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Viruses
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Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks
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Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viral Immunology, Vaccines, and Antivirals".

Deadline for manuscript submissions: closed (15 October 2024) | Viewed by 12169

Special Issue Editor

Prof. Dr. Jacques Fantini

E-Mail Website
Guest Editor
Department of Biology, Faculty of Medicine, University of Aix-Marseille, INSERM UMR_S 1072, 13015 Marseille, France
Interests: virus-host interactions; lipid rafts; gangliosides; virus receptors; RNA viruses; SARS-CoV-2 variants; antivirals; vaccines
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The COVID-19 pandemic has taught us a lot on public health strategies. Viruses mutate, spread among animal hosts in which they evolve, and sometimes acquire the capacity to infect humans. RNA viruses have exceptional mutational potential, producing a myriad of variants and quasispecies with potentially devastating pathogenic effects. DNA viruses are not left out, as evidenced by the recent detection of an abnormally high number of cases of the Monkeypox virus in Europe and in the USA. Faced with these acute public health problems, we must adapt therapeutic and vaccine strategies, design new ones, and, like viruses, we must constantly innovate. Our objective is to publish a series of articles on the mechanisms of infection of pathogenic viruses, including SARS-CoV-2 and its variants, influenza virus, Monkeypox virus or Nipah virus, and on the rational design of new prophylactic and therapeutic approaches. We hope to stimulate innovative ideas for vaccines and antiviral treatments capable of providing rapid responses in the event of new outbreaks. Research articles, reviews and perspectives are welcomed for this Special Issue.

Prof. Dr. Jacques Fantini
Guest Editor

Manuscript Submission Information

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Keywords

  • SARS-CoV-2 variants
  • Monkeypox virus
  • Nipah virus
  • virus–host interactions
  • antivirals
  • vaccines
  • mutations
  • lipid rafts
  • virus receptors
  • immune escape

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Published Papers (5 papers)

