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Microorganisms
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Advances in SARS-CoV-2 Infection 2.0
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Advances in SARS-CoV-2 Infection 2.0

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

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 8322

Special Issue Editor

Prof. Dr. Carlo Contini

E-Mail Website
Guest Editor
Infectious and Tropical Diseases, University of Ferrara, Ferrara, Italy
Interests: SARS-CoV-2 infection; opportunistic infections
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Advances in SARS-CoV-2 Infection”

More than a year has passed since the new coronavirus SARS-CoV-2 entered our lives, causing worldwide grief and economic devastation in the form of COVID-19. The virus made a species jump (spillover) from an animal (bat) to man and, in a short time through sequential waves, has caused an uncontrolled epidemic that has resulted in 295 million cases worldwide and almost 6 million deaths to date—an apocalyptic scenario caused by a highly contagious disease, which sees governments and experts of all medical disciplines committed to facing a common enemy that continues to claim thousands of victims around the world.

COVID-19 is multifaceted, with a variety of clinical expressions from mild or moderate symptoms that generally heal without the need for any treatment, to more severe and devastating effects, especially in unvaccinated patients over 60, or those who are frail or have other coexisting diseases. It can also seriously affect children, in whom the virus can cause a deadly disease: multisystem inflammatory syndrome (MIS-C), which is particularly perilous to the pediatric age group. Moreover, long-COVID syndrome is becoming increasingly recognized as a new clinical entity in the context of SARS-CoV-2 infection.

In the therapeutic field, there is still no definitive curative drug. However, monoclonal antibodies are available and new antivirals will soon be commercialized. Several currently available vaccines were manufactured in just 18 months, a unique event in the history of highly prevalent infectious diseases that have plagued humanity. The positive effects of the vaccination campaign are being seen in many parts of the world, with a reduction in admissions to intensive care units and in overall mortality. However, the disappearance of this new infection is still far from being a reality, as it is also threatened by the presence of numerous viral variants that could compromise the efficacy of the vaccine, especially when there are segments of the population not yet immunized.

The purpose of this Special Issue is to focus on the main biological, epidemiological and clinical aspects of the virus, but above all, on therapeutic and preventive aspects in light of newly acquired knowledge.

Prof. Dr. Carlo Contini
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 and COVID-19
  • epidemiology and pathogenesis
  • virus variants
  • clinical aspects and advanced diagnosis
  • new therapeutic strategies
  • vaccines
  • long-term COVID-19 pandemic
  • multisystem inflammatory syndrome (MIS-C)
  • COVID-related opportunistic infections

Published Papers (6 papers)

