Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders.

Autor: Dezordi FZ; Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife Pernambuco, 50670-420, Brazil; Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, 50670-420, Brazil., Júnior JVJS; Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, 97105-900, Brazil; Setor de Virologia, Instituto Keizo Asami, Universidade Federal de Pernambuco, Pernambuco, 50670-901, Brazil; Laboratório NB3 de Neuroimunologia, Universidade Federal de Santa Maria, Rio Grande do Sul, 97105-900, Brazil; Departamento de Microbiologia e Parasitologia, Universidade Federal de Santa Maria, Rio Grande do Sul, 97105-900, Brazil; Programa de Pós-graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, 97105-900, Brazil; Programa de Pós-graduação em Farmacologia, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil., Ruoso TF; Campus Palmeira das Missões, Universidade Federal de Santa Maria. Palmeira das Missões, Rio Grande do Sul, 98300-000, Brazil., Batista AG; Campus Palmeira das Missões, Universidade Federal de Santa Maria. Palmeira das Missões, Rio Grande do Sul, 98300-000, Brazil; Life Sciences Institute, Universidade Federal de Juiz de Fora. Governador Valadares, Minas Gerais, 35010-180, Brazil., Fonseca PM; Campus Palmeira das Missões, Universidade Federal de Santa Maria. Palmeira das Missões, Rio Grande do Sul, 98300-000, Brazil., Bernardo LP; Departamento de Ciências da Vida - DCVIDA, Universidade Regional do Noroeste do Estado do Rio Grande do Sul - UNIJUÍ, Ijuí, Rio Grande do Sul, 98700-000, Brazil., Salvato RS; Centro Estadual de Vigilância em Saúde. Secretaria Estadual da Saúde do Rio Grande do Sul. Porto Alegre, Rio Grande do Sul, 90610-000, Brazil., Gregianini TS; Centro Estadual de Vigilância em Saúde. Secretaria Estadual da Saúde do Rio Grande do Sul. Porto Alegre, Rio Grande do Sul, 90610-000, Brazil., Lopes TRR; Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, 97105-900, Brazil; Programa de Pós-graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, 97105-900, Brazil., Flores EF; Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, 97105-900, Brazil., Weiblen R; Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, 97105-900, Brazil., Brites PC; Hospital Universitário de Santa Maria (HUSM), Universidade Federal de Santa Maria (UFSM), Av. Roraima, 1000, Santa Maria, Rio Grande do Sul, 97105-900, Brazil., Silva MM; Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Av. Roraima, 1000, Santa Maria, Rio Grande do Sul, 97105-900, Brazil., da Rocha JBT; Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Av. Roraima, 1000, Santa Maria, Rio Grande do Sul, 97105-900, Brazil., Barbosa GL; Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, 50670-420, Brazil., Machado LC; Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife Pernambuco, 50670-420, Brazil., da Silva AF; Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife Pernambuco, 50670-420, Brazil; Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, 50670-420, Brazil., Paiva MHS; Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife Pernambuco, 50670-420, Brazil; Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste-Rodovia BR-104, Caruaru, Pernambuco, 55002-970, Brazil., Bezerra MF; Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, 50670-420, Brazil., Campos TL; Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, 50670-420, Brazil., Gräf T; Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil., Graichen DAS; Departamento de Zootecnia e Ciências Biológicas, Universidade Federal de Santa Maria, Palmera das Missões, Rio Grande do Sul 98300-000, Brazil., Loreto ELDS; Hospital Universitário de Santa Maria (HUSM), Universidade Federal de Santa Maria (UFSM), Av. Roraima, 1000, Santa Maria, Rio Grande do Sul, 97105-900, Brazil., Wallau GDL; Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife Pernambuco, 50670-420, Brazil; Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, 50670-420, Brazil; Department of Arbovirology and Entomology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research. National Reference Center for Tropical Infectious Diseases. Bernhard-Nocht-Straße 74 20359 Hamburg, Germany. Electronic address: gabriel.wallau@fiocruz.br.
Jazyk: angličtina
Zdroj: Virus research [Virus Res] 2024 Dec 17; Vol. 351, pp. 199500. Date of Electronic Publication: 2024 Dec 17.
DOI: 10.1016/j.virusres.2024.199500
Abstrakt: Brazil's COVID-19 response has faced challenges due to the continuous emergence of variants of concern (VOCs), emphasizing the need for ongoing genomic surveillance and retrospective analyses of past epidemic waves to reassess and fine tune containment protocols. Rio Grande do Sul (RS), Brazil's southernmost state, has international borders and trades with Argentina and Uruguay, along with significant domestic connections within Brazil. The identification of source and sink transmission chains at national and international scales can identify main hubs and pathways to target future interventions. In this study we investigated the RS state role in the national and international SARS-CoV-2 transmission chains, which has not been fully explored. Nasopharyngeal samples from various municipalities in RS were collected between June 2020 and July 2022. SARS-CoV-2 whole genome amplification and sequencing were performed using high-throughput Illumina sequencing. Bioinformatics analysis encompassed the development of scripts and tools to perform subsampling taking into account epidemiological information to reduce sequencing disparities bias among the regions/countries, genome assembly, and large-scale alignment and phylogenetic reconstruction. We sequenced a total of 1,480 SARS-CoV-2 genomes from RS, covering all major regions. Sequences predominantly represented Gamma (April-June 2021) and Omicron (January-July 2022) lineages. Phylogenetic analysis revealed a regional pattern for transmission dynamics, particularly with Southeast Brazil for Gamma, and a range of inter-regional connections for Delta and Omicron within the country. On the other hand, international and cross-border transmission with Argentina and Uruguay was rather limited. We evaluated the three VOCs circulation over two years in RS using a new subsampling strategy based on the number of cases in each state during the circulation of each VOC. In summary, the retrospective analysis of genomic surveillance data demonstrated that virus transmission was less intense between country borders than within the country. These findings suggest that while non-pharmacological interventions were effective to mitigate transmission across international RS land borders, they were insufficient to contain transmission at the domestic level.
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
Externí odkaz: