SARS-CoV-2 Variants, Vaccines, and Immune Responses

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Coronaviruses".

Deadline for manuscript submissions: closed (31 January 2025) | Viewed by 667

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Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Siena, Italy
Interests: innate immunity; antagonistic proteins; arboviruses; vaccines
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Special Issue Information

Dear Colleagues,

Our immune system responds promptly to the attack of pathogens in order to limit their spread in the body and prevent the development of disease. However, several factors affect the immune system’s efficiency. Virus genetic evolution, which determines antigenic variations, causes virus’ escape from the host’s acquired immunity, such as that induced by vaccines. A striking example of recent days is SARS-CoV-2, whose extremely rapid genetic evolution has led to the emergence of viral variants capable of escaping vaccine protection. In this Special Issue, researches highlighting the relationship between SARS-CoV-2 and host immune responses, mechanisms for enhancing SARS-CoV-2 immunity, or the viral escape strategies from the immune system to induce symptomatic infection are welcome.

You may choose our Joint Special Issue in Vaccines.

Dr. Gianni Gori Savellini
Guest Editor

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Keywords

  • acquired immunity
  • vaccine
  • virus escape
  • virus evolution
  • SARS-CoV-2 variants

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Published Papers (1 paper)

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Research

19 pages, 3982 KiB  
Article
Comparative Interactome Profiling of Nonstructural Protein 3 Across SARS-CoV-2 Variants Emerged During the COVID-19 Pandemic
by Valeria Garcia Lopez and Lars Plate
Viruses 2025, 17(3), 447; https://doi.org/10.3390/v17030447 - 20 Mar 2025
Viewed by 445
Abstract
SARS-CoV-2 virus and its variants remain a global health threat, due to their capacity for rapid evolution. Variants throughout the COVID-19 pandemic exhibited variations in virulence, impacting vaccine protection and disease severity. Investigating nonstructural protein variants is critical to understanding viral evolution and [...] Read more.
SARS-CoV-2 virus and its variants remain a global health threat, due to their capacity for rapid evolution. Variants throughout the COVID-19 pandemic exhibited variations in virulence, impacting vaccine protection and disease severity. Investigating nonstructural protein variants is critical to understanding viral evolution and manipulation of host protein interactions. We focus on nonstructural protein 3 (nsp3), with multiple domains with different activities, including viral polyprotein cleavage, host deubiquitylation, de-ISGylation, and double-membrane vesicle formation. Using affinity purification–mass spectrometry (AP-MS), we identify differential protein interactions in nsp3 caused by mutations found in variants identified between 2019 and 2024: Alpha 20I, Beta 20H, Delta 21I, Delta 21J, Gamma 20J, Kappa 21B, Lambda 21G, Omicron 21K, and Omicron 21L. A small set of amino acid substitutions in the N-terminal region of nsp3 (nsp3.1) could be traced to increased interactions with RNA-binding proteins, which are vital in viral replication. Meanwhile, variants of the central region of nsp3 (nsp3.2) were found to share interactions with protein quality control machinery, including ER-associated degradation. In this construct, shared trends in interactor enrichment are observed between Omicron 21K and Delta 21I. These results underscore how minor mutations reshape host interactions, emphasizing the evolutionary arms race between the host and virus. We provide a roadmap to track the interaction changes driven by SARS-CoV-2 variant evolution. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variants, Vaccines, and Immune Responses)
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