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Emergence and Spread of the SARS-CoV-2 Variant of Concern Delta across Different Brazilian Regions

2022; American Society for Microbiology; Volume: 10; Issue: 5 Linguagem: Inglês

10.1128/spectrum.02641-21

2165-0497

Ighor Arantes, Felipe Gomes Naveca, Tiago Gräf, Fábio Miyajima, Helisson Faoro, Gabriel Luz Wallau, Edson Delatorre, Luciana Appolinario, Elisa Cavalcante Pereira, Tainá Moreira Martins Venas, Alice Sampaio Barreto da Rocha, Renata Serrano Lopes, Marilda Mendonça Siqueira, Gonzalo Bello, Paola Cristina Resende, Carlos Leonardo Araújo, Cleber Furtado Akesenen, Fernando Braga Stehling Dias, Igor Oliveira Duarte, Jamille Mendes Bezerra, Joaquim Cesar Sousa, Pedro Miguel Carneiro Jerônimo, Suzana Almeida Porto, Thaís de Oliveira Costa, Thais Ferreira de Oliveira, Ticiane Cavalcante de Souza, Veridiana Pessoa Miyajima, Acacia Lourenço Francisco Nasr, Ana Carolina De la Vechia, Rosana Aparecida Piler, Tatiane Motta Huggler, Cristiano Fernandes, Marcelo Ferreira da Costa Gomes, Adriano Abbud, Katia Oliveira Correa, Alexandre Freitas da Silva, Antônio Marinho da Silva Neto, Cássia Docena, Filipe Zimmer Dezordi, Gustavo Barbosa de Lima, Laís Ceschini Machado, Lílian Caroliny Amorim Silva, Marcelo Henrique Santos Paiva, Matheus Filgueira Bezerra, Raul Emídio de Lima, Andréia Akemi Suzukawa, Mauro de Medeiros Oliveira, Michelle Orane Schemberger, Beatriz Grinsztejn, Patrícia Brasil, Valdiléa G. Veloso, Felicidade Mota Pereira, Dalane Loudal Florentino Teixeira, Haline Barroso, Anderson Brandão Leite, Vinicius Lemes da Silva, André Felipe Leal Bernardes, Felipe Campos de Melo Iani, Irina Nastassja Riediger, Maria do Carmo Debur, Themis Rocha, Andreia Santos Costa, Lindomar dos Anjos Silva, Tirza Mattos, Ana Barjud Marques, Maximo Liana Perdigão Mello, Vânia Angelica Feitosa Viana, Rodrigo Ribeiro Rodrigues, Darcita Büerger Rovaris, Sandra Bianchini Fernandes, Lídio Gonçãlves Lima Neto, Valnete Andrade, Andréa Cony Cavalcanti, Richard Steiner Salvato Tatiana Schäffer Gregianini, Jucimária Dantas Galvão, Ágatha Costa, André de Lima Guerra Corado, Fernanda Nascimento, George Silva, Karina Pessoa, Luciana Fé Gonçalves, Maria Júlia Brandão, Matilde Mejía, Michele Silva de Jesus, Valdinete Alves do Nascimento, Victor Costa de Souza, Bruna Mendonça da Silva, Fernando Couto Motta, Jéssica de Macedo Carvalho, Larissa Macedo Pinto, Fernando Vinhal, Isabela de Lucena Heráclio Morgana de Freitas Caraciolo, Roberta Mendes Abreu Silva, Silvio Rodrigues de Almeida, Thayna Karoline Sousa Silva, Alessandro Álvares Magalhães, Érika Lopes Rocha Batista, Greice Madeleine Ikeda do Carmo, Janaína Sallas, Walquíria Aparecida Ferreira de Almeida, Márcio Henrique de Oliveira Garcia, Cecília Leite Costa, Eduardo Ruback dos Santos, João Felipe Bezerra,

COVID-19 epidemiological studies

The SARS-CoV-2 variant of concern (VOC) Delta was first detected in India in October 2020. The first imported cases of the Delta variant in Brazil were identified in April 2021 in the southern region, followed by more cases in different regions during the following months. By early September 2021, Delta was already the dominant variant in the southeastern (87%), southern (73%), and northeastern (52%) Brazilian regions. This study aimed to understand the spatiotemporal dissemination dynamics of Delta in Brazil. To this end, we employed a combination of maximum likelihood (ML) and Bayesian methods to reconstruct the evolutionary relationship of 2,264 VOC Delta complete genomes (482 from this study) recovered across 21 of the 27 Brazilian federal units. Our phylogeographic analyses identified three major transmission clusters of Delta in Brazil. The clade BR-I (n = 1,560) arose in Rio de Janeiro in late April 2021 and was the major cluster behind the dissemination of the VOC Delta in the southeastern, northeastern, northern, and central-western regions. The AY.101 lineage (n = 207) that arose in the Paraná state in late April 2021 and aggregated the largest fraction of sampled genomes from the southern region. Lastly, the AY.46.3 lineage emerged in Brazil in the São Paulo state in early June 2021 and remained mostly restricted to this state. In the rapid turnover of viral variants characteristic of the SARS-CoV-2 pandemic, Brazilian regions seem to occupy different stages of an increasing prevalence of the VOC Delta in their epidemic profiles. This process demands continuous genomic and epidemiological surveillance toward identifying and mitigating new introductions, limiting their dissemination, and preventing the establishment of more significant outbreaks in a population already heavily affected by the COVID-19 pandemic. IMPORTANCE Amid the SARS-CoV-2 continuously changing epidemic profile, this study details the space-time dynamics of the emergence of the Delta lineage across Brazilian territories, pointing out its multiple introductions in the country and its most prevalent sublineages. Some of these sublineages have their emergence, alongside their genomic composition and geographic distribution, detailed here for the first time. A special focus is given to the emergence process of Delta outside the country's south and southeast regions, the most populated and subjects of most published SARS-CoV-2 studies in Brazil. In summary, the study allows a better comprehension of the evolution process of a SARS-CoV-2 lineage that would be associated with a significant recrudescence of the pandemic in Brazil.