Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders
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&...
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Elsevier
2025-01-01
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| Series: | Virus Research |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S016817022400193X |
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| author | Filipe Zimmer Dezordi José Valter Joaquim Silva Júnior Terimar Facin Ruoso Angela Giovana Batista Pedro Mesquita Fonseca Larissa Paim Bernardo Richard Steiner Salvato Tatiana Schäffer Gregianini Thaísa Regina Rocha Lopes Eduardo Furtado Flores Rudi Weiblen Patrícia Chaves Brites Mônica de Medeiros Silva João Batista Teixeira da Rocha Gustavo de Lima Barbosa Lais Ceschini Machado Alexandre Freitas da Silva Marcelo Henrique Santos Paiva Matheus Filgueira Bezerra Tulio de Lima Campos Tiago Gräf Daniel Angelo Sganzerla Graichen Elgion Lucio da Silva Loreto Gabriel da Luz Wallau |
| author_facet | Filipe Zimmer Dezordi José Valter Joaquim Silva Júnior Terimar Facin Ruoso Angela Giovana Batista Pedro Mesquita Fonseca Larissa Paim Bernardo Richard Steiner Salvato Tatiana Schäffer Gregianini Thaísa Regina Rocha Lopes Eduardo Furtado Flores Rudi Weiblen Patrícia Chaves Brites Mônica de Medeiros Silva João Batista Teixeira da Rocha Gustavo de Lima Barbosa Lais Ceschini Machado Alexandre Freitas da Silva Marcelo Henrique Santos Paiva Matheus Filgueira Bezerra Tulio de Lima Campos Tiago Gräf Daniel Angelo Sganzerla Graichen Elgion Lucio da Silva Loreto Gabriel da Luz Wallau |
| author_sort | Filipe Zimmer Dezordi |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-aaf844fc6548499992b5d794888741e5 |
| institution | Kabale University |
| issn | 1872-7492 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
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| series | Virus Research |
| spelling | doaj-art-aaf844fc6548499992b5d794888741e52025-01-09T06:12:14ZengElsevierVirus Research1872-74922025-01-01351199500Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state bordersFilipe Zimmer Dezordi0José Valter Joaquim Silva Júnior1Terimar Facin Ruoso2Angela Giovana Batista3Pedro Mesquita Fonseca4Larissa Paim Bernardo5Richard Steiner Salvato6Tatiana Schäffer Gregianini7Thaísa Regina Rocha Lopes8Eduardo Furtado Flores9Rudi Weiblen10Patrícia Chaves Brites11Mônica de Medeiros Silva12João Batista Teixeira da Rocha13Gustavo de Lima Barbosa14Lais Ceschini Machado15Alexandre Freitas da Silva16Marcelo Henrique Santos Paiva17Matheus Filgueira Bezerra18Tulio de Lima Campos19Tiago Gräf20Daniel Angelo Sganzerla Graichen21Elgion Lucio da Silva Loreto22Gabriel da Luz Wallau23Departamento 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, BrazilSetor 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, BrazilCampus Palmeira das Missões, Universidade Federal de Santa Maria. Palmeira das Missões, Rio Grande do Sul, 98300-000, BrazilCampus 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, BrazilCampus Palmeira das Missões, Universidade Federal de Santa Maria. Palmeira das Missões, Rio Grande do Sul, 98300-000, BrazilDepartamento de Ciências da Vida - DCVIDA, Universidade Regional do Noroeste do Estado do Rio Grande do Sul - UNIJUÍ, Ijuí, Rio Grande do Sul, 98700-000, BrazilCentro Estadual de Vigilância em Saúde. Secretaria Estadual da Saúde do Rio Grande do Sul. Porto Alegre, Rio Grande do Sul, 90610-000, BrazilCentro Estadual de Vigilância em Saúde. Secretaria Estadual da Saúde do Rio Grande do Sul. Porto Alegre, Rio Grande do Sul, 90610-000, BrazilSetor 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, BrazilSetor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, 97105-900, BrazilSetor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, 97105-900, BrazilHospital Universitário de Santa Maria (HUSM), Universidade Federal de Santa Maria (UFSM), Av. Roraima, 1000, Santa Maria, Rio Grande do Sul, 97105-900, BrazilDepartamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Av. Roraima, 1000, Santa Maria, Rio Grande do Sul, 97105-900, BrazilDepartamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Av. Roraima, 1000, Santa Maria, Rio Grande do Sul, 97105-900, BrazilNúcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, 50670-420, BrazilDepartamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife Pernambuco, 50670-420, BrazilDepartamento 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, BrazilDepartamento 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, BrazilDepartamento de Microbiologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, 50670-420, BrazilNúcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, 50670-420, BrazilLaboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, BrazilDepartamento de Zootecnia e Ciências Biológicas, Universidade Federal de Santa Maria, Palmera das Missões, Rio Grande do Sul 98300-000, BrazilHospital Universitário de Santa Maria (HUSM), Universidade Federal de Santa Maria (UFSM), Av. Roraima, 1000, Santa Maria, Rio Grande do Sul, 97105-900, BrazilDepartamento 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; Corresponding author.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.http://www.sciencedirect.com/science/article/pii/S016817022400193XSARS-Cov-2BrazilRio Grande do SulGenomic Surveillance |
| spellingShingle | Filipe Zimmer Dezordi José Valter Joaquim Silva Júnior Terimar Facin Ruoso Angela Giovana Batista Pedro Mesquita Fonseca Larissa Paim Bernardo Richard Steiner Salvato Tatiana Schäffer Gregianini Thaísa Regina Rocha Lopes Eduardo Furtado Flores Rudi Weiblen Patrícia Chaves Brites Mônica de Medeiros Silva João Batista Teixeira da Rocha Gustavo de Lima Barbosa Lais Ceschini Machado Alexandre Freitas da Silva Marcelo Henrique Santos Paiva Matheus Filgueira Bezerra Tulio de Lima Campos Tiago Gräf Daniel Angelo Sganzerla Graichen Elgion Lucio da Silva Loreto Gabriel da Luz Wallau Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders Virus Research SARS-Cov-2 Brazil Rio Grande do Sul Genomic Surveillance |
| title | Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders |
| title_full | Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders |
| title_fullStr | Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders |
| title_full_unstemmed | Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders |
| title_short | Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders |
| title_sort | higher frequency of interstate over international transmission chains of sars cov 2 virus at the rio grande do sul brazil state borders |
| topic | SARS-Cov-2 Brazil Rio Grande do Sul Genomic Surveillance |
| url | http://www.sciencedirect.com/science/article/pii/S016817022400193X |
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