 10.1007/s11356-023-27019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Municipal solid waste leachate-based epidemiology is an alternative viral tracking tool that applies fresh truck leachate as an early warning of public health emergencies. This study aimed to investigate the potential of SARS-CoV-2 surveillance based on solid waste fresh truck leachate. Twenty truck leachate samples were ultracentrifugated, nucleic acid extracted, and real-time RT-qPCR SARS-CoV-2 N1/N2 applied. Viral isolation, variant of concern (N1/N2) inference, and whole genome sequencing were also performed. SARS-CoV-2 was detected on 40% (8/20) of samples, with a concentration from 2.89 to 6.96 RNA Log10 100 mL-1. The attempt to isolate SARS-CoV-2 and recover the whole genome was not successful; however, positive samples were characterized as possible pre-variant of concern (pre-VOC), VOC Alpha (B.1.1.7) and variant of interest Zeta (P.2). This approach revealed an alternative tool to infer SARS-CoV-2 in the environment and may help the management of local surveillance, health, and social policies.
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Affiliation(s)
- Natália Maria Lanzarini
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil.
| | - Camille Ferreira Mannarino
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - André Vinicius Costa Ribeiro
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Leonardo Saboia Vahia
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | | | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
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44
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Silva JDP, Lima ABD, Alvim LB, Malta FSV, Mendonça CPTB, Carvalho AHBD, Rios JSH, Fonseca PLC, Queiroz DC, Santos LCGDAE, Ferreira ACDS, Souza RPD, Aguiar RSD, Zauli DAG. Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil. Viruses 2023; 15:v15041017. [PMID: 37112997 PMCID: PMC10145299 DOI: 10.3390/v15041017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The introduction of SARS-CoV-2 variants of concern (VOCs) in Brazil has been associated with major impacts on the epidemiological and public health scenario. In this study, 291,571 samples were investigated for SARS-CoV-2 variants from August 2021 to March 2022 (the highest peak of positive cases) in four geographical regions of Brazil. To identify the frequency, introduction, and dispersion of SARS-CoV-2 variants in 12 Brazilian capitals, VOCs defining spike mutations were identified in 35,735 samples through genotyping and viral genome sequencing. Omicron VOC was detected in late November 2021 and replaced the Delta VOC in approximately 3.5 weeks. We estimated viral load differences between SARS-CoV-2 Delta and Omicron through the evaluation of the RT-qPCR cycle threshold (Ct) score in 77,262 samples. The analysis demonstrated that the Omicron VOC has a lower viral load in infected patients than the Delta VOC. Analyses of clinical outcomes in 17,586 patients across the country indicated that individuals infected with Omicron were less likely to need ventilatory support. The results of our study reinforce the importance of surveillance programs at the national level and showed the introduction and faster dispersion of Omicron over Delta VOC in Brazil without increasing the numbers of severe cases of COVID-19.
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Affiliation(s)
- Joice do Prado Silva
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, Brazil
| | - Aline Brito de Lima
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 31270-901, Brazil
| | - Luige Biciati Alvim
- Departamento de Produtos e Inovação, Instituto Hermes Pardini, Belo Horizonte 31270-901, Brazil
| | | | | | | | | | - Paula Luize Camargos Fonseca
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Daniel Costa Queiroz
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Luíza Campos Guerra de Araújo E Santos
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Renan Pedra de Souza
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Renato Santana de Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro 22281-100, Brazil
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45
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Arantes I, Bello G, Nascimento V, Souza V, da Silva A, Silva D, Nascimento F, Mejía M, Brandão MJ, Gonçalves L, Silva G, da Costa CF, Abdalla L, Santos JH, Ramos TCA, Piantham C, Ito K, Siqueira MM, Resende PC, Wallau GL, Delatorre E, Gräf T, Naveca FG. Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas. Nat Commun 2023; 14:2048. [PMID: 37041143 PMCID: PMC10089528 DOI: 10.1038/s41467-023-37541-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/21/2023] [Indexed: 04/13/2023] Open
Abstract
The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil's most heavily affected regions. We sequenced the virus genome from 4128 patients collected in Amazonas between July 1st, 2021, and January 31st, 2022, and investigated the viral dynamics using a phylodynamic approach. The VOCs Delta and Omicron BA.1 displayed similar patterns of phylogeographic spread but different epidemic dynamics. The replacement of Gamma by Delta was gradual and occurred without an upsurge of COVID-19 cases, while the rise of Omicron BA.1 was extremely fast and fueled a sharp increase in cases. Thus, the dissemination dynamics and population-level impact of new SARS-CoV-2 variants introduced in the Amazonian population after mid-2021, a setting with high levels of acquired immunity, greatly vary according to their viral phenotype.
