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Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa

Author

Listed:
  • Kaiyuan Sun

    (Fogarty International Center, National Institutes of Health)

  • Stefano Tempia

    (National Institute for Communicable Diseases of the National Health Laboratory Service
    University of the Witwatersrand
    Centers for Disease Control and Prevention)

  • Jackie Kleynhans

    (National Institute for Communicable Diseases of the National Health Laboratory Service
    University of the Witwatersrand)

  • Anne Gottberg

    (National Institute for Communicable Diseases of the National Health Laboratory Service
    University of the Witwatersrand)

  • Meredith L. McMorrow

    (Centers for Disease Control and Prevention)

  • Nicole Wolter

    (National Institute for Communicable Diseases of the National Health Laboratory Service
    University of the Witwatersrand)

  • Jinal N. Bhiman

    (National Institute for Communicable Diseases of the National Health Laboratory Service
    University of the Witwatersrand)

  • Jocelyn Moyes

    (National Institute for Communicable Diseases of the National Health Laboratory Service
    University of the Witwatersrand)

  • Maimuna Carrim

    (National Institute for Communicable Diseases of the National Health Laboratory Service
    University of the Witwatersrand)

  • Neil A. Martinson

    (University of the Witwatersrand
    Johns Hopkins University Center for TB Research)

  • Kathleen Kahn

    (University of the Witwatersrand)

  • Limakatso Lebina

    (University of the Witwatersrand)

  • Jacques D. Toit

    (University of the Witwatersrand)

  • Thulisa Mkhencele

    (National Institute for Communicable Diseases of the National Health Laboratory Service)

  • Cécile Viboud

    (Fogarty International Center, National Institutes of Health)

  • Cheryl Cohen

    (National Institute for Communicable Diseases of the National Health Laboratory Service
    University of the Witwatersrand)

Abstract

South Africa was among the first countries to detect the SARS-CoV-2 Omicron variant. However, the size of its Omicron BA.1 and BA.2 subvariants (BA.1/2) wave remains poorly understood. We analyzed sequential serum samples collected through a prospective cohort study before, during, and after the Omicron BA.1/2 wave to infer infection rates and monitor changes in the immune histories of participants over time. We found that the Omicron BA.1/2 wave infected more than half of the cohort population, with reinfections and vaccine breakthroughs accounting for > 60% of all infections in both rural and urban sites. After the Omicron BA.1/2 wave, we found few (

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-022-35652-0
    DOI: 10.1038/s41467-022-35652-0
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    as
    1. Yunlong Cao & Jing Wang & Fanchong Jian & Tianhe Xiao & Weiliang Song & Ayijiang Yisimayi & Weijin Huang & Qianqian Li & Peng Wang & Ran An & Jing Wang & Yao Wang & Xiao Niu & Sijie Yang & Hui Liang &, 2022. "Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies," Nature, Nature, vol. 602(7898), pages 657-663, February.
    2. 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.
    3. Bo Meng & Adam Abdullahi & Isabella A. T. M. Ferreira & Niluka Goonawardane & Akatsuki Saito & Izumi Kimura & Daichi Yamasoba & Pehuén Pereyra Gerber & Saman Fatihi & Surabhi Rathore & Samantha K. Zep, 2022. "Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity," Nature, Nature, vol. 603(7902), pages 706-714, March.
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    Cited by:

    1. Sheikh Jarju & Rhys D. Wenlock & Madikoi Danso & Dawda Jobe & Ya Jankey Jagne & Alansana Darboe & Michelle Kumado & Yusupha Jallow & Mamlie Touray & Ebrima A. Ceesay & Hoja Gaye & Biran Gaye & Abdouli, 2024. "High SARS-CoV-2 incidence and asymptomatic fraction during Delta and Omicron BA.1 waves in The Gambia," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. 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.

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