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Research

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17 pages, 3039 KiB  
Article
Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection
by William Bourumeau, Karine Tremblay, Guillaume Jourdan, Catherine Girard and Catherine Laprise
Microorganisms 2023, 11(11), 2703; https://doi.org/10.3390/microorganisms11112703 - 04 Nov 2023
Cited by 1 | Viewed by 1131
Abstract
(1) Background: Individuals with COVID-19 display different forms of disease severity and the upper respiratory tract microbiome has been suggested to play a crucial role in the development of its symptoms. (2) Methods: The present study analyzed the microbial profiles of the oral [...] Read more.
(1) Background: Individuals with COVID-19 display different forms of disease severity and the upper respiratory tract microbiome has been suggested to play a crucial role in the development of its symptoms. (2) Methods: The present study analyzed the microbial profiles of the oral cavity and oropharynx of 182 COVID-19 patients compared to 75 unaffected individuals. The samples were obtained from gargle screening samples. 16S rRNA amplicon sequencing was applied to analyze the samples. (3) Results: The present study shows that SARS-CoV-2 infection induced significant differences in bacterial community assemblages, with Prevotella and Veillonella as biomarkers for positive-tested people and Streptococcus and Actinomyces for negative-tested people. It also suggests a state of dysbiosis on the part of the infected individuals due to significant differences in the bacterial community in favor of a microbiome richer in opportunistic pathogens. (4) Conclusions: SARS-CoV-2 infection induces dysbiosis in the upper respiratory tract. The identification of these opportunistic pathogenic biomarkers could be a new screening and prevention tool for people with prior dysbiosis. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection 2.0)
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17 pages, 2736 KiB  
Article
Metatranscriptome Analysis of Nasopharyngeal Swabs across the Varying Severity of COVID-19 Disease Demonstrated Unprecedented Species Diversity
by Michaela Hyblova, Dominik Hadzega, Klaudia Babisova, Patrik Krumpolec, Andrej Gnip, Peter Sabaka, Stefan Lassan and Gabriel Minarik
Microorganisms 2023, 11(7), 1804; https://doi.org/10.3390/microorganisms11071804 - 14 Jul 2023
Viewed by 1078
Abstract
The recent global emergence of the SARS-CoV-2 pandemic has accelerated research in several areas of science whose valuable outputs and findings can help to address future health challenges in the event of emerging infectious agents. We conducted a comprehensive shotgun analysis targeting multiple [...] Read more.
The recent global emergence of the SARS-CoV-2 pandemic has accelerated research in several areas of science whose valuable outputs and findings can help to address future health challenges in the event of emerging infectious agents. We conducted a comprehensive shotgun analysis targeting multiple aspects to compare differences in bacterial spectrum and viral presence through culture-independent RNA sequencing. We conducted a comparative analysis of the microbiome between healthy individuals and those with varying degrees of COVID-19 severity, including a total of 151 participants. Our findings revealed a noteworthy increase in microbial species diversity among patients with COVID-19, irrespective of disease severity. Specifically, our analysis revealed a significant difference in the abundance of bacterial phyla between healthy individuals and those infected with COVID-19. We found that Actinobacteria, among other bacterial phyla, showed a notably higher abundance in healthy individuals compared to infected individuals. Conversely, Bacteroides showed a lower abundance in the latter group. Infected people, regardless of severity and symptoms, have the same proportional representation of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteriales. In addition to SARS-CoV-2 and numerous phage groups, we identified sequences of clinically significant viruses such as Human Herpes Virus 1, Human Mastadenovirus D, and Rhinovirus A in several samples. Analyses were performed retrospectively, therefore, in the case of SARS-CoV-2 various WHO variants such as Alpha (B.1.1.7), Delta (B.1.617.2), Omicron (B.1.1.529), and 20C strains are represented. Additionally, the presence of specific virus strains has a certain effect on the distribution of individual microbial taxa. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection 2.0)
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12 pages, 508 KiB  
Article
Association of Toxoplasmosis and COVID-19 in a Mexican Population
by María de la Luz Galván-Ramírez, Angel Gustavo Salas-Lais, José Esteban Muñoz-Medina, Larissa Fernandes-Matano, Laura Rocío Rodríguez Pérez and Karen Franco de León
Microorganisms 2023, 11(6), 1441; https://doi.org/10.3390/microorganisms11061441 - 30 May 2023
Cited by 3 | Viewed by 1783
Abstract
SARS-CoV-2 is the causal agent of COVID-19; the first report of SARS-CoV-2 infection was in December 2019 in Wuhan, China. This virus has since caused the largest pandemic in history, and the number of deaths and infections has been significant. Nevertheless, the development [...] Read more.
SARS-CoV-2 is the causal agent of COVID-19; the first report of SARS-CoV-2 infection was in December 2019 in Wuhan, China. This virus has since caused the largest pandemic in history, and the number of deaths and infections has been significant. Nevertheless, the development of vaccines has helped to reduce both deaths and infections. Comorbidities such as diabetes, hypertension, heart and lung diseases, and obesity have been identified as additional risk factors for infection and the progression of COVID-19. Additionally, latent toxoplasmosis has been reported to be a risk factor for acquiring COVID-19 in some studies, but other studies have suggested a negative association between these two infections. Furthermore, in patients after vaccination or with COVID-19 and coinfection, an increase in the lethality and mortality of toxoplasmosis has been observed. Therefore, the objective of the current study is to determine the association of toxoplasmosis with COVID-19 in patients diagnosed with COVID-19. Serum samples from 384 patients previously diagnosed with COVID-19 using IgG antibodies against the S1/S2 antigens of SARS-CoV-2 were collected. Subsequently, anti-Toxoplasma IgG and IgM antibodies were analyzed with ELISA. Statistical analysis was performed using SPSS Version 20.0 frequencies, percentages, 2 × 2 tables, and the Pearson correlation coefficient. IgG and IgM anti-Toxoplasma antibodies were positive in 105/384 (27.34%) and (26/191) 13.6% of patients, respectively. The positivity for both infections was higher in patients aged >40 years old. Subjects who were overweight or obese were mainly positive for both IgG antibodies against S1/S2 SARS-CoV-2 and Toxoplasma antibodies. In conclusion, the coinfection rate was 21.7%. The prevalence of S1/S2 SARS-CoV-2 was 308/384 (80.2%), and the percentage of Toxoplasma antibodies was 27.34%. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection 2.0)
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21 pages, 3216 KiB  
Article
Blood Biomarkers from the Emergency Department Disclose Severe Omicron COVID-19-Associated Outcomes
by Fiorenza Pennacchia, Eqrem Rusi, Wael Abu Ruqa, Maria Antonella Zingaropoli, Patrizia Pasculli, Giuseppina Talarico, Giuseppe Bruno, Christian Barbato, Antonio Minni, Luigi Tarani, Gioacchino Galardo, Francesco Pugliese, Marco Lucarelli, Giampiero Ferraguti, Maria Rosa Ciardi and Marco Fiore
Microorganisms 2023, 11(4), 925; https://doi.org/10.3390/microorganisms11040925 - 02 Apr 2023
Cited by 2 | Viewed by 1573
Abstract
Background: Since its outbreak, Coronavirus disease 2019 (COVID-19), a life-threatening respiratory illness, has rapidly become a public health emergency with a devastating social impact. Lately, the Omicron strain is considered the main variant of concern. Routine blood biomarkers are, indeed, essential for stratifying [...] Read more.
Background: Since its outbreak, Coronavirus disease 2019 (COVID-19), a life-threatening respiratory illness, has rapidly become a public health emergency with a devastating social impact. Lately, the Omicron strain is considered the main variant of concern. Routine blood biomarkers are, indeed, essential for stratifying patients at risk of severe outcomes, and a huge amount of data is available in the literature, mainly for the previous variants. However, only a few studies are available on early routine biochemical blood biomarkers for Omicron-afflicted patients. Thus, the aim and novelty of this study were to identify routine blood biomarkers detected at the emergency room for the early prediction of severe morbidity and/or mortality. Methods: 449 COVID-19 patients from Sapienza University Hospital of Rome were divided into four groups: (1) the emergency group (patients with mild forms who were quickly discharged); (2) the hospital ward group (patients that after the admission in the emergency department were hospitalized in a COVID-19 ward); (3) the intensive care unit (ICU) group (patients that after the admission in the emergency department required intensive assistance); (4) the deceased group (patients that after the admission in the emergency department had a fatal outcome). Results: ANOVA and ROC data showed that high-sensitivity troponin-T (TnT), fibrinogen, glycemia, C-reactive protein, lactate dehydrogenase, albumin, D-dimer myoglobin, and ferritin for both men and women may predict lethal outcomes already at the level of the emergency department. Conclusions: Compared to previous Delta COVID-19 parallel emergency patterns of prediction, Omicron-induced changes in TnT may be considered other early predictors of severe outcomes. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection 2.0)
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Review