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Affiliation(s)
- Ighor Arantes
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Victor Souza
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Arlesson da Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Dejanane Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Matilde Mejía
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Maria Júlia Brandão
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Luciana Gonçalves
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto, Manaus, Brazil
| | - George Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- Fundação Centro de Controle de Oncologia do Estado do Amazonas, Manaus, Brazil
| | - Cristiano Fernandes da Costa
- Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto, Manaus, Brazil
- Conselho de Secretários Municipais de Saúde do Amazonas COSEMS - AM, Manaus, Brazil
| | | | | | | | - Chayada Piantham
- Graduate School of Infectious Diseases, Hokkaido University, Hokkaido, Japan
| | - Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - 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
| | - Gabriel Luz Wallau
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil.
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
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46
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Paz M, Moreno P, Moratorio G. Perspective Chapter: Real-Time Genomic Surveillance for SARS-CoV-2 on Center Stage. Infect Dis (Lond) 2023. [DOI: 10.5772/intechopen.107842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
The course of the COVID-19 pandemic depends not only on how the SARS-CoV-2 virus mutates but on the actions taken to respond to it. Important public health decisions can only be taken if we know viral dynamics, viral variants distribution, and whether new variants are emerging that may be more transmissible or/and more virulent, displaying evasion to vaccines or antiviral treatments. This situation has put the use of different approaches, such as molecular techniques and real-time genomic sequencing, to support public health decision-making on center stage. To achieve this, robust programs based on: (i) diagnostic capacity; (ii) high-throughput sequencing technologies; and (iii) high-performance bioinformatic resources, need to be established. This chapter focuses on how SARS-CoV-2 evolved since its discovery and it summarizes the scientific efforts to obtain genomic data as the virus spread throughout the globe.
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47
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Neves JMM, Belo VS, Catita CMS, de Oliveira BFA, Horta MAP. Modeling the Climatic Suitability of COVID-19 Cases in Brazil. Trop Med Infect Dis 2023; 8:tropicalmed8040198. [PMID: 37104323 PMCID: PMC10142792 DOI: 10.3390/tropicalmed8040198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023] Open
Abstract
Studies have shown that climate may affect the distribution of coronavirus disease (COVID-19) and its incidence and fatality rates. Here, we applied an ensemble niche modeling approach to project the climatic suitability of COVID-19 cases in Brazil. We estimated the cumulative incidence, mortality rate, and fatality rate of COVID-19 between 2020 and 2021. Seven statistical algorithms (MAXENT, MARS, RF, FDA, CTA, GAM, and GLM) were selected to model the climate suitability for COVID-19 cases from diverse climate data, including temperature, precipitation, and humidity. The annual temperature range and precipitation seasonality showed a relatively high contribution to the models, partially explaining the distribution of COVID-19 cases in Brazil based on the climatic suitability of the territory. We observed a high probability of climatic suitability for high incidence in the North and South regions and a high probability of mortality and fatality rates in the Midwest and Southeast regions. Despite the social, viral, and human aspects regulating COVID-19 cases and death distribution, we suggest that climate may play an important role as a co-factor in the spread of cases. In Brazil, there are regions with a high probability that climatic suitability will contribute to the high incidence and fatality rates of COVID-19 in 2020 and 2021.
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48
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Pereira-Gómez M, Arce R, Ferla D, Simón D, Salazar C, Perbolianachis P, Costábile A, Fajardo A, Aldunate F, Nin N, Hurtado J, Iraola G, Moreno P, Moratorio G. One-year monitoring SARS-CoV-2 RNA surface contamination in hospitals reveals no correlation with organic material and negative pressure as a limiting factor for contamination. Heliyon 2023; 9:e13875. [PMID: 36845037 PMCID: PMC9938536 DOI: 10.1016/j.heliyon.2023.e13875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Understanding transmission routes of SARS-CoV-2 is crucial to establish effective interventions in healthcare institutions. Although the role of surface contamination in SARS-CoV-2 transmission has been controversial, fomites have been proposed as a contributing factor. Longitudinal studies about SARS-CoV-2 surface contamination in hospitals with different infrastructure (presence or absence of negative pressure systems) are needed to improve our understanding of their effectiveness on patient healthcare and to advance our knowledge about the viral spread. We performed a one-year longitudinal study to evaluate surface contamination with SARS-CoV-2 RNA in reference hospitals. These hospitals have to admit all COVID-19 patients from public health services that require hospitalization. Surfaces samples were molecular tested for SARS-CoV-2 RNA presence considering three factors: the dirtiness by measuring organic material, the circulation of a high transmissibility variant, and the presence or absence of negative pressure systems in hospitalized patients' rooms. Our results show that: (i) There is no correlation between the amount of organic material dirtiness and SARS-CoV-2 RNA detected on surfaces; (ii) SARS-CoV-2 high transmissible Gamma variant introduction significantly increased surface contamination; (iii) the hospital with negative pressure systems was associated with lower levels of SARS-CoV-2 surface contamination and, iv) most environmental samples recovered from contaminated surfaces were assigned as non-infectious. This study provides data gathered for one year about the surface contamination with SARS-CoV-2 RNA sampling hospital settings. Our results suggest that spatial dynamics of SARS-CoV-2 RNA contamination varies according with the type of SARS-CoV-2 genetic variant and the presence of negative pressure systems. In addition, we showed that there is no correlation between the amount of organic material dirtiness and the quantity of viral RNA detected in hospital settings. Our findings suggest that SARS CoV-2 RNA surface contamination monitoring might be useful for the understanding of SARS-CoV-2 dissemination with impact on hospital management and public health policies. This is of special relevance for the Latin-American region where ICU rooms with negative pressure are insufficient.
