IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37541-6.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37541-6
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-37541-6?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Oliver Eales & Leonardo Oliveira Martins & Andrew J. Page & Haowei Wang & Barbara Bodinier & David Tang & David Haw & Jakob Jonnerby & Christina Atchison & Deborah Ashby & Wendy Barclay & Graham Taylo, 2022. "Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Emanuele Andreano & Ida Paciello & Giulia Piccini & Noemi Manganaro & Piero Pileri & Inesa Hyseni & Margherita Leonardi & Elisa Pantano & Valentina Abbiento & Linda Benincasa & Ginevra Giglioli & Conc, 2021. "Hybrid immunity improves B cells and antibodies against SARS-CoV-2 variants," Nature, Nature, vol. 600(7889), pages 530-535, December.
    3. Raquel Viana & Sikhulile Moyo & Daniel G. Amoako & Houriiyah Tegally & Cathrine Scheepers & Christian L. Althaus & Ugochukwu J. Anyaneji & Phillip A. Bester & Maciej F. Boni & Mohammed Chand & Wonderf, 2022. "Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa," Nature, Nature, vol. 603(7902), pages 679-686, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Emanuele Andreano & Ida Paciello & Silvia Marchese & Lorena Donnici & Giulio Pierleoni & Giulia Piccini & Noemi Manganaro & Elisa Pantano & Valentina Abbiento & Piero Pileri & Linda Benincasa & Ginevr, 2022. "Anatomy of Omicron BA.1 and BA.2 neutralizing antibodies in COVID-19 mRNA vaccinees," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    2. Tiago Gräf & Alexander A. Martinez & Gonzalo Bello & Simon Dellicour & Philippe Lemey & Vittoria Colizza & Mattia Mazzoli & Chiara Poletto & Vanessa Leiko Oikawa Cardoso & Alexandre Freitas Silva & Fe, 2024. "Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Alvin X. Han & Emma Hannay & Sergio Carmona & Bill Rodriguez & Brooke E. Nichols & Colin A. Russell, 2023. "Estimating the potential impact and diagnostic requirements for SARS-CoV-2 test-and-treat programs," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Joseph A. Lewnard & Vennis Hong & Jeniffer S. Kim & Sally F. Shaw & Bruno Lewin & Harpreet Takhar & Sara Y. Tartof, 2023. "Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    5. X. Tong & R. P. McNamara & M. J. Avendaño & E. F. Serrano & T. García-Salum & C. Pardo-Roa & H. L. Bertera & T. M. Chicz & J. Levican & E. Poblete & E. Salinas & A. Muñoz & A. Riquelme & G. Alter & R., 2023. "Waning and boosting of antibody Fc-effector functions upon SARS-CoV-2 vaccination," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    6. Dapeng Li & David R. Martinez & Alexandra Schäfer & Haiyan Chen & Maggie Barr & Laura L. Sutherland & Esther Lee & Robert Parks & Dieter Mielke & Whitney Edwards & Amanda Newman & Kevin W. Bock & Mahn, 2022. "Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    7. Meriem Bekliz & Kenneth Adea & Pauline Vetter & Christiane S. Eberhardt & Krisztina Hosszu-Fellous & Diem-Lan Vu & Olha Puhach & Manel Essaidi-Laziosi & Sophie Waldvogel-Abramowski & Caroline Stephan , 2022. "Neutralization capacity of antibodies elicited through homologous or heterologous infection or vaccination against SARS-CoV-2 VOCs," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    8. Fanglei Zuo & Hassan Abolhassani & Likun Du & Antonio Piralla & Federico Bertoglio & Leire Campos-Mata & Hui Wan & Maren Schubert & Irene Cassaniti & Yating Wang & Josè Camilla Sammartino & Rui Sun & , 2022. "Heterologous immunization with inactivated vaccine followed by mRNA-booster elicits strong immunity against SARS-CoV-2 Omicron variant," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    9. Sapna Sharma & Thomas Vercruysse & Lorena Sanchez-Felipe & Winnie Kerstens & Madina Rasulova & Lindsey Bervoets & Carolien Keyzer & Rana Abdelnabi & Caroline S. Foo & Viktor Lemmens & Dominique Loover, 2022. "Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    10. Zhennan Zhao & Yufeng Xie & Bin Bai & Chunliang Luo & Jingya Zhou & Weiwei Li & Yumin Meng & Linjie Li & Dedong Li & Xiaomei Li & Xiaoxiong Li & Xiaoyun Wang & Junqing Sun & Zepeng Xu & Yeping Sun & W, 2023. "Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    11. Kaiyuan Sun & Stefano Tempia & Jackie Kleynhans & Anne Gottberg & Meredith L. McMorrow & Nicole Wolter & Jinal N. Bhiman & Jocelyn Moyes & Maimuna Carrim & Neil A. Martinson & Kathleen Kahn & Limakats, 2023. "Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    12. Oliver Eales & Leonardo Oliveira Martins & Andrew J. Page & Haowei Wang & Barbara Bodinier & David Tang & David Haw & Jakob Jonnerby & Christina Atchison & Deborah Ashby & Wendy Barclay & Graham Taylo, 2022. "Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    13. Chihiro Motozono & Mako Toyoda & Toong Seng Tan & Hiroshi Hamana & Yoshihiko Goto & Yoshiki Aritsu & Yusuke Miyashita & Hiroyuki Oshiumi & Kimitoshi Nakamura & Seiji Okada & Keiko Udaka & Mizuki Kitam, 2022. "The SARS-CoV-2 Omicron BA.1 spike G446S mutation potentiates antiviral T-cell recognition," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    14. Alief Moulana & Thomas Dupic & Angela M. Phillips & Jeffrey Chang & Serafina Nieves & Anne A. Roffler & Allison J. Greaney & Tyler N. Starr & Jesse D. Bloom & Michael M. Desai, 2022. "Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    15. Hailey Hornsby & Alexander R. Nicols & Stephanie Longet & Chang Liu & Adriana Tomic & Adrienn Angyal & Barbara Kronsteiner & Jessica K. Tyerman & Tom Tipton & Peijun Zhang & Marta Gallis & Piyada Supa, 2023. "Omicron infection following vaccination enhances a broad spectrum of immune responses dependent on infection history," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    16. Adam Abdullahi & David Oladele & Michael Owusu & Steven A. Kemp & James Ayorinde & Abideen Salako & Douglas Fink & Fehintola Ige & Isabella A. T. M. Ferreira & Bo Meng & Augustina Angelina Sylverken &, 2022. "SARS-COV-2 antibody responses to AZD1222 vaccination in West Africa," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    17. Delphine Planas & Isabelle Staropoli & Vincent Michel & Frederic Lemoine & Flora Donati & Matthieu Prot & Francoise Porrot & Florence Guivel-Benhassine & Banujaa Jeyarajah & Angela Brisebarre & Océane, 2024. "Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    18. Emanuele Andreano & Ida Paciello & Giulio Pierleoni & Giuseppe Maccari & Giada Antonelli & Valentina Abbiento & Piero Pileri & Linda Benincasa & Ginevra Giglioli & Giulia Piccini & Concetta De Santi &, 2023. "mRNA vaccines and hybrid immunity use different B cell germlines against Omicron BA.4 and BA.5," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    19. Duggan, Jim & Andrade, Jair & Murphy, Thomas Brendan & Gleeson, James P. & Walsh, Cathal & Nolan, Philip, 2024. "An age-cohort simulation model for generating COVID-19 scenarios: A study from Ireland's pandemic response," European Journal of Operational Research, Elsevier, vol. 313(1), pages 343-358.
    20. Simone Lanini & Stefano Milleri & Emanuele Andreano & Sarah Nosari & Ida Paciello & Giulia Piccini & Alessandra Gentili & Adhuna Phogat & Inesa Hyseni & Margherita Leonardi & Alessandro Torelli & Eman, 2022. "Safety and serum distribution of anti-SARS-CoV-2 monoclonal antibody MAD0004J08 after intramuscular injection," Nature Communications, Nature, vol. 13(1), pages 1-8, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37541-6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.