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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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Rey LMR, Delai RM, Batista ACCA, Ferreira L, Santos ICD, Del Vecchio MAC, Andrade ACS, Teles P, Pereira UDP, Gerber AL, Guimarães APDC, Almeida LGPD, Lamarca AP, Vasconcelos ATRD, Gonçalves DD. SARS-CoV-2 Research in Dogs ( Canis lupus familiaris) and Felines ( Felis silvestris catus) Domiciled in an International Border Region (Paraguay and Brazil). Vector Borne Zoonotic Dis 2024. [PMID: 38829161 DOI: 10.1089/vbz.2023.0154] [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: 06/05/2024] Open
Abstract
Introduction: COVID-19 is an infectious disease caused by SARS-CoV-2 that has become a serious threat to public health owing to its rapid spread from aerosols from infected people. Despite being considered a strictly human disease, there are reports in the literature about animals with confirmed presence of the virus. Aim: Owing to the scarcity of scientific literature on the potential for infection of animals and their importance for One Health, the objective of this work was to research SARS-CoV-2 RNA in felines (Felis silvestris catus) and dogs (Canis lupus familiaris) domiciled. Materials and Methods: Oropharyngeal swabs were collected from domestic dogs and cats belonging to patients diagnosed with COVID-19 from August to October 2021 and residents of the northwest and west regions of Paraná, Brazil. Results: Of the 34 samples collected, 14 were from dogs and 20 from cats. Three of these samples tested positive in real-time PCR, and two of them were also positive in the immunochromatographic test. After testing positive in real-time PCR, the samples underwent genetic sequencing using the Illumina COVIDSeq test. Of the 34 samples collected, three (9%), all of them female and from the feline species, tested positive in real-time PCR, with two of these (67%) also testing positive in the immunochromatographic test. Regarding sequencing, it was possible to sequence the three samples aligned with the AY.101 lineage, corresponding to the Delta variant. Conclusion: The occurrence of SARS-CoV-2 infection in dogs and cats is seen as an unintended event with significant implications for public health, including its potential transmission to other animal species. Further research is required to enhance our understanding of how this disease spreads among these animals and its broader impact on One Health initiatives.
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Affiliation(s)
- Laisa Marina Rosa Rey
- Pós-Graduandos do Programa de Pós-Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense (UNIPAR), Umuarama, Brasil
| | - Robson Michael Delai
- Pós-Graduandos do Programa de Pós-Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense (UNIPAR), Umuarama, Brasil
- Centro de Medicina Tropical da Fundação de Saúde Itaiguapy, Foz do Iguaçu, Brasil
| | - Aline Cristiane Cechinel Assing Batista
- Pós-Graduandos do Programa de Pós-Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense (UNIPAR), Umuarama, Brasil
- Centro de Medicina Tropical da Fundação de Saúde Itaiguapy, Foz do Iguaçu, Brasil
| | - Leonardo Ferreira
- Centro de Medicina Tropical da Fundação de Saúde Itaiguapy, Foz do Iguaçu, Brasil
| | - Isabela Carvalho Dos Santos
- Pós-Graduandos do Programa de Pós-Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense (UNIPAR), Umuarama, Brasil
| | - Marco Aurélio Cunha Del Vecchio
- Pós-Graduandos do Programa de Pós-Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense (UNIPAR), Umuarama, Brasil
| | - Ana Cláudia Souza Andrade
- Pós-Graduandos do Programa de Pós-Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense (UNIPAR), Umuarama, Brasil
| | - Pedro Teles
- Médico Veterinário autônomo, Self-employed veterinarian, Cascavel, Paraná, Brasil
| | - Ulisses de Pádua Pereira
- Docente do Programa de Pós-Graduação em Ciência Animal, Universidade Estadual de Londrina (UEL), Londrina, Brasil
| | | | | | | | - Alessandra Pavan Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brasil
| | | | - Daniela Dib Gonçalves
- Docente do Programa de Pós-Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense (UNIPAR), Umuarama, Brasil
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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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Ferrareze PAG, Cybis GB, de Oliveira LFV, Zimerman RA, Schiavon DEB, Peter C, Thompson CE. Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study. Microbes Infect 2024; 26:105216. [PMID: 37827275 DOI: 10.1016/j.micinf.2023.105216] [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: 07/04/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 10/14/2023]
Abstract
The analyses of genetic traits, dispersion patterns and phylogenomics are essential for understanding the evolutionary forces driving SARS-CoV-2 viruses in these three years of COVID-19 pandemics. Brazil is one of the most affected countries in the world and not sufficient genomic studies have been performed. The emergence of P.1 lineage led to one of the most serious public health crises on record. Our study presents the genomic sequencing and characterization of 412 samples from Rio Grande do Sul state, in the Brazilian Southern region, during Gamma and Delta epidemic waves, in 2021. Additionally, molecular evolution tests were performed to identify positively selected sites in Brazil between 2020 and 2022, as well as offer some evolutionary perspective about the maintenance of multiple spike mutations in Omicron lineages. Genomic epidemiology analysis has indicated an intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil.
