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Life
Special Issues
An Update on SARS‐CoV‐2: Mutations, Variants, and Their Potential Impact
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An Update on SARS‐CoV‐2: Mutations, Variants, and Their Potential Impact

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Epidemiology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 13664

Special Issue Editors

Dr. Romina Salpini

E-Mail Website
Guest Editor
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Interests: SARS-CoV-2; drug resistance; vaccine escape; HBV chronic infection; HBV reactivation; hepatocellular carcinoma; HIV
Dr. Valentina Svicher

E-Mail Website
Guest Editor
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Interests: SARS-CoV-2; drug resistance; immune escape; HBV chronic infection; HBV reactivation; hepatocellular carcinoma; HIV; HDV
Special Issues, Collections and Topics in MDPI journals
Dr. Mohammad Alkhatib

E-Mail Website
Guest Editor
Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
Interests: SARS-CoV-2; coronaviruses; HCV; genetic variability; HBV markers

Special Issue Information

Dear Colleagues,

Since the beginning of the 21st century, coronaviruses have been considered highly pathogenic and transmissible emerging viruses causing SARS, MERS, and COVID-19. SARS-CoV-2, the etiological agent of COVID-19, is currently undergoing a process of genetic diversification during its spread across humans. An increasing body of evidence highlights that emerging SARS-CoV-2 mutations and variants could play crucial roles in promoting viral evasion from immune responses, including those elicited by vaccination, in hampering the effectiveness of the current diagnostic assays, and in favoring reinfection events. Knowledge about viral mutations and genetic variations can help to better understand viral pathogenicity, immunity, and design of accurate diagnostic assays.

This Special Issue is aimed at providing a comprehensive overview of the key areas of genetic diversification, adaptation, and evolution underlying SARS-CoV-2 infection. Original research, review, clinical reports that afford up-to-date findings in the topics of SARS-CoV-2 viral genetic variation, intergenic co-evolution, geographical adaptation, immune and diagnostic evasion, natural drug resistance, mutational impact on SARS-CoV-2 structural protein stability, and genetic compartmentalization in body districts are of great interest and will be welcome.

Dr. Romina Salpini
Prof. Dr. Valentina Svicher
Dr. Mohammad Alkhatib
Guest Editors

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. Life 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 mutations and variants
  • genetic adaptation
  • genetic conservation and diversification
  • sequence variations
  • coronaviruses
  • phylogenetic analysis
  • mutation impact
  • immune evasion
  • drug resistance
  • 3D structural analysis
  • pandemic

Published Papers (3 papers)

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Research

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10 pages, 697 KiB  
Article
A Rare STXBP2 Mutation in Severe COVID-19 and Secondary Cytokine Storm Syndrome
by Daniel D. Reiff, Mingce Zhang, Emily A. Smitherman, Melissa L. Mannion, Matthew L. Stoll, Peter Weiser and Randy Q. Cron
Life 2022, 12(2), 149; https://doi.org/10.3390/life12020149 - 20 Jan 2022
Cited by 7 | Viewed by 3494
Abstract
Background: Primary (familial) hemophagocytic lymphohistiocytosis (pHLH) is a potentially lethal syndrome of infancy, caused by genetic defects in natural killer (NK) cell and CD8 T cell cytotoxicity, leading to hyperinflammation, elevated cytokine levels, and a disorganized immune response resulting in multi-organ system failure [...] Read more.
Background: Primary (familial) hemophagocytic lymphohistiocytosis (pHLH) is a potentially lethal syndrome of infancy, caused by genetic defects in natural killer (NK) cell and CD8 T cell cytotoxicity, leading to hyperinflammation, elevated cytokine levels, and a disorganized immune response resulting in multi-organ system failure and frequently death. Secondary HLH (sHLH) can be triggered in the setting of malignances, diseases of chronic immune system activation, or by infectious etiologies. While pHLH is usually a result of homozygous gene mutations, monoallelic hypomorphic and dominant-negative mutations in pHLH genes have been implicated in sHLH. Coronavirus disease 2019 (COVID-19) has been an omnipresent viral infection since its arrival, and severe cases can present with cytokine storm and have clinical features and laboratory findings consistent with sHLH. Herein, we report an adolescent with severe COVID-19, decreased NK cell function, and features of sHLH. Her genetic evaluation identified a monoallelic missense mutation in the pHLH gene STXBP2, and NK cell assays of her blood showed decreased cytolysis and degranulation ex vivo. Methods: Patient data was extracted through an electronic medical record review. Using a lentiviral approach, the patient’s STXBP2 mutation and wild-type (WT) STXBP2 were separately transduced into the NK-92 human NK cell line. The WT and mutant STXBP2 transduced NK-92 cells were stimulated with NK-sensitive K562 erythroleukemia target cells in vitro, and NK cell degranulation and cytolysis were measured via CD107a expression and Live/Dead near-IR dye, respectively. Results: Compared to WT STXBP2, the patient’s STXBP2 mutation caused significantly decreased NK cell cytolysis and associated degranulation in vitro. Conclusion: These findings add weight to the hypothesis that some severe cases of COVID-19 may be accompanied by sHLH and hyperinflammation, especially in the setting of heterozygous pHLH genetic mutations. This has implications both diagnostically and therapeutically for severe COVID-19. Full article
(This article belongs to the Special Issue An Update on SARS‐CoV‐2: Mutations, Variants, and Their Potential Impact)
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Review

