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

Author

Listed:
  • Ighor Arantes

    (Instituto Oswaldo Cruz, Fiocruz
    Enterovírus e Emergências Virais, 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
    Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto)

  • George Silva

    (Instituto Leônidas e Maria Deane, Fiocruz
    Fundação Centro de Controle de Oncologia do Estado do Amazonas)

  • Cristiano Fernandes Costa

    (Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto
    Conselho de Secretários Municipais de Saúde do Amazonas COSEMS – AM)

  • 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
    Bernhard Nocht Institute for Tropical Medicine)

  • Edson Delatorre

    (Universidade Federal do Espírito Santo)

  • Tiago Gräf

    (Instituto Carlos Chagas, Fiocruz)

  • Felipe Gomes Naveca

    (Instituto Leônidas e Maria Deane, Fiocruz
    Instituto Oswaldo Cruz, Fiocruz)

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.

Suggested Citation

  • Ighor Arantes & Gonzalo Bello & Valdinete Nascimento & Victor Souza & Arlesson Silva & Dejanane Silva & Fernanda Nascimento & Matilde Mejía & Maria Júlia Brandão & Luciana Gonçalves & George Silva & C, 2023. "Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37541-6
    DOI: 10.1038/s41467-023-37541-6
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