Open Access

Nature Communications

, volume 14 , issue 1 , publication number 149

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

Oksana V Stanevich ¹

Evgeniia I Alekseeva ²

Maria V Sergeeva ¹

Artem V Fadeev ¹

Kseniya S Komissarova ¹

Anna A Ivanova ¹

Tamara Simakova ³

Kirill A Vasiliev ¹

Anna Polina Shurygina ¹

Marina A Stukova ¹

Ksenia R Safina ²

Elena R Nabieva ⁴

Sofya K Garushyants ^{4, 5}

Galya V. Klink ⁴

Evgeny A Bakin ^{6, 7}

Jullia V Zabutova ⁸

Anastasia N Kholodnaia ^{6, 8}

Olga V Lukina ⁶

Irina A Skorokhod ⁸

Viktoria V Ryabchikova ⁸

Nadezhda V Medvedeva ⁸

Dmitry A Lioznov ^{1, 6}

Daria Danilenko ¹

Dmitry M. Chudakov ^{2, 9}

Andrey B Komissarov ¹

Georgii A. Bazykin ^{2, 4}

Hide authors affiliations Show authors affiliations: 9 affiliations

Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia |

Skolkovo Institute of Science and Technology (SKOLTECH), Moscow, Russia |

Parseq Lab Co. Ltd, Saint Petersburg, Russia |

⁴

A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia |

⁵

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA

United States National Library of Medicine

National Center for Biotechnology Information

⁶

First Pavlov State Medical University, Saint-Petersburg, Russia |

⁷

Bioinformatics Institute, Saint Petersburg, Russia |

⁸

City Hospital 31, Saint-Petersburg, Russia |

⁹

Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia |

Publication type: Journal Article

Publication date: 2023-01-10

Springer Nature

Nature Communications

scimago Q1

wos Q1

SJR: 4.761

CiteScore: 23.4

Impact factor: 15.7

ISSN: 20411723

DOI: 10.1038/s41467-022-34033-x

Copy DOI

PubMed ID: 36627290

General Chemistry

General Biochemistry, Genetics and Molecular Biology

Multidisciplinary

General Physics and Astronomy

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.

Found

2 citations

Bogolyubova Apollinariya

PhD in Biological/biomedical sciences

36 publications, 176 citations, 2 reviews

h-index: 9

National Medical Research Center for Hematology

1 citation

Korobova Zoia

🤝

PhD in Health sciences

33 publications, 264 citations

h-index: 10

Saint-Petersburg Pasteur Institute

First Pavlov State Medical University of St. Petersburg

Research interests

Cytokines

Immunology

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Stanevich O. V. et al. SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19 // Nature Communications. 2023. Vol. 14. No. 1. 149

GOST all authors (up to 50) Copy

Stanevich O. V., Alekseeva E. I., Sergeeva M. V., Fadeev A. V., Komissarova K. S., Ivanova A. A., Simakova T., Vasiliev K. A., Shurygina A. P., Stukova M. A., Safina K. R., Nabieva E. R., Garushyants S. K., Klink G. V., Bakin E. A., Zabutova J. V., Kholodnaia A. N., Lukina O. V., Skorokhod I. A., Ryabchikova V. V., Medvedeva N. V., Lioznov D. A., Danilenko D., Chudakov D. M., Komissarov A. B., Bazykin G. A. SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19 // Nature Communications. 2023. Vol. 14. No. 1. 149

RIS |

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RIS Copy

TY - JOUR

DO - 10.1038/s41467-022-34033-x

UR - https://doi.org/10.1038/s41467-022-34033-x

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

T2 - Nature Communications

AU - Stanevich, Oksana V

AU - Alekseeva, Evgeniia I

AU - Sergeeva, Maria V

AU - Fadeev, Artem V

AU - Komissarova, Kseniya S

AU - Ivanova, Anna A

AU - Simakova, Tamara

AU - Vasiliev, Kirill A

AU - Shurygina, Anna Polina

AU - Stukova, Marina A

AU - Safina, Ksenia R

AU - Nabieva, Elena R

AU - Garushyants, Sofya K

AU - Klink, Galya V.

AU - Bakin, Evgeny A

AU - Zabutova, Jullia V

AU - Kholodnaia, Anastasia N

AU - Lukina, Olga V

AU - Skorokhod, Irina A

AU - Ryabchikova, Viktoria V

AU - Medvedeva, Nadezhda V

AU - Lioznov, Dmitry A

AU - Danilenko, Daria

AU - Chudakov, Dmitry M.

AU - Komissarov, Andrey B

AU - Bazykin, Georgii A.

PY - 2023

DA - 2023/01/10

PB - Springer Nature

IS - 1

VL - 14

PMID - 36627290

SN - 2041-1723

ER -

BibTex

Cite this

BibTex (up to 50 authors) Copy

@article{2023_Stanevich,

author = {Oksana V Stanevich and Evgeniia I Alekseeva and Maria V Sergeeva and Artem V Fadeev and Kseniya S Komissarova and Anna A Ivanova and Tamara Simakova and Kirill A Vasiliev and Anna Polina Shurygina and Marina A Stukova and Ksenia R Safina and Elena R Nabieva and Sofya K Garushyants and Galya V. Klink and Evgeny A Bakin and Jullia V Zabutova and Anastasia N Kholodnaia and Olga V Lukina and Irina A Skorokhod and Viktoria V Ryabchikova and Nadezhda V Medvedeva and Dmitry A Lioznov and Daria Danilenko and Dmitry M. Chudakov and Andrey B Komissarov and Georgii A. Bazykin},

title = {SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19},

journal = {Nature Communications},

year = {2023},

volume = {14},

publisher = {Springer Nature},

month = {jan},

url = {https://doi.org/10.1038/s41467-022-34033-x},

number = {1},

pages = {149},

doi = {10.1038/s41467-022-34033-x}

}

Publisher

Springer Nature

Journal

Nature Communications

scimago Q1

wos Q1

SJR

4.761

CiteScore

23.4

Impact factor

15.7

ISSN

20411723 (Print, Electronic)

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