Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency

Nathan M Markarian; Gaël Galli; Dhanesh Patel; Mark Hemmings; Priya Nagpal; Albert M Berghuis; Levon Abrahamyan; Silvia M Vidal

doi:10.3389/fmicb.2022.933983

Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency

Front Microbiol. 2022 Jul 1:13:933983. doi: 10.3389/fmicb.2022.933983. eCollection 2022.

Authors

Nathan M Markarian^{1

2

3}, Gaël Galli^{2

4

5

6}, Dhanesh Patel^{1

2}, Mark Hemmings⁷, Priya Nagpal⁸, Albert M Berghuis⁷, Levon Abrahamyan³, Silvia M Vidal^{1

2}

Affiliations

¹ Department of Human Genetics, McGill University, Montréal, QC, Canada.
² McGill University Research Centre on Complex Traits, Montréal, QC, Canada.
³ Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada.
⁴ Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.
⁵ CNRS, ImmunoConcEpT, UMR 5164, Université de Bordeaux, Bordeaux, France.
⁶ CHU de Bordeaux, FHU ACRONIM, Centre National de Référence des Maladies Auto-Immunes et Systémiques Rares Est/Sud-Ouest, Bordeaux, France.
⁷ Department of Biochemistry, McGill University, Montréal, QC, Canada.
⁸ Department of Pharmacology, McGill University, Montréal, QC, Canada.

Abstract

Since the end of 2019, the world has been challenged by the coronavirus disease 2019 (COVID-19) pandemic. With COVID-19 cases rising globally, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, resulting in the emergence of variants of interest (VOI) and of concern (VOC). Of the hundreds of millions infected, immunodeficient patients are one of the vulnerable cohorts that are most susceptible to this virus. These individuals include those with preexisting health conditions and/or those undergoing immunosuppressive treatment (secondary immunodeficiency). In these cases, several researchers have reported chronic infections in the presence of anti-COVID-19 treatments that may potentially lead to the evolution of the virus within the host. Such variations occurred in a variety of viral proteins, including key structural ones involved in pathogenesis such as spike proteins. Tracking and comparing such mutations with those arisen in the general population may provide information about functional sites within the SARS-CoV-2 genome. In this study, we reviewed the current literature regarding the specific features of SARS-CoV-2 evolution in immunocompromised patients and identified recurrent de novo amino acid changes in virus isolates of these patients that can potentially play an important role in SARS-CoV-2 pathogenesis and evolution.

Keywords: COVID-19; SARS-CoV-2; mutations; secondary immunodeficiency; spike protein; viral evolution.

Publication types

Review