Evidence of recurrent selection of mutations commonly found in SARS-CoV-2 variants of concern in viruses infecting immunocompromised patients

Livia R Goes; Juliana D Siqueira; Marianne M Garrido; Brunna M Alves; Claudia Cicala; James Arthos; João P B Viola; Marcelo A Soares

doi:10.3389/fmicb.2022.946549

Evidence of recurrent selection of mutations commonly found in SARS-CoV-2 variants of concern in viruses infecting immunocompromised patients

Front Microbiol. 2022 Jul 26:13:946549. doi: 10.3389/fmicb.2022.946549. eCollection 2022.

Authors

Livia R Goes^{1

2}, Juliana D Siqueira¹, Marianne M Garrido³, Brunna M Alves¹, Claudia Cicala², James Arthos², João P B Viola⁴, Marcelo A Soares^{1

5}

Affiliations

¹ Oncovirology Program, Brazilian National Cancer Institute, Rio de Janeiro, Brazil.
² Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States.
³ Hospital Infection Control Committee, Brazilian National Cancer Institute, Rio de Janeiro, Brazil.
⁴ Immunology and Tumor Biology Program, Brazilian National Cancer Institute, Rio de Janeiro, Brazil.
⁵ Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.

Abstract

Chronically immunosuppressed patients infected with SARS-CoV-2 often experience prolonged virus shedding, and may pave the way to the emergence of mutations that render viral variants of concern (VOC) able to escape immune responses induced by natural infection or by vaccination. We report herein a SARS-CoV-2⁺ cancer patient from the beginning of the COVID-19 pandemic whose virus quasispecies across multiple timepoints carried several immune escape mutations found in more contemporary VOC, such as alpha, delta and omicron, that appeared to be selected for during infection. We hypothesize that immunosuppressed patients may represent the source of VOC seen throughout the COVID-19 pandemics.

Keywords: Nsp6; SARS-CoV2 infection; VOC; deletions/mutations; immunocompromised patient; long term virus shedding; spike.