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Affiliation(s)
- Marianoel Pereira-Gómez
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Rodrigo Arce
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Diego Ferla
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Diego Simón
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Cecilia Salazar
- Laboratorio de Genómica Microbiana, Institut Pasteur de Montevideo, Uruguay,Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur de Montevideo, Uruguay
| | - Paula Perbolianachis
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Alicia Costábile
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay,Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur de Montevideo, Uruguay,Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Alvaro Fajardo
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Fabián Aldunate
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Nicolás Nin
- Unidad de Cuidados Intensivos, Hospital Español “Juan José Crottoggini”, Administración de Servicios de Salud del Estado, Uruguay
| | - Javier Hurtado
- Unidad de Cuidados Intensivos, Hospital Español “Juan José Crottoggini”, Administración de Servicios de Salud del Estado, Uruguay
| | - Gregorio Iraola
- Laboratorio de Genómica Microbiana, Institut Pasteur de Montevideo, Uruguay,Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur de Montevideo, Uruguay
| | - Pilar Moreno
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay,Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur de Montevideo, Uruguay,Corresponding author.Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay
| | - Gonzalo Moratorio
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay,Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Uruguay,Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur de Montevideo, Uruguay,Corresponding author.Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Uruguay
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49
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Rep Med 2023; 4:100943. [PMID: 36791724 PMCID: PMC9906997 DOI: 10.1016/j.xcrm.2023.100943] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, CT, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott C Roberts
- Infectious Disease, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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50
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Badin RC, de Amorim RLO, Aguila A, Manaças LRA. Clinical and pharmacological factors associated with mortality in patients with COVID-19 in a high complexity hospital in Manaus: A retrospective study. PLoS One 2023; 18:e0280891. [PMID: 36763604 PMCID: PMC9916623 DOI: 10.1371/journal.pone.0280891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/10/2023] [Indexed: 02/11/2023] Open
Abstract
COVID-19 is a contagious infection caused by the SARS-CoV-2 virus, responsible for more than 5 million deaths worldwide, and has been a significant challenge for healthcare systems worldwide. Characterized by multiple manifestations, the most common symptoms are fever, cough, anosmia, ageusia, and myalgia. However, several organs can be affected in more severe cases, causing encephalitis, myocarditis, respiratory distress, hypercoagulable state, pulmonary embolism, and stroke. Despite efforts to identify appropriate clinical protocols for its management, there are still no fully effective therapies to prevent patient death. The objective of this study was to describe the demographic, clinical, and pharmacotherapeutic management characteristics employed in patients hospitalized for diagnosis of COVID-19, in addition to identifying predictive factors for mortality. This is a single-center, retrospective cohort study carried out in a reference hospital belonging to the Brazilian public health system, in Manaus, from March 2020 to July 2021. Data were obtained from analyzing medical records, physical and electronic forms, medical prescriptions, and antimicrobial use authorization forms. During the study period, 530 patients were included, 51.70% male, with a mean age of 58.74 ± 15.91 years. The overall mortality rate was 23.58%. The variables age, number of comorbidities, admission to the ICU, length of stay, oxygen saturation, serum aspartate transaminase, and use of mechanical ventilation showed a positive correlation with the mortality rate. Regarding pharmacological management, 88.49% of patients used corticosteroids, 86.79% used antimicrobials, 94.15% used anticoagulant therapy, and 3.77% used immunotherapy. Interestingly, two specific classes of antibiotics showed a positive correlation with the mortality rate: penicillins and glycopeptides. After multivariate logistic regression analysis, age, number of comorbidities, need for mechanical ventilation, length of hospital stay, and penicillin or glycopeptide antibiotics use were associated with mortality (AUC = 0.958).
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Affiliation(s)
- Rebeka Caribé Badin
- Department of Neurosurgery, Getúlio Vargas University Hospital, Manaus, Amazonas, Brazil
- * E-mail:
| | | | - Alian Aguila
- Department of Cardiology, Memorial Hospital System, Hollywood, Florida, United States of America
| | - Liliane Rosa Alves Manaças
- Department of Pharmacology, Brazilian National Cancer Institute José Alencar Gomes da Silva (INCA)/ Hospital II, Rio de Janeiro, Rio de Janeiro, Brazil
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