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Microorganisms
Special Issues
SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines, Second Edition
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SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines, Second Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Public Health Microbiology".

Deadline for manuscript submissions: closed (31 July 2024) | Viewed by 133318

Special Issue Editor

Dr. Rana Abdelnabi

E-Mail Website
Guest Editor
Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
Interests: antivirals and animals models for emerging viruses including SARS-CoV-2
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue, entitled “SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines”.

Almost two years after the emergence of SAR-CoV-2, more than 330 million cases of infection and 5.5 million fatal cases have been reported worldwide. Since the end of 2020, new SARS-CoV-2 variants of concern (VOCs) have been emerging worldwide. These variants present new challenges to the control of the COVID-19 pandemic by greatly threatening the efficacies of available monoclonal antibody therapies and vaccines, which have been developed to target the parent strain of SARS-CoV-2. Therefore, continued efforts are required to evaluate the efficacy of currently available and newly developed therapeutics and vaccines against SARS-CoV-2 (including new variants) in relevant infection models in order to contain and combat this virus efficiently.

Therefore, the aim of this Special Issue is to provide a collection of articles that highlight recent advancements in the battle against the SARS-CoV-2 pandemic. As the Guest Editor of this Special Issue, I invite you to submit research articles, review articles, and short communications related to SARS-CoV-2 infection models and the development of therapeutics and vaccines for use against this virus.

I look forward to receiving your contributions.

Dr. Rana Abdelnabi
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. Microorganisms 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 2700 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
  • animal models
  • antivirals
  • vaccine
  • monoclonal antibodies
  • assay models

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Published Papers (5 papers)

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Research

14 pages, 1822 KiB  
Article
Antigenic Imprinting Dominates Humoral Responses to New Variants of SARS-CoV-2 in a Hamster Model of COVID-19
by Joran Degryse, Elke Maas, Ria Lassaunière, Katrien Geerts, Yana Kumpanenko, Birgit Weynand, Piet Maes, Johan Neyts, Hendrik Jan Thibaut, Yeranddy A. Alpizar and Kai Dallmeier
Microorganisms 2024, 12(12), 2591; https://doi.org/10.3390/microorganisms12122591 - 14 Dec 2024
Cited by 1 | Viewed by 1481
Abstract
The emergence of SARS-CoV-2 variants escaping immunity challenges the efficacy of current vaccines. Here, we investigated humoral recall responses and vaccine-mediated protection in Syrian hamsters immunized with the third-generation Comirnaty® Omicron XBB.1.5-adapted COVID-19 mRNA vaccine, followed by infection with either antigenically closely [...] Read more.
The emergence of SARS-CoV-2 variants escaping immunity challenges the efficacy of current vaccines. Here, we investigated humoral recall responses and vaccine-mediated protection in Syrian hamsters immunized with the third-generation Comirnaty® Omicron XBB.1.5-adapted COVID-19 mRNA vaccine, followed by infection with either antigenically closely (EG.5.1) or distantly related (JN.1) Omicron subvariants. Vaccination with the YF17D vector encoding a modified Gamma spike (YF-S0*) served as a control for SARS-CoV-2 immunity restricted to pre-Omicron variants. Our results show that both Comirnaty® XBB.1.5 and YF-S0* induce robust, however, poorly cross-reactive, neutralizing antibody (nAb) responses. In either case, total antibody and nAb levels increased following infection. Intriguingly, the specificity of these boosted nAbs did not match the respective challenge virus, but was skewed towards the primary antigen used for immunization, suggesting a marked impact of antigenic imprinting, confirmed by antigenic cartography. Furthermore, limited cross-reactivity and rapid decline in nAbs induced by Comirnaty® XBB.1.5 with EG.5.1 and, more concerning, JN.1, raises doubts about sustained vaccine efficacy against recent circulating Omicron subvariants. In conclusion, we demonstrate that antigenic imprinting plays a dominant role in shaping humoral immunity against emerging SARS-CoV-2 variants. Future vaccine design may have to address two major issues: (i) overcoming original antigenic sin that limits the breadth of a protective response towards emerging variants, and (ii) achieving sustained immunity that lasts for at least one season. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines, Second Edition)
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11 pages, 897 KiB  
Article
Comparable Efficacy of Lopinavir/Ritonavir and Remdesivir in Reducing Viral Load and Shedding Duration in Patients with COVID-19
by Choon-Mee Kim, Jae Keun Chung, Sadia Tamanna, Mi-Seon Bang, Misbah Tariq, You Mi Lee, Jun-Won Seo, Da Young Kim, Na Ra Yun, Jinjong Seo, Yuri Kim, Min Ji Kim, Dong-Min Kim and Nam-Hyuk Cho
Microorganisms 2024, 12(8), 1696; https://doi.org/10.3390/microorganisms12081696 - 16 Aug 2024
Cited by 3 | Viewed by 1575
Abstract
The spread of COVID-19 has significantly increased research on antiviral drugs and measures such as case isolation and contact tracing. This study compared the effects of lopinavir/ritonavir and remdesivir on COVID-19 patients with a control group receiving no antiviral drugs. Patients confirmed to [...] Read more.
The spread of COVID-19 has significantly increased research on antiviral drugs and measures such as case isolation and contact tracing. This study compared the effects of lopinavir/ritonavir and remdesivir on COVID-19 patients with a control group receiving no antiviral drugs. Patients confirmed to have a SARS-CoV-2 infection via real-time RT-PCR were divided into three groups: lopinavir/ritonavir, remdesivir, and control. We assessed the efficacy of these drugs in reducing viral load and viral shedding duration using real-time RT-PCR and Vero E6 cell cultures. Lopinavir/ritonavir led to no detectable infectious SARS-CoV-2, with a median viral clearance time of one day, whereas one remdesivir-treated case remained culture-positive until day 12. Lopinavir/ritonavir significantly reduced viral load compared to remdesivir and control groups (p = 0.0117 and p = 0.0478). No infectious virus was detected in the lopinavir/ritonavir group, and the non-infectious SARS-CoV-2 proportion remained constant at 90%, higher than in the remdesivir and control groups (p = 0.0097). There was a significant difference in culture positivity among the groups (p = 0.0234), particularly between the lopinavir/ritonavir and remdesivir groups (p = 0.0267). These findings suggest that lopinavir/ritonavir reduces viral load and shortens the viral shedding duration compared to remdesivir, despite not being an effective treatment option. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines, Second Edition)
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Figure 1