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Research

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11 pages, 1455 KiB  
Article
Modeling the Dynamic of Multiwave Diseases: The Model of Hand, Foot and Mouth Disease
by Patrice Ravel, Nghia Ngu Duy, Guilhem Kister, Le Thi Song Huong, Ankit Dwivedi, Christian A. Devaux, Tran Nhu Duong, Nguyen Tran Hien, Laurent Gavotte, Emmanuel Cornillot and Roger Frutos
Viruses 2024, 16(8), 1217; https://doi.org/10.3390/v16081217 - 29 Jul 2024
Viewed by 688
Abstract
An HFMD outbreak spread over the city of Hải Phòng from summer 2011 to autumn 2012. This epidemic was chosen because it was the very first HFMD epidemic in North Vietnam, eliminating thus interferences with previous outbreaks. This epidemic displayed three separate waves. [...] Read more.
An HFMD outbreak spread over the city of Hải Phòng from summer 2011 to autumn 2012. This epidemic was chosen because it was the very first HFMD epidemic in North Vietnam, eliminating thus interferences with previous outbreaks. This epidemic displayed three separate waves. A complete dataset was collected for more than 9500 patients during this period, which enabled us to analyze this epidemic at different scales. Access to the healthcare system was crucial during this period, which was possible due to a reorganization of the system in February–March 2012. An analysis at the commune level enabled us to track the epidemic along certain communication routes. The three-waves structure reveals a wide disparity at the district level. We developed a mathematical model showing high accuracy at the adjustment of data for both the total number of cases and for the number of cases per week. As a consequence, the model was able to accurately determine the dates of the beginning and end of each wave and to show that they overlapped. Using mathematical functions associated with this model, it was possible to calculate the probability for a patient to belong to a specific wave. Full article
(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)
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22 pages, 11640 KiB  
Article
A T-Cell-Derived 3-Gene Signature Distinguishes SARS-CoV-2 from Common Respiratory Viruses
by Yang Li, Xinya Tao, Sheng Ye, Qianchen Tai, Yu-Ang You, Xinting Huang, Mifang Liang, Kai Wang, Haiyan Wen, Chong You, Yan Zhang and Xiaohua Zhou
Viruses 2024, 16(7), 1029; https://doi.org/10.3390/v16071029 - 26 Jun 2024
Viewed by 4336
Abstract
Research on the host responses to respiratory viruses could help develop effective interventions and therapies against the current and future pandemics from the host perspective. To explore the pathogenesis that distinguishes SARS-CoV-2 infections from other respiratory viruses, we performed a multi-cohort analysis with [...] Read more.
Research on the host responses to respiratory viruses could help develop effective interventions and therapies against the current and future pandemics from the host perspective. To explore the pathogenesis that distinguishes SARS-CoV-2 infections from other respiratory viruses, we performed a multi-cohort analysis with integrated bioinformatics and machine learning. We collected 3730 blood samples from both asymptomatic and symptomatic individuals infected with SARS-CoV-2, seasonal human coronavirus (sHCoVs), influenza virus (IFV), respiratory syncytial virus (RSV), or human rhinovirus (HRV) across 15 cohorts. First, we identified an enhanced cellular immune response but limited interferon activities in SARS-CoV-2 infection, especially in asymptomatic cases. Second, we identified a SARS-CoV-2-specific 3-gene signature (CLSPN, RBBP6, CCDC91) that was predominantly expressed by T cells, could distinguish SARS-CoV-2 infection, including Omicron, from other common respiratory viruses regardless of symptoms, and was predictive of SARS-CoV-2 infection before detectable viral RNA on RT-PCR testing in a longitude follow-up study. Thereafter, a user-friendly online tool, based on datasets collected here, was developed for querying a gene of interest across multiple viral infections. Our results not only identify a unique host response to the viral pathogenesis in SARS-CoV-2 but also provide insights into developing effective tools against viral pandemics from the host perspective. Full article
(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)
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15 pages, 8013 KiB  
Article
An In Silico Analysis of PCR-Based Monkeypox Virus Detection Assays: A Case Study for Ongoing Clinical Surveillance
by Kuncheng Song, Hayden N. Brochu, Qimin Zhang, Jonathan D. Williams and Lakshmanan K. Iyer
Viruses 2023, 15(12), 2327; https://doi.org/10.3390/v15122327 - 27 Nov 2023
Cited by 1 | Viewed by 2582
Abstract
The 2022 global Mpox outbreak swiftly introduced unforeseen diversity in the monkeypox virus (MPXV) population, resulting in numerous Clade IIb sublineages. This propagation of new MPXV mutations warrants the thorough re-investigation of previously recommended or validated primers designed to target MPXV genomes. In [...] Read more.
The 2022 global Mpox outbreak swiftly introduced unforeseen diversity in the monkeypox virus (MPXV) population, resulting in numerous Clade IIb sublineages. This propagation of new MPXV mutations warrants the thorough re-investigation of previously recommended or validated primers designed to target MPXV genomes. In this study, we explored 18 PCR primer sets and examined their binding specificity against 5210 MPXV genomes, representing all the established MPXV lineages. Our results indicated that only five primer sets resulted in almost all perfect matches against the targeted MPXV lineages, and the remaining primer sets all contained 1–2 mismatches against almost all the MPXV lineages. We further investigated the mismatched primer-genome pairs and discovered that some of the primers overlapped with poorly sequenced and assembled regions of the MPXV genomes, which are consistent across multiple lineages. However, we identified 173 99% genome-wide conserved regions across all 5210 MPXV genomes, representing 30 lineages/clades with at least 80% lineage-specific consensus for future primer development and primer binding evaluation. This exercise is crucial to ensure that the current detection schemes are robust and serve as a framework for primer evaluation in clinical testing development for other infectious diseases. Full article
(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)
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Review

