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Genomic Studies Related to SARS-CoV-2 and Other Common Pathogens
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Genomic Studies Related to SARS-CoV-2 and Other Common Pathogens

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 September 2024) | Viewed by 4284

Special Issue Editor

Dr. Łukasz Huminiecki

E-Mail Website
Guest Editor
Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Warszawa, Poland
Interests: genomics; biostatistics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Functional genomics can be a preferable tool to study expression changes induced by viral infections, such as COVID-19, as the changes tend to be dynamic or multilevel, as well as irreducibly complex. The corollary of the complexity is that there is no simple reductionist explanation of how an animal cell reacts to a pathogen, either in the early or late stages of an infection. Rather, a genome of the infected cell can move as a whole to a new transcriptomic state. If this hypothesis is generally true, science can benefit from microarray profiling of gene expression patterns during infections.

In the planned Special Issue of the International Journal of Molecular Sciences, I would like to invite the submission of further genomic studies of responses to common pathogens. Transcriptomic or statistical studies are of most interest (genomic studies are also of interest if they are correlated with host responses to an infection).

Dr. Łukasz Huminiecki
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • functional genomics
  • microarrays
  • RNAseq
  • bioinformatics
  • SARS-CoV-2
  • COVID-19
  • viral infection

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Published Papers (2 papers)

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Research

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17 pages, 1181 KiB  
Article
Sex-Specific HLA Alleles Contribute to the Modulation of COVID-19 Severity
by Serena Spartano, Maria Vittoria Faggiano, Giovanna Guidi, Pino D’Ambrosio, Alessandro Vaisfeld, Agnese Novelli, Salvatore Falqui, Antonella Cingolani, Lorenza Lambertenghi, Alessandro Visentin, Annamaria Azzini, Elda Righi, Enrico Maria Trecarichi, Maria Mazzitelli, Silvano Coletti, Jan Mous, Thomas W. Rademacher, Carlo Torti, Evelina Tacconelli, Massimo Fantoni, Roberto Cauda and Francesco Danilo Tizianoadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2024, 25(23), 13198; https://doi.org/10.3390/ijms252313198 - 8 Dec 2024
Viewed by 936
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, responsible for Coronavirus Disease 2019 (COVID-19), exhibits a spectrum of clinical manifestations, ranging from asymptomatic to severe pulmonary dysfunction or death. The variability in COVID-19 severity has largely been attributed to the host’s genetic characteristics, [...] Read more.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, responsible for Coronavirus Disease 2019 (COVID-19), exhibits a spectrum of clinical manifestations, ranging from asymptomatic to severe pulmonary dysfunction or death. The variability in COVID-19 severity has largely been attributed to the host’s genetic characteristics, suggesting a polygenic genetic architecture, without significant strong evidence of sex-related genetic differences. In this Italian retrospective case–control study, we investigated the association between COVID-19 severity (severe vs. asymptomatic/oligosymptomatic healed individuals) and HLA gene variants, analyzed by next-generation sequencing (NGS). We identified significant HLA alleles (according to the conventional nomenclature), SNPs and haplotypes in the HLA-B, -C, -F, -DQA1, -DRB1, and -DRB5 genes associated with COVID-19 severity. Interestingly, these variants showed biological sex-related effects. Also, we identified specific haplotypes associated with COVID-19 severity that are shared by different conventional HLA alleles, indicated here as “super-haplotypes”. These haplotypes had a biological sex-specific impact on disease severity and markedly increased the risk of severe COVID-19 compared to the conventional HLA alleles (odds ratio of up to 15). Our data suggest that the revision of the current HLA nomenclature may help to identify variants with a stronger effect on disease susceptibility and that association studies could benefit from the stratification of patients by biological sex. If replicated in other disease models, these findings could help to define the functional diversity in immune response between sexes, also based on the HLA system. Finally, due to the global pandemic’s mortality rate, we hypothesize here that SARS-CoV-2 may have acted as a natural selection trigger, leading to a drift in HLA allelic frequencies in the general population. Full article
(This article belongs to the Special Issue Genomic Studies Related to SARS-CoV-2 and Other Common Pathogens)
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Review

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34 pages, 3292 KiB  
Review
Bulk and Single-Cell RNA Sequencing Elucidate the Etiology of Severe COVID-19
by Łukasz Huminiecki
Int. J. Mol. Sci. 2024, 25(6), 3280; https://doi.org/10.3390/ijms25063280 - 14 Mar 2024
Viewed by 2644
Abstract
Coronavirus disease 2019 (COVID-19) is a type of pneumonia caused by the SARS-CoV-2 coronavirus. It can cause acute pulmonary and systemic inflammation, which can lead to death in severely ill patients. This study explores the potential reasons behind severe COVID-19 and its similarities [...] Read more.
Coronavirus disease 2019 (COVID-19) is a type of pneumonia caused by the SARS-CoV-2 coronavirus. It can cause acute pulmonary and systemic inflammation, which can lead to death in severely ill patients. This study explores the potential reasons behind severe COVID-19 and its similarities to systemic autoimmune diseases. This study reviewed unbiased high-throughput gene expression datasets, including next-generation and single-cell RNA sequencing. A total of 27 studies and eight meta-analyses were reviewed. The studies indicated that severe COVID-19 is associated with the upregulation of genes involved in pro-inflammatory, interferon, and cytokine/chemokine pathways. Additionally, changes were observed in the proportions of immune cell types in the blood and tissues, along with degenerative alterations in lung epithelial cells. Genomic evidence also supports the association of severe COVID-19 with various inflammatory syndromes, such as neuronal COVID-19, acute respiratory distress syndrome, vascular inflammation, and multisystem inflammatory syndrome. In conclusion, this study suggests that gene expression profiling plays a significant role in elucidating the etiology of severe COVID-19. Full article
(This article belongs to the Special Issue Genomic Studies Related to SARS-CoV-2 and Other Common Pathogens)
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