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Viruses
Special Issues
Emerging Variants of SARS-CoV-2
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Emerging Variants of SARS-CoV-2

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

Deadline for manuscript submissions: 31 March 2025 | Viewed by 1505

Special Issue Editor

Dr. Pengfei Wang

E-Mail Website
Guest Editor
State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, China
Interests: coronavirus; HIV-1; antibody; vaccine
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The SARS-CoV-2 virus has undergone substantial evolution, leading to new variants such as JN.1 and KP.2, among others. These new variants continue to shape the trajectory of the COVID-19 pandemic, underscoring the need for continuous monitoring and adaptive response strategies to effectively address their challenges. These variants can significantly impact transmission, disease severity, and immune evasion, necessitating ongoing research to understand and mitigate their effects.

Last year, we successfully organized the Special Issue "Recombinant Variants of SARS-CoV-2," which published six papers. In this reopened Special Issue, "Emerging Variants of SARS-CoV-2," we invite original research articles and reviews exploring the dynamics and implications of newly emerging variants. This includes, but is not limited to:

  • The evolution and epidemiology of emerging SARS-CoV-2 variants.
  • Real-time assessment of the risk posed by new variants.
  • Virological characteristics of emerging variants, including transmissibility, immune evasion, ACE2 binding affinity, infectivity, fusogenicity, structural information, and pathogenicity in animal models.
  • Development and efficacy of vaccines, antibodies, and drugs against new SARS-CoV-2 variants.

Your contributions will be instrumental in advancing our understanding of these emerging threats and informing public health strategies. I look forward to your valuable submissions.

Dr. Pengfei Wang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SARS-CoV-2
  • variants
  • evolution and epidemiology
  • immune evasion
  • ACE2
  • structure
  • vaccines
  • antibodies
  • drugs

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Published Papers (1 paper)

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Research

37 pages, 6270 KiB  
Article
AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance
by Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta and Gennady Verkhivker
Viruses 2024, 16(9), 1458; https://doi.org/10.3390/v16091458 - 13 Sep 2024
Viewed by 1358
Abstract
The most recent wave of SARS-CoV-2 Omicron variants descending from BA.2 and BA.2.86 exhibited improved viral growth and fitness due to convergent evolution of functional hotspots. These hotspots operate in tandem to optimize both receptor binding for effective infection and immune evasion efficiency, [...] Read more.
The most recent wave of SARS-CoV-2 Omicron variants descending from BA.2 and BA.2.86 exhibited improved viral growth and fitness due to convergent evolution of functional hotspots. These hotspots operate in tandem to optimize both receptor binding for effective infection and immune evasion efficiency, thereby maintaining overall viral fitness. The lack of molecular details on structure, dynamics and binding energetics of the latest FLiRT and FLuQE variants with the ACE2 receptor and antibodies provides a considerable challenge that is explored in this study. We combined AlphaFold2-based atomistic predictions of structures and conformational ensembles of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the most dominant Omicron variants JN.1, KP.1, KP.2 and KP.3 to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and computations of binding affinities, we identified binding energy hotspots and characterized the molecular basis underlying epistatic couplings between convergent mutational hotspots. The results suggested the existence of epistatic interactions between convergent mutational sites at L455, F456, Q493 positions that protect and restore ACE2-binding affinity while conferring beneficial immune escape. To examine immune escape mechanisms, we performed structure-based mutational profiling of the spike protein binding with several classes of antibodies that displayed impaired neutralization against BA.2.86, JN.1, KP.2 and KP.3. The results confirmed the experimental data that JN.1, KP.2 and KP.3 harboring the L455S and F456L mutations can significantly impair the neutralizing activity of class 1 monoclonal antibodies, while the epistatic effects mediated by F456L can facilitate the subsequent convergence of Q493E changes to rescue ACE2 binding. Structural and energetic analysis provided a rationale to the experimental results showing that BD55-5840 and BD55-5514 antibodies that bind to different binding epitopes can retain neutralizing efficacy against all examined variants BA.2.86, JN.1, KP.2 and KP.3. The results support the notion that evolution of Omicron variants may favor emergence of lineages with beneficial combinations of mutations involving mediators of epistatic couplings that control balance of high ACE2 affinity and immune evasion. Full article
(This article belongs to the Special Issue Emerging Variants of SARS-CoV-2)
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