16 pages, 263 KiB  
Article
A Critical Analysis of All-Cause Deaths during COVID-19 Vaccination in an Italian Province
by Marco Alessandria, Giovanni M. Malatesta, Franco Berrino and Alberto Donzelli
Microorganisms 2024, 12(7), 1343; https://doi.org/10.3390/microorganisms12071343 - 30 Jun 2024
Cited by 5 | Viewed by 125631
Abstract
Immortal time bias (ITB) is common in cohort studies and distorts the association estimates between the treated and untreated. We used data from an Italian study on COVID-19 vaccine effectiveness, with a large cohort, long follow-up, and adjustment for confounding factors, affected by [...] Read more.
Immortal time bias (ITB) is common in cohort studies and distorts the association estimates between the treated and untreated. We used data from an Italian study on COVID-19 vaccine effectiveness, with a large cohort, long follow-up, and adjustment for confounding factors, affected by ITB, with the aim to verify the real impact of the vaccination campaign by comparing the risk of all-cause death between the vaccinated population and the unvaccinated population. We aligned all subjects on a single index date and considered the “all-cause deaths” outcome to compare the survival distributions of the unvaccinated group versus various vaccination statuses. The all-cause-death hazard ratios in univariate analysis for vaccinated people with 1, 2, and 3/4 doses versus unvaccinated people were 0.88, 1.23, and 1.21, respectively. The multivariate values were 2.40, 1.98, and 0.99. Possible explanations of this trend of the hazard ratios as vaccinations increase could be a harvesting effect; a calendar-time bias, accounting for seasonality and pandemic waves; a case-counting window bias; a healthy-vaccinee bias; or some combination of these factors. With 2 and even with 3/4 doses, the calculated Restricted Mean Survival Time and Restricted Mean Time Lost have shown a small but significant downside for the vaccinated populations. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines, Second Edition)
11 pages, 1335 KiB  
Article
Validation of a Pseudovirus Neutralization Assay for Severe Acute Respiratory Syndrome Coronavirus 2: A High-Throughput Method for the Evaluation of Vaccine Immunogenicity
by Zhaohui Cai, Raj Kalkeri, Mi Wang, Benjamin Haner, Dominic Dent, Bahar Osman, Paul Skonieczny, Jeremy Ross, Sheau-Line Feng, Rongman Cai, Mingzhu Zhu, Shane Cloney-Clark and Joyce S. Plested
Microorganisms 2024, 12(6), 1201; https://doi.org/10.3390/microorganisms12061201 - 14 Jun 2024
Cited by 4 | Viewed by 2166
Abstract
The evaluation of coronavirus disease 2019 (COVID-19) vaccine immunogenicity remains essential as the severe acute respiratory syncytial virus 2 (SARS-CoV-2) pandemic continues to evolve and as additional variants emerge. Neutralizing antibodies are a known correlate of protection for SARS-CoV-2 vaccines. A pseudovirus neutralization [...] Read more.
The evaluation of coronavirus disease 2019 (COVID-19) vaccine immunogenicity remains essential as the severe acute respiratory syncytial virus 2 (SARS-CoV-2) pandemic continues to evolve and as additional variants emerge. Neutralizing antibodies are a known correlate of protection for SARS-CoV-2 vaccines. A pseudovirus neutralization (PNT) assay was developed and validated at Novavax Clinical Immunology Laboratories to allow for the detection of neutralizing antibodies in vaccine clinical trial sera. The PNT assay was