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18 pages, 1616 KiB  
Review
A Review: The Potential Involvement of Growth Arrest-Specific 6 and Its Receptors in the Pathogenesis of Lung Damage and in Coronavirus Disease 2019
by Daria Apostolo, Luciana L. Ferreira, Alice Di Tizio, Barbara Ruaro, Filippo Patrucco and Mattia Bellan
Microorganisms 2023, 11(8), 2038; https://doi.org/10.3390/microorganisms11082038 - 08 Aug 2023
Cited by 1 | Viewed by 1144
Abstract
The tyrosine kinase receptors of the TAM family—Tyro3, Axl and Mer—and their main ligand Gas6 (growth arrest-specific 6) have been implicated in several human diseases, having a particularly important role in the regulation of innate immunity and inflammatory response. The Gas6/TAM system is [...] Read more.
The tyrosine kinase receptors of the TAM family—Tyro3, Axl and Mer—and their main ligand Gas6 (growth arrest-specific 6) have been implicated in several human diseases, having a particularly important role in the regulation of innate immunity and inflammatory response. The Gas6/TAM system is involved in the recognition of apoptotic debris by immune cells and this mechanism has been exploited by viruses for cell entry and infection. Coronavirus disease 2019 (COVID-19) is a multi-systemic disease, but the lungs are particularly affected during the acute phase and some patients may suffer persistent lung damage. Among the manifestations of the disease, fibrotic abnormalities have been observed among the survivors of COVID-19. The mechanisms of COVID-related fibrosis remain elusive, even though some parallels may be drawn with other fibrotic diseases, such as idiopathic pulmonary fibrosis. Due to the still limited number of scientific studies addressing this question, in this review we aimed to integrate the current knowledge of the Gas6/TAM axis with the pathophysiological mechanisms underlying COVID-19, with emphasis on the development of a fibrotic phenotype. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection 2.0)
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Other

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7 pages, 748 KiB  
Opinion
Macrophage Activation in Follicular Conjunctivitis during the COVID-19 Pandemic
by Carla Enrica Gallenga, Martina Maritati, Marco Mura, Francesco Di Virgilio, Pio Conti and Carlo Contini
Microorganisms 2023, 11(9), 2198; https://doi.org/10.3390/microorganisms11092198 - 31 Aug 2023
Viewed by 988
Abstract
Among the symptoms of SARS-CoV-2, follicular conjunctivitis has become relevant. The conjunctiva acts as an open lymph node, reacting to the viral antigen that binds the epithelial cells, forming follicles of B cells with activated T cells and NK cells on its surface, [...] Read more.
Among the symptoms of SARS-CoV-2, follicular conjunctivitis has become relevant. The conjunctiva acts as an open lymph node, reacting to the viral antigen that binds the epithelial cells, forming follicles of B cells with activated T cells and NK cells on its surface, which, in turn, talk to monocyte-derived inflammatory infected macrophages. Here, the NLRP3 inflammasome is a major driver in releasing pro-inflammatory factors such as IL-6 and caspase-1, leading to follicular conjunctivitis and bulbar congestion, even as isolated signs in the ‘asymptomatic’ patient. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection 2.0)
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