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SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19

Author

Listed:
  • Oksana V. Stanevich

    (Smorodintsev Research Institute of Influenza)

  • Evgeniia I. Alekseeva

    (Skolkovo Institute of Science and Technology (Skoltech))

  • Maria Sergeeva

    (Smorodintsev Research Institute of Influenza)

  • Artem V. Fadeev

    (Smorodintsev Research Institute of Influenza)

  • Kseniya S. Komissarova

    (Smorodintsev Research Institute of Influenza)

  • Anna A. Ivanova

    (Smorodintsev Research Institute of Influenza)

  • Tamara S. Simakova

    (Parseq Lab Co. Ltd)

  • Kirill A. Vasilyev

    (Smorodintsev Research Institute of Influenza)

  • Anna-Polina Shurygina

    (Smorodintsev Research Institute of Influenza)

  • Marina A. Stukova

    (Smorodintsev Research Institute of Influenza)

  • Ksenia R. Safina

    (Skolkovo Institute of Science and Technology (Skoltech))

  • Elena R. Nabieva

    (A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences)

  • Sofya K. Garushyants

    (A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences
    National Library of Medicine, National Institutes of Health)

  • Galya V. Klink

    (A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences)

  • Evgeny A. Bakin

    (First Pavlov State Medical University
    Bioinformatics Institute)

  • Jullia V. Zabutova

    (City Hospital 31)

  • Anastasia N. Kholodnaia

    (First Pavlov State Medical University
    City Hospital 31)

  • Olga V. Lukina

    (First Pavlov State Medical University)

  • Irina A. Skorokhod

    (City Hospital 31)

  • Viktoria V. Ryabchikova

    (City Hospital 31)

  • Nadezhda V. Medvedeva

    (City Hospital 31)

  • Dmitry A. Lioznov

    (Smorodintsev Research Institute of Influenza
    First Pavlov State Medical University)

  • Daria M. Danilenko

    (Smorodintsev Research Institute of Influenza)

  • Dmitriy M. Chudakov

    (Skolkovo Institute of Science and Technology (Skoltech)
    Institute of Translational Medicine, Pirogov Russian National Research Medical University)

  • Andrey B. Komissarov

    (Smorodintsev Research Institute of Influenza)

  • Georgii A. Bazykin

    (Skolkovo Institute of Science and Technology (Skoltech)
    A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences)

Abstract

Evolution of SARS-CoV-2 in immunocompromised hosts may result in novel variants with changed properties. While escape from humoral immunity certainly contributes to intra-host evolution, escape from cellular immunity is poorly understood. Here, we report a case of long-term COVID-19 in an immunocompromised patient with non-Hodgkin’s lymphoma who received treatment with rituximab and lacked neutralizing antibodies. Over the 318 days of the disease, the SARS-CoV-2 genome gained a total of 40 changes, 34 of which were present by the end of the study period. Among the acquired mutations, 12 reduced or prevented the binding of known immunogenic SARS-CoV-2 HLA class I antigens. By experimentally assessing the effect of a subset of the escape mutations, we show that they resulted in a loss of as much as ~1% of effector CD8 T cell response. Our results indicate that CD8 T cell escape represents a major underappreciated contributor to SARS-CoV-2 evolution in humans.

Suggested Citation

  • Oksana V. Stanevich & Evgeniia I. Alekseeva & Maria Sergeeva & Artem V. Fadeev & Kseniya S. Komissarova & Anna A. Ivanova & Tamara S. Simakova & Kirill A. Vasilyev & Anna-Polina Shurygina & Marina A. , 2023. "SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-022-34033-x
    DOI: 10.1038/s41467-022-34033-x
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    References listed on IDEAS

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