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Microorganisms
Special Issues
SARS-CoV-2/COVID-19 Infection: Molecular and Clinical Aspects
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SARS-CoV-2/COVID-19 Infection: Molecular and Clinical Aspects

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

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 8365

Special Issue Editors

Prof. Dr. Davide Gibellini

E-Mail Website
Guest Editor
Section of Microbiology, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
Interests: virology; pathogenesis of viral infection; molecular virology
Special Issues, Collections and Topics in MDPI journals
Dr. Erica Diani

E-Mail Website
Guest Editor
Department of Diagnostic and Public Health, Verona University, 37134 Verona, Italy
Interests: clinical genetics; genomics; epilepsy; genetics; biomedical science; cell biology; cell signaling; virology; bacteriology; microbiology; alternative splicing; infectious disease; sequencing; molecular virology; diagnostics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The onset of the SARS-CoV-2 virus infection has deeply changed our vision of virology and infectious diseases. After three years of the pandemic, an increasing number of papers were published on this subject, but our knowledge of virus biology, pathogenesis, and clinical impact is partially notwithstanding all efforts performed.

The study of basic characteristics of SARS-CoV-2 replication, the virological and immunological aspects of the infection, and the analysis of specific clinical evolution including the problem of comorbidities, long-Covid, vaccine impact, and treatment choices, represent a fundamental field of scientific interest.

In this Special Issue of Microorganisms, we should like to offer the reader a collection of papers on these SARS-CoV-2-related items in order to describe these pivotal aspects and display new observations to shed light on the SARS-CoV-2 “mystery”. We think that only a multidisciplinary approach may represent a better way to achieve a more exhaustive comprehension of SARS-CoV-2 infection as a model to study other present and future infections by viruses.

Prof. Dr. Davide Gibellini
Dr. Erica Diani
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. 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

  • molecular virology
  • clinical aspects
  • COVID-19
  • omics study

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Published Papers (6 papers)

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Editorial

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2 pages, 133 KiB  
Editorial
An Open View on SARS-CoV-2 Infection
by Erica Diani and Davide Gibellini
Microorganisms 2024, 12(1), 156; https://doi.org/10.3390/microorganisms12010156 - 12 Jan 2024
Viewed by 878
Abstract
The onset of the SARS-CoV-2 virus led to the appearance of a devastating pandemic, which once again demonstrated the practical importance of virology [...] Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19 Infection: Molecular and Clinical Aspects)

