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Molecular Epidemiology of SARS-CoV-2, 3rd Edition
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Molecular Epidemiology of SARS-CoV-2, 3rd Edition

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 2233

Special Issue Editor

Dr. Marta Giovanetti

E-Mail Website
Guest Editor
1. Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte 30.190-009, Minas Gerais, Brazil 2. Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, 00128 Rome, Italy
Interests: phylogenetic; phylodynamic; molecular evolution; genomic surveillance; WGS; emerging and re-emerging viral pathogens
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the course of the SARS-CoV-2 pandemic, extensive global sustained transmission allowed for the evolution of the virus, leading to the emergence of the so-called ‘variants of concern’ (VOCs). These VOCs are characterized by several lineage-specific mutations that are suggested to impact viral transmissibility, resistance to neutralizing antibodies, and virulence. The identification of such variants has recently challenged public health authorities in terms of tracking transmission and mitigating the impact of the ongoing pandemic. This Special Issue will provide new genomic data on the SARS-CoV-2 strains circulating worldwide and present an overview of the real-time global evolution of SARS-CoV-2.

Dr. Marta Giovanetti
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
  • genomic monitoring
  • phylodynamic
  • molecular epidemiology

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Published Papers (4 papers)

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Research

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12 pages, 5072 KiB  
Article
Mutations in the Receptor Binding Domain of Severe Acute Respiratory Coronavirus-2 Omicron Variant Spike Protein Significantly Stabilizes Its Conformation
by Michael H. Peters
Viruses 2024, 16(6), 912; https://doi.org/10.3390/v16060912 - 4 Jun 2024
Viewed by 151
Abstract
The Omicron variant and its sub-lineages are the only current circulating SARS-CoV-2 viruses worldwide. In this study, the conformational stability of the isolated Receptor Binding Domain (RBD) of Omicron’s spike protein is examined in detail. The parent Omicron lineage has over ten mutations [...] Read more.
The Omicron variant and its sub-lineages are the only current circulating SARS-CoV-2 viruses worldwide. In this study, the conformational stability of the isolated Receptor Binding Domain (RBD) of Omicron’s spike protein is examined in detail. The parent Omicron lineage has over ten mutations in the ACE2 binding region of the RBD that are specifically associated with its β hairpin loop domain. It is demonstrated through biophysical molecular computations that the mutations in the β hairpin loop domain significantly increase the intra-protein interaction energies of intra-loop and loop–RBD interactions. The interaction energy increases include the formation of new hydrogen bonds in the β hairpin loop domain that help stabilize this critical ACE2 binding region. Our results also agree with recent experiments on the stability of Omicron’s core β barrel domain, outside of its loop domain, and help demonstrate the overall conformational stability of the Omicron RBD. It is further shown here through dynamic simulations that the unbound state of the Omicron RBD remains closely aligned with the bound state configuration, which was not observed for the wild-type RBD. Overall, these studies demonstrate the significantly increased conformational stability of Omicron over its wild-type configuration and raise a number of questions on whether conformational stability could be a positive selection feature of SARS-CoV-2 viral mutational changes. Full article
(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 3rd Edition)
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22 pages, 4111 KiB  
Article
Exploring Cannabinoids as Potential Inhibitors of SARS-CoV-2 Papain-like Protease: Insights from Computational Analysis and Molecular Dynamics Simulations
by Jamie Holmes, Shahidul M. Islam and Kimberly A. Milligan
Viruses 2024, 16(6), 878; https://doi.org/10.3390/v16060878 - 30 May 2024
Viewed by 288
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a global COVID-19 pandemic, challenging healthcare systems worldwide. Effective therapeutic strategies against this novel coronavirus remain limited, underscoring the urgent need for innovative approaches. The present research investigates the potential [...] Read more.
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a global COVID-19 pandemic, challenging healthcare systems worldwide. Effective therapeutic strategies against this novel coronavirus remain limited, underscoring the urgent need for innovative approaches. The present research investigates the potential of cannabis compounds as therapeutic agents against SARS-CoV-2 through their interaction with the virus’s papain-like protease (PLpro) protein, a crucial element in viral replication and immune evasion. Computational methods, including molecular docking and molecular dynamics (MD) simulations, were employed to screen cannabis compounds against PLpro and analyze their binding mechanisms and interaction patterns. The results showed cannabinoids with binding affinities ranging from −6.1 kcal/mol to −4.6 kcal/mol, forming interactions with PLpro. Notably, Cannabigerolic and Cannabidiolic acids exhibited strong binding contacts with critical residues in PLpro’s active region, indicating their potential as viral replication inhibitors. MD simulations revealed the dynamic behavior of cannabinoid–PLpro complexes, highlighting stable binding conformations and conformational changes over time. These findings shed light on the mechanisms underlying cannabis interaction with SARS-CoV-2 PLpro, aiding in the rational design of antiviral therapies. Future research will focus on experimental validation, optimizing binding affinity and selectivity, and preclinical assessments to develop effective treatments against COVID-19. Full article
(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 3rd Edition)
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15 pages, 2838 KiB  
Article
Distribution of SARS-CoV-2 Genomes in Wastewaters and the Associated Potential Infection Risk for Plant Workers in Typical Urban and Peri-Urban Communities of the Buffalo City Region, South Africa
by Balisa Ngqwala, Luyanda Msolo, Kingsley Ehi Ebomah, Nolonwabo Nontongana and Anthony Ifeanyi Okoh
Viruses 2024, 16(6), 871; https://doi.org/10.3390/v16060871 - 29 May 2024
Viewed by 208
Abstract
The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater has been reported in several studies and similar research can be used as a proxy for an early warning of potential Coronavirus disease 2019 (COVID-19) outbreaks. This study focused on profiling [...] Read more.
The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater has been reported in several studies and similar research can be used as a proxy for an early warning of potential Coronavirus disease 2019 (COVID-19) outbreaks. This study focused on profiling the incidence of SARS-CoV-2 genomes in wastewater samples obtained from facilities located in the Buffalo City Municipality. Raw samples were collected weekly using the grab technique for a period of 48 weeks. Ribonucleic acids were extracted from the samples, using the QIAGEN Powersoil Total RNA Extraction kit, and extracted RNA samples were further profiled for the presence of SARS-CoV-2 genomes using Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) technique. Furthermore, various environmental matrices were utilized to estimate the potential health risk to plant operators associated with exposure to SARS-CoV-2 viral particles using the quantitative microbiological risk assessment (QMRA) model. Our findings revealed the prevalence of SARS-CoV-2 genomes with concentrations that ranged from 0.22 × 103 to 17.60 × 103 genome copies per milliliter (GC/mL). Different exposure scenarios were employed for the QMRA model, and the findings indicate a probability of infection (P(i)) ranging from 0.93% to 37.81% across the study sites. Similarly, the P(i) was highly significant (p < 0.001) for the 20 mL volumetric intake as compared to other volumetric intake scenarios, and high P(i) was also observed in spring, autumn, and winter for all WWTPs. The P(i) was significantly different (p < 0.05) with respect to the different seasons and with respect to different volume scenarios. Full article
(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 3rd Edition)
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Review

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19 pages, 1768 KiB  
Review
SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies
by Hailong Guo, Sha Ha, Jason W. Botten, Kai Xu, Ningyan Zhang, Zhiqiang An, William R. Strohl, John W. Shiver and Tong-Ming Fu
Viruses 2024, 16(5), 697; https://doi.org/10.3390/v16050697 - 28 Apr 2024
Viewed by 1154
Abstract
Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative [...] Read more.
Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection. Full article
(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 3rd Edition)
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