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12 pages, 1028 KiB  
Review
Breaking the Barrier: SARS-CoV-2 Infections in Wild and Companion Animals and Their Implications for Public Health
by Zhandos Abay, Sandugash Sadikaliyeva, Ainur Nurpeisova, Kuanysh Jekebekov, Kamshat Shorayeva, Bolat Yespembetov, Sergazy Nurabayev, Aslan Kerimbayev, Berik Khairullin, Hansang Yoo, Lespek Kutumbetov, Markhabat Kassenov and Kunsulu Zakarya
Viruses 2024, 16(6), 956; https://doi.org/10.3390/v16060956 - 13 Jun 2024
Cited by 2 | Viewed by 1280
Abstract
The emergence of the novel coronavirus SARS-CoV-2 has led to significant interest in its potential transmission between animals and humans, especially pets. This review article summarises the literature on coronavirus infections in domestic animals, emphasising epidemiology, transmission dynamics, clinical manifestations, and public health [...] Read more.
The emergence of the novel coronavirus SARS-CoV-2 has led to significant interest in its potential transmission between animals and humans, especially pets. This review article summarises the literature on coronavirus infections in domestic animals, emphasising epidemiology, transmission dynamics, clinical manifestations, and public health implications. This article highlights current understandings of the relationship between infections in companion animals and humans, identifies research gaps, and suggests directions for future research. Cases of disease in cats, dogs, and other domestic animals, often occurring through close contact with infected owners, are reviewed, raising concerns about possible zoonotic and reverse zoonotic transmission. Precautions and recommendations for pet owners and healthcare workers are also discussed. The scientific evidence presented in the article highlights the need for a One Health approach that considers the health of people, animals, and the environment to combat future pandemics. Full article
(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)
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Other

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23 pages, 942 KiB  
Systematic Review
Epidemiological and Clinical Characteristics of Mpox in Cisgender and Transgender Women and Non-Binary Individuals Assigned to the Female Sex at Birth: A Comprehensive, Critical Global Perspective
by Nicola Luigi Bragazzi, Woldegebriel Assefa Woldegerima, Jianhong Wu, Manlio Converti, Lukasz Szarpak, Andrea Crapanzano, Marwan Odeh, Raymond Farah and Rola Khamisy-Farah
Viruses 2024, 16(3), 325; https://doi.org/10.3390/v16030325 - 21 Feb 2024
Cited by 3 | Viewed by 2510
Abstract
The 2022–2023 Mpox multi-country outbreak, identified in over 110 WHO Member States, revealed a predominant impact on cisgender men, particularly those engaging in sex with men, while less frequently affecting women. This disparity prompted a focused investigation into the gender-specific characteristics of Mpox [...] Read more.
The 2022–2023 Mpox multi-country outbreak, identified in over 110 WHO Member States, revealed a predominant impact on cisgender men, particularly those engaging in sex with men, while less frequently affecting women. This disparity prompted a focused investigation into the gender-specific characteristics of Mpox infections, particularly among women, to address a notable knowledge gap. This review systematically gathers and analyzes the scientific literature and case reports concerning Mpox infections in women, covering a broad geographical spectrum including regions such as Argentina, Brazil, Colombia, Nigeria, Europe, Vietnam, and the United States. The analysis delves into various aspects of Mpox in women, including clinical features, epidemiology, psychological impacts, preparedness strategies, and case studies, with particular attention to pregnant women and those with underlying health conditions. Empirical data from multiple studies underscore the unique epidemiological and clinical patterns of Mpox in women. In the United States, a small percentage of Mpox cases were reported among cisgender women, with a notable portion involving non-Hispanic Black or African American, non-Hispanic White, and Hispanic or Latino ethnicities. The primary transmission route was identified as sexual or close intimate contact, with the virus predominantly manifesting on the legs, arms, and genital areas. Further, a study in Spain highlighted significant disparities in diagnosis delays, transmission modes, and clinical manifestations between genders, indicating a different risk profile and disease progression in women. Additionally, a case from Vietnam, linked to a new Mpox sub-lineage in women, emphasized the role of women in the transmission dynamics and the importance of genomic monitoring. This review emphasizes the necessity for inclusive surveillance and research to fully understand Mpox dynamics across diverse population groups, including women. Highlighting gender and sexual orientation in public health responses is crucial for an effective approach to managing the spread and impact of this disease. The findings advocate for a gender-diverse assessment in health services and further research to explore the nuances of Mpox transmission, behavior, and progression among different groups, thereby enhancing the global response to Mpox and similar public health challenges. Full article
(This article belongs to the Special Issue Advanced Strategies against SARS-CoV-2 Variants and Future Emerging Virus Outbreaks)
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