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Affiliation(s)
- Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Gabriela Betella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | - Dieine Estela Bernieri Schiavon
- Undergraduate Program in Biomedical Informatics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Claudia Elizabeth Thompson
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
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5
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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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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: 4] [Impact Index Per Article: 4.0] [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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7
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Lamarca AP, Souza UJBD, Moreira FRR, Almeida LGPD, Menezes MTD, Souza ABD, Ferreira ACDS, Gerber AL, Lima ABD, Guimarães APDC, Cavalcanti AC, Silva ABPE, Lima BI, Lobato C, Silva CGD, Mendonça CPTB, Queiroz DC, Zauli DAG, Menezes D, Possebon FS, Cardoso FDP, Malta FSV, Braga-Paz I, Silva JDP, Ferreira JGG, Galvão JD, Souza LMD, Ferreira L, Possuelo LG, Cavalcante LTDF, Alvim LB, Souza LFAD, Santos LCGDAE, Dias RC, Souza RB, Castro TRY, Valim ARDM, Campos FS, Araujo JP, Trindade PDA, Aguiar RS, Michael Delai R, Vasconcelos ATRD. The Omicron Lineages BA.1 and BA.2 ( Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub. Viruses 2023; 15:888. [PMID: 37112869 PMCID: PMC10146814 DOI: 10.3390/v15040888] [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: 02/13/2023] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.
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Affiliation(s)
- Alessandra P Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-075, Brazil
| | - Ueric José Borges de Souza
- Laboratório de Bioinformática e Biotecnologia, Universidade Federal do Tocantins, Campus de Gurupi, Palmas 77410-570, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Luiz G P de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-075, Brazil
| | - Mariane Talon de Menezes
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | | | - Alexandra L Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-075, Brazil
| | - Aline B de Lima
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 30140-070, Brazil
| | - Ana Paula de C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-075, Brazil
| | | | - Aryel B Paz E Silva
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Bruna Israel Lima
- Laboratório de Biologia Molecular, Parque Científico e Tecnológico Regional, Universidade de Santa Cruz do Sul, Santa Cruz do Sul 96815-900, Brazil
| | - Cirley Lobato
- Centro de Ciências de Saúde e do Desporto, Universidade Federal do Acre, Rio Branco 69920-900, Brazil
| | | | - Cristiane P T B Mendonça
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 30140-070, Brazil
| | - Daniel Costa Queiroz
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Diego Menezes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Fábio Sossai Possebon
- Instituto de Biotecnologia, Universidade Estadual Paulista, Botucatu 18618-689, Brazil
| | | | | | - Isabela Braga-Paz
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Joice do Prado Silva
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 30140-070, Brazil
| | - Jorge Gomes Goulart Ferreira
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | | | - Leonardo Ferreira
- Centro de Medicina Tropical da Tríplice Fronteira, Foz do Iguaçu 85866-010, Brazil
| | - Lia Gonçalves Possuelo
- Departmento de Ciências da Vida, Universidade de Santa Cruz do Sul, Santa Cruz do Sul 96815-900, Brazil
| | | | - Luige B Alvim
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 30140-070, Brazil
| | - Luiz Fellype Alves de Souza
- Centro de Infectologia Charles Mérieux and Laboratório Rodolphe Mérieux, Hospital das Clínicas do Acre, Rio Branco 69920-223, Brazil
| | - Luiza C G de Araújo E Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Rillery Calixto Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Rutilene Barbosa Souza
- Centro de Infectologia Charles Mérieux and Laboratório Rodolphe Mérieux, Hospital das Clínicas do Acre, Rio Branco 69920-223, Brazil
| | - Thaís Regina Y Castro
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | | | - Fabrício Souza Campos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, Brazil
| | - João Pessoa Araujo
- Instituto de Biotecnologia, Universidade Estadual Paulista, Botucatu 18618-689, Brazil
| | - Priscila de Arruda Trindade
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Robson Michael Delai
- Centro de Medicina Tropical da Tríplice Fronteira, Foz do Iguaçu 85866-010, Brazil
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8