Research

Jump to: Editorial

13 pages, 214 KiB  
Article
Gastrointestinal and Hepatological Manifestations in Severe Acute Respiratory Syndrome Coronavirus 2 Infection: Results from the Major COVID Hospital in Serbia
by Dragana Mijac, Samir Vucelj, Kristina Todorovic, Marko Vojnovic, Biljana Milicic, Snezana Lukic, Branka Filipovic, Marija Marjanovic Haljilji, Dusan Popovic and Tatjana Adzic Vukicevic
Microorganisms 2024, 12(1), 27; https://doi.org/10.3390/microorganisms12010027 - 22 Dec 2023
Cited by 2 | Viewed by 1017
Abstract
The coronavirus disease of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), includes a clinical spectrum of diseases from mild to severe progressive pneumonia, which has affected and still affects the human population worldwide. Most commonly, it is presented [...] Read more.
The coronavirus disease of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), includes a clinical spectrum of diseases from mild to severe progressive pneumonia, which has affected and still affects the human population worldwide. Most commonly, it is presented by respiratory symptoms, but studies have shown that about 50% of patients with SARS-CoV-2 infection have at least one gastrointestinal symptom (GI), predominantly nausea, diarrhea, vomiting, or loss of appetite. In addition, abnormal liver functional tests are commonly present in the SARS-CoV-2 virus. The aim of our study was to examine the GI and hepatic manifestations of COVID-19 in patients hospitalized due to COVID-19 pneumonia in “COVID hospital Batajnica”, University Clinical Center of Serbia in Belgrade. The study included 498 consecutive patients, and the data was obtained from the patient’s electronic medical history. GI symptoms included nausea, vomiting, diarrhea, and anorexia. Collected laboratory values included baseline and peak values of blood count, inflammatory parameters, liver function tests, renal function tests, and cardiac enzyme tests. The results have shown that GI symptoms occurred in 26% of cases at diagnosis, which indicates the great susceptibility of the GI system to SARS-CoV-2. There was a high risk of liver injury in patients with COVID-19 pneumonia (>60%). The level of AST is more often increased compared to ALT, which is different from other virus-induced liver lesions and may be a useful indicator of SARS-CoV-2 infection. Further research should focus on the causes of liver damage in SARS-CoV-2 virus and the impact on treatment and outcome of COVID-19 disease. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19 Infection: Molecular and Clinical Aspects)
19 pages, 5345 KiB  
Article
Molecular Mimicry between SARS-CoV-2 Proteins and Human Self-Antigens Related with Autoimmune Central Nervous System (CNS) Disorders
by Elisa Gouvea Gutman, Renan Amphilophio Fernandes, Jéssica Vasques Raposo-Vedovi, Andreza Lemos Salvio, Larissa Araujo Duarte, Caio Faria Tardim, Vinicius Gabriel Coutinho Costa, Valéria Coelho Santa Rita Pereira, Paulo Roberto Valle Bahia, Marcos Martins da Silva, Fabrícia Lima Fontes-Dantas and Soniza Vieira Alves-Leon
Microorganisms 2023, 11(12), 2902; https://doi.org/10.3390/microorganisms11122902 - 1 Dec 2023
Cited by 7 | Viewed by 1678
Abstract
SARS-CoV-2 can trigger autoimmune central nervous system (CNS) diseases in genetically susceptible individuals, a mechanism poorly understood. Molecular mimicry (MM) has been identified in other viral diseases as potential triggers of autoimmune CNS events. This study investigated if MM is the process through [...] Read more.
SARS-CoV-2 can trigger autoimmune central nervous system (CNS) diseases in genetically susceptible individuals, a mechanism poorly understood. Molecular mimicry (MM) has been identified in other viral diseases as potential triggers of autoimmune CNS events. This study investigated if MM is the process through which SARS-CoV-2 induces the breakdown of immune tolerance. The frequency of autoimmune CNS disorders was evaluated in a prospective cohort with patients admitted to the COVID-19 Intense Care Unity (ICU) in Rio de Janeiro. Then, an in silico analysis was performed to identify the conserved regions that share a high identity between SARS-CoV-2 antigens and human proteins. The sequences with significant identity and antigenic properties were then assessed for their binding capacity to HLA subtypes. Of the 112 patients included, 3 were classified as having an autoimmune disorder. A total of eleven combinations had significant linear and three-dimensional overlap. NMDAR1, MOG, and MPO were the self-antigens with more significant combinations, followed by GAD65. All sequences presented at least one epitope with strong or intermediate binding capacity to the HLA subtypes selected. This study underscores the possibility that CNS autoimmune attacks observed in COVID-19 patients, including those in our population, could be driven by MM in genetically predisposed individuals. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19 Infection: Molecular and Clinical Aspects)
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9 pages, 741 KiB  
Article
Prevalence of Pneumocystis jirovecii Colonization in Non-Critical Immunocompetent COVID-19 Patients: A Single-Center Prospective Study (JiroCOVID Study)
by Antonio Riccardo Buonomo, Giulio Viceconte, Ludovica Fusco, Marina Sarno, Isabella di Filippo, Luca Fanasca, Paola Salvatore and Ivan Gentile
Microorganisms 2023, 11(12), 2839; https://doi.org/10.3390/microorganisms11122839 - 22 Nov 2023
Cited by 2 | Viewed by 1064
Abstract
Background: Pneumocystis jirovecii pneumonia (PJP) is an invasive fungal infection (IFI) that occurs mainly in immunocompromised hosts. After observing a high prevalence of PJP as a complication of COVID-19 in immunocompetent patients, we conducted a study to evaluate the prevalence of P. jirovecii [...] Read more.