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22 pages, 1232 KiB  
Review
Emergence of SARS-CoV-2 Variants in the World: How Could This Happen?
by Alfredo Parra-Lucares, Paula Segura, Verónica Rojas, Catalina Pumarino, Gustavo Saint-Pierre and Luis Toro
Life 2022, 12(2), 194; https://doi.org/10.3390/life12020194 - 28 Jan 2022
Cited by 30 | Viewed by 4951
Abstract
The COVID-19 pandemic has had a significant global impact, with more than 280,000,000 people infected and 5,400,000 deaths. The use of personal protective equipment and the anti-SARS-CoV-2 vaccination campaigns have reduced infection and death rates worldwide. However, a recent increase in infection rates [...] Read more.
The COVID-19 pandemic has had a significant global impact, with more than 280,000,000 people infected and 5,400,000 deaths. The use of personal protective equipment and the anti-SARS-CoV-2 vaccination campaigns have reduced infection and death rates worldwide. However, a recent increase in infection rates has been observed associated with the appearance of SARS-CoV-2 variants, including the more recently described lineage B.1.617.2 (Delta variant) and lineage B.1.1.529/BA.1 (Omicron variant). These new variants put the effectiveness of international vaccination at risk, with the appearance of new outbreaks of COVID-19 throughout the world. This emergence of new variants has been due to multiple predisposing factors, including molecular characteristics of the virus, geographic and environmental conditions, and the impact of social determinants of health that favor the genetic diversification of SARS-CoV-2. We present a literature review on the most recent information available on the emergence of new variants of SARS-CoV-2 in the world. We analyzed the biological, geographical, and sociocultural factors that favor the development of these variants. Finally, we evaluate the surveillance strategies for the early detection of new variants and prevent their distribution outside these regions. Full article
(This article belongs to the Special Issue An Update on SARS‐CoV‐2: Mutations, Variants, and Their Potential Impact)
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Other

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21 pages, 1403 KiB  
Systematic Review
SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review
by Indira R. Mendiola-Pastrana, Eduardo López-Ortiz, José G. Río de la Loza-Zamora, James González, Anel Gómez-García and Geovani López-Ortiz
Life 2022, 12(2), 170; https://doi.org/10.3390/life12020170 - 25 Jan 2022
Cited by 37 | Viewed by 4352
Abstract
Background: From the start of the COVID-19 pandemic, new SARS-CoV-2 variants have emerged that potentially affect transmissibility, severity, and immune evasion in infected individuals. In the present systematic review, the impact of different SARS-CoV-2 variants on clinical outcomes is analyzed. Methods: A systematic [...] Read more.
Background: From the start of the COVID-19 pandemic, new SARS-CoV-2 variants have emerged that potentially affect transmissibility, severity, and immune evasion in infected individuals. In the present systematic review, the impact of different SARS-CoV-2 variants on clinical outcomes is analyzed. Methods: A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020. Two databases (PubMed and ScienceDirect) were searched for original articles published from 1 January 2020 to 23 November 2021. The articles that met the selection criteria were appraised according to the Newcastle–Ottawa Quality Assessment Scale. Results: Thirty-three articles were included, involving a total of 253,209 patients and 188,944 partial or complete SARS-CoV-2 sequences. The most reported SARS-CoV-2 variants showed changes in the spike protein, N protein, RdRp and NSP3. In 28 scenarios, SARS-CoV-2 variants were found to be associated with a mild to severe or even fatal clinical outcome, 15 articles reported such association to be statistically significant. Adjustments in eight of them were made for age, sex and other covariates. Conclusions: SARS-CoV-2 variants can potentially have an impact on clinical outcomes; future studies focused on this topic should consider several covariates that influence the clinical course of the disease. Full article
(This article belongs to the Special Issue An Update on SARS‐CoV‐2: Mutations, Variants, and Their Potential Impact)
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