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Machado TL, Santos AC, Azamor T, da Silva AMV, Pimenta VR, Tubarão LN, da Silva ADS, Flores Rodrigues DDR, Müller R, Pinto MA, Villar LM, Bom APA, Melgaço JG. CLEC5A expression can be triggered by spike glycoprotein and may be a potential target for COVID-19 therapy. J Med Virol 2023; 95:e28427. [PMID: 36571274 PMCID: PMC9880667 DOI: 10.1002/jmv.28427] [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: 09/13/2022] [Revised: 12/02/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
The immune response is crucial for coronavirus disease 19 (COVID-19) progression, with the participation of proinflammatory cells and cytokines, inducing lung injury and loss of respiratory function. CLEC5A expression on monocytes can be triggered by viral and bacterial infections, leading to poor outcomes. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is able to induce neutrophil activation by CLEC5A and Toll-like receptor 2, leading to an aggressive inflammatory cascade, but little is known about the molecular interactions between CLEC5A and SARS-CoV-2 proteins. Here, we aimed to explore how CLEC5A expression could be affected by SARS-CoV-2 infection using immunological tools with in vitro, in vivo, and in silico assays. The findings revealed that high levels of CLEC5A expression were found in monocytes from severe COVID-19 patients in comparison with mild COVID-19 and unexposed subjects, but not in vaccinated subjects who developed mild COVID-19. In hamsters, we detected CLEC5A gene expression during 3-15 days of Omicron strain viral challenge. Our results also showed that CLEC5A can interact with SARS-CoV-2, promoting inflammatory cytokine production, probably through an interaction with the receptor-binding domain in the N-acetylglucosamine binding site (NAG-601). The high expression of CLEC5A and high levels of proinflammatory cytokine production were reduced in vitro by a human CLEC5A monoclonal antibody. Finally, CLEC5A was triggered by spike glycoprotein, suggesting its involvement in COVID-19 progression; therapy with a monoclonal antibody could be a good strategy for COVID-19 treatment, but vaccines are still the best option to avoid hospitalization/deaths.
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Affiliation(s)
- Thiago L. Machado
- Instituto de Tecnologia em Imunobiológicos, Bio‐Manguinhos, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Alanna C. Santos
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Tamiris Azamor
- Instituto de Tecnologia em Imunobiológicos, Bio‐Manguinhos, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Andrea M. V. da Silva
- Instituto de Tecnologia em Imunobiológicos, Bio‐Manguinhos, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Vanessa R. Pimenta
- Instituto de Tecnologia em Imunobiológicos, Bio‐Manguinhos, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Luciana N. Tubarão
- Instituto de Tecnologia em Imunobiológicos, Bio‐Manguinhos, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Alexandre dos Santos da Silva
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | | | - Rodrigo Müller
- Instituto de Tecnologia em Imunobiológicos, Bio‐Manguinhos, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Marcelo A. Pinto
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Livia M. Villar
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Ana P. A. Bom
- Instituto de Tecnologia em Imunobiológicos, Bio‐Manguinhos, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
| | - Juliana G. Melgaço
- Instituto de Tecnologia em Imunobiológicos, Bio‐Manguinhos, Fundação Oswaldo Cruz, FiocruzRio de JaneiroBrazil
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9
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SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis. Viruses 2022; 14:v14122715. [PMID: 36560720 PMCID: PMC9784312 DOI: 10.3390/v14122715] [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: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/09/2022] Open
Abstract
Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 were included. Ninety-six different strains were reported, with variant of concern (VOC) gamma (n = 35,398), VOC delta (n = 15,780), and the variant of interest zeta (n = 1983) being the most common. The top three states with the most samples in the published articles were São Paulo, Rio de Janeiro, and Minas Gerais. Whereas the first year of the pandemic presented primary circulation of B.1.1.28 and B.1.1.33 variants, consecutive replacements were observed between them and VOI zeta, VOC gamma, VOC delta, and VOC omicron. VOI mu, VOI lambda, VOC alpha, and VOC beta were also detected but failed to reach significant circulation. Co-infection, re-infection, and vaccine breakthrough reports were found. Article co-citation differed from the co-authorship structure. Despite the limitations, we expect to give an overview of Brazil's genomic surveillance studies and contribute to future research execution.
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