Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas

Ighor Arantes, Gonzalo Bello (), Valdinete Nascimento, Victor Souza, Arlesson Silva, Dejanane Silva, Fernanda Nascimento, Matilde Mejía, Maria Júlia Brandão, Luciana Gonçalves, George Silva, Cristiano Fernandes Costa, Ligia Abdalla, João Hugo Santos, Tatyana Costa Amorim Ramos, Chayada Piantham, Kimihito Ito, Marilda Mendonça Siqueira, Paola Cristina Resende, Gabriel Luz Wallau, Edson Delatorre, Tiago Gräf and Felipe Gomes Naveca ()
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Ighor Arantes: Instituto Oswaldo Cruz, Fiocruz
Gonzalo Bello: Instituto Oswaldo Cruz, Fiocruz
Valdinete Nascimento: Instituto Leônidas e Maria Deane, Fiocruz
Victor Souza: Instituto Leônidas e Maria Deane, Fiocruz
Arlesson Silva: Instituto Leônidas e Maria Deane, Fiocruz
Dejanane Silva: Instituto Leônidas e Maria Deane, Fiocruz
Fernanda Nascimento: Instituto Leônidas e Maria Deane, Fiocruz
Matilde Mejía: Instituto Leônidas e Maria Deane, Fiocruz
Maria Júlia Brandão: Instituto Leônidas e Maria Deane, Fiocruz
Luciana Gonçalves: Instituto Leônidas e Maria Deane, Fiocruz
George Silva: Instituto Leônidas e Maria Deane, Fiocruz
Cristiano Fernandes Costa: Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto
Ligia Abdalla: Universidade do Estado do Amazonas
João Hugo Santos: Hospital Adventista de Manaus
Tatyana Costa Amorim Ramos: Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto
Chayada Piantham: Hokkaido University
Kimihito Ito: Hokkaido University
Marilda Mendonça Siqueira: Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz
Paola Cristina Resende: Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz
Gabriel Luz Wallau: Instituto Aggeu Magalhães, Fundação Oswaldo Cruz
Edson Delatorre: Universidade Federal do Espírito Santo
Tiago Gräf: Instituto Carlos Chagas, Fiocruz
Felipe Gomes Naveca: Instituto Leônidas e Maria Deane, Fiocruz

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-37541-6

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