Background: Pneumocystis jirovecii pneumonia (PJP) is an invasive fungal infection (IFI) that occurs mainly in immunocompromised hosts. After observing a high prevalence of PJP as a complication of COVID-19 in immunocompetent patients, we conducted a study to evaluate the prevalence of P. jirovecii colonization with PCR on oral washing samples (OWS) among non-immunocompromised and non-critical patients admitted with COVID-19 pneumonia at our university hospital. Methods: All patients over 18 years of age admitted to the Infectious Diseases Unit for SARS-CoV-2 pneumonia between July 2021 and December 2022 were included. Patients undergoing invasive mechanical ventilation or ECMO, those with risk factors for developing PJP, and those receiving prophylaxis for P. jirovecii were excluded. Samples were collected by gargling with 10 mL of 0.9% NaCl on day 14 of the hospital stay or at discharge. Results: Of 290 screened patients, 59 (20%) met the inclusion criteria and were enrolled. Only 1 of 59 patients (1.7%) tested positive for P. jirovecii detection with PCR, and the same patient was the only one to develop PJP in the follow-up period. Conclusions: Our results are in line with the previous findings of other studies that confirmed a very low prevalence of P. jirovecii colonization on OWS in the immunocompetent population. Despite the limitations of the study, the fact that the only patient who tested positive for P. jirovecii was the only one in our cohort to develop PJP leads us to reflect on the role of this non-invasive sample in predicting the risk of PJP in patients with COVID-19. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19 Infection: Molecular and Clinical Aspects)
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13 pages, 4084 KiB  
Article
Detection of SARS-CoV-2 Δ426 ORF8 Deletion Mutant Cluster in NGS Screening
by Riccardo Cecchetto, Emil Tonon, Nicoletta Medaina, Giona Turri, Erica Diani, Pier Paolo Piccaluga, Angela Salomoni, Michela Conti, Evelina Tacconelli, Anna Lagni, Virginia Lotti, Mosé Favarato and Davide Gibellini
Microorganisms 2023, 11(10), 2378; https://doi.org/10.3390/microorganisms11102378 - 23 Sep 2023
Cited by 2 | Viewed by 1244
Abstract
Next-generation sequencing (NGS) from SARS-CoV-2-positive swabs collected during the last months of 2022 revealed a large deletion spanning ORF7b and ORF8 (426 nt) in six patients infected with the BA.5.1 Omicron variant. This extensive genome loss removed a large part of these two [...] Read more.
Next-generation sequencing (NGS) from SARS-CoV-2-positive swabs collected during the last months of 2022 revealed a large deletion spanning ORF7b and ORF8 (426 nt) in six patients infected with the BA.5.1 Omicron variant. This extensive genome loss removed a large part of these two genes, maintaining in frame the first 22 aminoacids of ORF7b and the last three aminoacids of ORF8. Interestingly, the deleted region was flanked by two small repeats, which were likely involved in the formation of a hairpin structure. Similar rearrangements, comparable in size and location to the deletion, were also identified in 15 sequences in the NCBI database. In this group, seven out of 15 cases from the USA and Switzerland presented both the BA.5.1 variant and the same 426 nucleotides deletion. It is noteworthy that three out of six cases were detected in patients with immunodeficiency, and it is conceivable that this clinical condition could promote the replication and selection of these mutations. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19 Infection: Molecular and Clinical Aspects)
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17 pages, 1386 KiB  
Article
Comparative Longitudinal Serological Study of Anti-SARS-CoV-2 Antibody Profiles in People with COVID-19
by Marilou H. Barrios, Suellen Nicholson, Rowena A. Bull, Marianne Martinello, William Rawlinson, Michael Mina, Jeffrey J. Post, Bernard Hudson, Nicole Gilroy, Andrew R. Lloyd, Pamela Konecny, Francesca Mordant, Mike Catton, Kanta Subbarao, Leon Caly, Julian Druce and Hans J. Netter
Microorganisms 2023, 11(8), 1985; https://doi.org/10.3390/microorganisms11081985 - 2 Aug 2023
Cited by 1 | Viewed by 1836
Abstract
Serological diagnostic assays are essential tools for determining an individual’s protection against viruses like SARS-CoV-2, tracking the spread of the virus in the community, and evaluating population immunity. To assess the diversity and quality of the anti-SARS-CoV-2 antibody response, we have compared the [...] Read more.
Serological diagnostic assays are essential tools for determining an individual’s protection against viruses like SARS-CoV-2, tracking the spread of the virus in the community, and evaluating population immunity. To assess the diversity and quality of the anti-SARS-CoV-2 antibody response, we have compared the antibody profiles of people with mild, moderate, and severe COVID-19 using a dot blot assay. The test targeted the four major structural proteins of SARS-CoV-2, namely the nucleocapsid (N), spike (S) protein domains S1 and S2, and receptor-binding domain (RBD). Serum samples were collected from 63 participants at various time points for up to 300 days after disease onset. The dot blot assay revealed patient-specific differences in the anti-SARS-CoV-2 antibody profiles. Out of the 63 participants with confirmed SARS-CoV-2 infections and clinical COVID-19, 35/63 participants exhibited diverse and robust responses against the tested antigens, while 14/63 participants displayed either limited responses to a subset of antigens or no detectable antibody response to any of the antigens. Anti-N-specific antibody levels decreased within 300 days after disease onset, whereas anti-S-specific antibodies persisted. The dynamics of the antibody response did not change during the test period, indicating stable antibody profiles. Among the participants, 28/63 patients with restricted anti-S antibody profiles or undetectable anti-S antibody levels in the dot blot assay also exhibited weak neutralization activity, as measured by a surrogate virus neutralization test (sVNT) and a microneutralization test. These results indicate that in some cases, natural infections do not lead to the production of neutralizing antibodies. Furthermore, the study revealed significant serological variability among patients, regardless of the severity of their COVID-19 illness. These differences need to be carefully considered when evaluating the protective antibody status of individuals who have experienced primary SARS-CoV-2 infections. Full article
(This article belongs to the Special Issue SARS-CoV-2/COVID-19 Infection: Molecular and Clinical Aspects)
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