precise, accurate, linear, and specific in measuring SARS-CoV-2 neutralization titers in human serum for ancestral strain and the Omicron subvariants BA.5 and XBB.1.5, with an overall geometric coefficient of variation of ≤43.4%, a percent relative bias within the expected range of −60% to 150%, and a linearity value of R2 > 0.98 for all three strains. This pseudovirus assay will be useful for the analysis of vaccine clinical trial samples to assess vaccine immunogenicity. Future work will focus on modifying the assay for emerging variants, including XBB.1.16, EG.5.1, BA.2.86, and any other variants that emerge in the ongoing pandemic. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines, Second Edition)
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10 pages, 216 KiB  
Article
Determinants of COVID-19 Vaccine Hesitancy: A Cross-Sectional Study in Three Communities in the United States and Lebanon
by Mohamad Yasmin, Mohamad Ali Tfaily, Rayyan Wazzi Mkahal, Rita Obeid, Rebecca P. Emery, Habiba Hassouna, Mudita Bhugra, Robert A. Bonomo and Zeina A. Kanafani
Microorganisms 2024, 12(6), 1200; https://doi.org/10.3390/microorganisms12061200 - 14 Jun 2024
Cited by 2 | Viewed by 1243
Abstract
The COVID-19 pandemic underscores the significance of vaccine hesitancy in shaping vaccination outcomes. Understanding the factors underpinning COVID-19 vaccination hesitancy is crucial for tailoring effective vaccination strategies. This cross-sectional study, conducted in three communities across the United States and Lebanon, employed surveys to [...] Read more.
The COVID-19 pandemic underscores the significance of vaccine hesitancy in shaping vaccination outcomes. Understanding the factors underpinning COVID-19 vaccination hesitancy is crucial for tailoring effective vaccination strategies. This cross-sectional study, conducted in three communities across the United States and Lebanon, employed surveys to assess respondents’ knowledge, attitudes, and perceptions regarding COVID-19 infection and vaccination. Among the 7196 participants, comprising 6775 from the US and 422 from Lebanon, vaccine hesitancy rates were comparable at 12.2% and 12.8%, respectively. Notably, a substantial proportion of respondents harbored misconceptions, such as attributing the potential to alter DNA (86.4%) or track individuals (92.8%) to COVID-19 vaccines and believing in the virus’s artificial origins (81%). US participants had more misconceptions about the COVID-19 vaccine, such as altering DNA or causing infertility. Lebanese participants were more likely to question the origins of the virus and the speed of vaccine development. Additionally, US respondents were less worried about infection, while Lebanese respondents were more indecisive but less likely to outright reject the vaccine. Primary determinants of hesitancy included perceptions that the vaccine poses a greater risk than the infection itself (aOR = 8.7 and 9.4, respectively) and negative recommendations from healthcare providers (aOR = 6.5 and 5.4, respectively). Conversely, positive endorsements from healthcare providers were associated with reduced hesitancy (aOR = 0.02 and 0.4, respectively). Targeting healthcare providers to dispel misinformation and elucidate COVID-19 vaccine risks holds promise for enhancing vaccination uptake. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines, Second Edition)
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