Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

Giovanetti, Marta; Slavov, Svetoslav Nanev; Fonseca, Vagner; Wilkinson, Eduan; Tegally, Houriiyah; Patané, José Salvatore Leister; Viala, Vincent Louis; San, James Emmanuel; Rodrigues, Evandra Strazza; Santos, Elaine Vieira; Aburjaile, Flávia Figueira; Xavier, Joilson; Fritsch, Hegger; Adelino, Talita; Pereira, Felicidade Mota; Leal, Arabela; Iani, Felipe Campos de Melo; Pereira, Glauco de Carvalho; Vázquez, Cynthia; Sanabria, Gladys Mercedes Estigarribia; Oliveira, Elaine Cristina de; Demarchi, Luiz Henrique Ferraz; Croda, Júlio; Bezerra, Rafael dos Santos; Lima, Loyze Paola Oliveira de; Martins, Antonio Jorge; Barros, Cláudia; Marqueze, Elaine Cristina; Bernardino, Jardelina de Souza Todão; Moretti, Débora Botéquio; Brassaloti, Ricardo Augusto; Cassano, Raquel de Lello Rocha Campos; Mariani, Pilar Drummond Sampaio Corrêa; Kitajima, João Paulo; Santos, Bibiana; Proto‐Siqueira, Rodrigo; Cantarelli, Vlademir Vicente; Tosta, Stephane; Nardy, Vanessa Brandão; Silva, Luciana Reboredo de Oliveira da; Gómez, Marcela; Lima, Jaqueline Gomes; Ribeiro, Adriana Aparecida; Guimarães, Natália Rocha; Watanabe, Luiz Takao; Silva, Luana Barbosa Da; Ferreira, Raquel da Silva; Penha, Mara Patricia F. da; Ortega, María José Cilleruelo; Fuente, Andrea Gómez de la; Villalba, Shirley; Torales, Juan; Gamarra, María Liz; Aquino, Carolina Lessa; Figueredo, Gloria Patricia Martínez; Fava, Wellington Santos; Motta-Castro, Ana Rita Coimbra; Venturini, James; Oliveira, Sandra Maria do Vale Leone de; Gonçalves, Crhistinne Cavalheiro Maymone; Rossa, Maria do Carmo Debur; Becker, Guilherme Nardi; Giacomini, Mayra Presibella; Marques, Nelson Quallio; Riediger, Irina Nastassja; Raboni, Sônia Mara; Mattoso, Gabriela; Cataneo, Allan D.; Zanluca, Camila; Santos, Claudia Nunes Duarte dos; Assato, Patrícia Akemi; Costa, Felipe da Silva da Allan; Poleti, Mirele Daiana; Lesbon, Jéssika Cristina Chagas; Mattos, E. C.; Banho, Cecília Ártico; Sacchetto, Lívia; Moraes, Marília Mazzi; Grotto, Rejane Maria Tommasini; Souza-Neto, Jayme A.; Nogueira, Maurício Lacerda; Fukumasu, Heidge; Coutinho, Luiz Lehmann; Calado, Rodrigo T.; Neto, Raul Machado; Filippis, Ana María Bispo de; Cunha, Rivaldo Venâncio da; Freitas, Carla; Peterka, Cassio Roberto Leonel; Fernandes, Cássia de Fátima Rangel; Araújo, Wildo Navegantes de; Said, Rodrigo Fabiano do Carmo; Melo, Carlos Frederico Campelo de Albuquerque e; Almirón, María; Lourenço, José; Oliveira, Túlio de; Holmes, Edward C.; Haddad, Ricardo; Sampaio, Sandra Coccuzzo; Elias, Maria Carolina; Kashima, Simone; Alcântara, Luíz Carlos Júnior; Covas, Dimas Tadeu

doi:10.1038/s41564-022-01191-z

Cited by 61 publications

(41 citation statements)

References 49 publications

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“…With a focus on this, we adopted a large-scale sequencing survey on the circulating SARS-CoV-2 variants which was aimed at the sequencing of all of the positive cases in this location. By this way, we estimated the SARS-CoV-2 substitution dynamics which followed the trends of emergence and VOCs’ dissemination in Brazil from the introduction of the parenteral strains in the region [ 21 ], and the emergence of the first epidemic Gamma VOC wave [ 22 ]. This profile was also observed for the Delta epidemic wave [ 23 ].…”

Section: Discussionmentioning

confidence: 99%

Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil

Slavov

La-Roque²,

Costa³

et al. 2022

Viruses

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From a country with one of the highest SARS-CoV-2 morbidity and mortality rates, Brazil has implemented one of the most successful vaccination programs. Brazil’s first model city vaccination program was performed by the CoronaVac vaccine (Sinovac Biotech) in the town of Serrana, São Paulo State. To evaluate the vaccination effect on the SARS-CoV-2 molecular dynamics and clinical outcomes, we performed SARS-CoV-2 molecular surveillance on 4375 complete genomes obtained between June 2020 and April 2022 in this location. This study included the period between the initial SARS-CoV-2 introduction and during the vaccination process. We observed that the SARS-CoV-2 substitution dynamics in Serrana followed the viral molecular epidemiology in Brazil, including the initial identification of the ancestral lineages (B.1.1.28 and B.1.1.33) and epidemic waves of variants of concern (VOC) including the Gamma, Delta, and, more recently, Omicron. Most probably, as a result of the immunization campaign, the mortality during the Gamma and Delta VOC was significantly reduced compared to the rest of Brazil, which was also related to lower morbidity. Our phylogenetic analysis revealed the evolutionary history of the SARS-CoV-2 in this location and showed that multiple introduction events have occurred over time. The evaluation of the COVID-19 clinical outcome revealed that most cases were mild (88.9%, 98.1%, 99.1% to Gamma, Delta, and Omicron, respectively) regardless of the infecting VOC. In conclusion, we observed that vaccination was responsible for reducing the death toll rate and related COVID-19 morbidity, especially during the gamma and Delta VOC; however, it does not prevent the rapid substitution rate and morbidity of the Omicron VOC.

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Section: Discussionmentioning

confidence: 99%

Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil

Slavov

La-Roque²,

Costa³

et al. 2022

Viruses

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“…The first identified SARS-CoV-2 variant carried a single point mutation in the spike protein (D614G), emerged early in the pandemic and spread rapidly through Europe and North America. Several lines of evidence now suggest that SARS-CoV-2 variants carrying this mutation have increased transmissibility ( Korber et al, 2020 ; Plante et al, 2021 ; Volz et al, 2021 ; Yurkovetskiy et al, 2020 ; Giovanetti et al, 2022a ; Nonaka et al, 2021 ).…”

Section: Sars-cov-2 Real-time Evolutionmentioning

confidence: 99%

Global SARS-CoV-2 genomic surveillance: What we have learned (so far)

Tosta

Moreno

Schuab

et al. 2023

Infection, Genetics and Evolution

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“…Genomic surveillance in Brazil was limited during the beginning of the pandemic, but specific initiatives successfully detected and characterized the international introduction of lineages and community transmission of distinct lineages as well as the introduction and spread of VOCs[18–20]. With the establishment of research networks, SARS-CoV-2 surveillance has improved substantially in the country, providing country-wide views of lineage introduction, spread, establishment and transmission patterns between states[21–24]. But, although interstate SARS-CoV-2 dynamics were more thoroughly investigated, up to October 2022 there were limited intrastate SARS-CoV-2 studies.…”

Section: Introductionmentioning

confidence: 99%

“…But, although interstate SARS-CoV-2 dynamics were more thoroughly investigated, up to October 2022 there were limited intrastate SARS-CoV-2 studies. Only Amazonas, Santa Catarina, Tocantins, Paraná, São Paulo and Rio de Janeiro intrastate dynamics have been investigated[21,24–28] as well as some reports from Rio Grande do Sul and Minas Gerais states focussing on specific lineage replacements[18,29,30]. Our group published the first genomes from Pernambuco state showing multiple introductions and ongoing community transmission at the beginning of the pandemic in Brazil[31].…”

Section: Introductionmentioning

confidence: 99%

“…Interstate transmission has been investigated for specific lineages such as P.1 Gamma and P.2 lineages in Pernambuco[32]. Although these studies provided crucial information to understand the SARS-CoV-2 dynamics in Brazil, states or region-specific SARS-CoV-2 lineage dynamics are expected due to the large differences between inter and intra states population sizes, concentration and human movement dynamics in Brazil[21]. In addition, non-pharmacological strategies to control SARS-CoV-2 were implemented with highly distinct adoption patterns across the country[33].…”

Section: Introductionmentioning

confidence: 99%

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Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco - Brazil

Machado

Dezordi

Lima

et al. 2023

Preprint

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In recent years, the SARS-CoV-2 viruses emerged and spread around the world, leaving a large death toll and long-lasting impact on survivors. As of January 2023, Brazil is still among the countries with the highest number of registered deaths. This continental-size and pluralistic country experienced a heterogenous implementation of non-pharmacological and pharmacological interventions which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics across the country. Here we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and its dynamics in distinct epidemiological scenarios in the first two years of the pandemics in the Pernambuco state (Northeast Brazil). We generated a total of 1389 new SARS-CoV-2 genomes from June 2020 to August 2021 covering all major regions of the state. This sampling captured the arrival, communitary transmission and the circulation of the B1.1, B.1.1.28 and B.1.1.33 lineages in the first eight months of the pandemics, 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) lineage. Based on the incidence and lineage spread pattern we observed that there was 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. Nevertheless, inter-state traffic was also another important source of lineage introduction and spread into the state. Our results highlight that the fine grained intrastate analysis of lineages and incidence spread can provide actionable insights for planning future non-pharmacological intervention for air-borne transmissible human pathogens.

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Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

Cited by 61 publications

References 49 publications

Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil

Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil

Global SARS-CoV-2 genomic surveillance: What we have learned (so far)

Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco - Brazil

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