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New Knowledge in the Study of Coronaviruses: Towards One Health...
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New Knowledge in the Study of Coronaviruses: Towards One Health and Whole Genome Sequencing Approaches, 2nd Edition

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 6824

Special Issue Editor

Dr. Simone Peletto

E-Mail Website
Guest Editor
Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy
Interests: microbiota; metagenomics; viral WGS; phylogeny; molecular typing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue, “New Knowledge in the Study of Coronaviruses: Towards One Health and Whole Genome Sequencing Approaches”

Coronaviruses, belonging to the order Nidovirales, are enveloped, positive single-stranded RNA viruses that have the largest and most complex genomes among riboviruses. Their name derives from the protrusions (spikes) present in the viral envelope. The Coronaviridae family includes four genera (Alpha-, Beta-, Gamma- and Deltacoronavirus), which include several species of viruses capable of infecting humans, mammals and birds.

The advent of the SARS-CoV-2 pandemic has enormously increased the attention on these viruses, which were previously known in human pathology, especially for SARS-CoV and MERS-CoV. Often, the coronavirus environmental reservoir is represented by different animal species, especially bats; humans are the final hosts of these viruses or become infected due to spillover events. Therefore, given the presence of coronaviruses in animal hosts and their ability to spillover, it is essential to adopt a One Health approach.

Coronaviruses research should be based on molecular approaches—in particular, by adopting Whole Genome Sequencing (WGS) techniques that are needed to characterize these viruses and track possible spillover events, in order to prevent new pandemic events. In fact, if from a diagnostic point of view, it may still be sufficient to adopt classical techniques of the amplification of nucleic acids (NAATs). It is necessary to encourage the research to adopt the full genome approach to constantly increase the available knowledge about these viruses.

For these reasons, this Special Issue was designed to collect works concerning the study of coronaviruses in both humans and animals. We welcome articles that may concern both diagnostic and research aspects, with a particular emphasis on works based on WGS approaches.

Dr. Simone Peletto
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

  • coronaviruses
  • whole genome sequencing Approaches
  • one health

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Related Special Issue

Published Papers (5 papers)

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Research

13 pages, 2716 KiB  
Article
Tracing Emergence of SARS-CoV-2 Variants: Insights from Comprehensive Assessment Using Reverse Transcription Polymerase Chain Reaction and Whole Genome Sequencing
by Duyeon Na, Yuna Hong, Chaeyeon Lee and Myungshin Kim
Microorganisms 2025, 13(2), 311; https://doi.org/10.3390/microorganisms13020311 - 31 Jan 2025
Viewed by 360
Abstract
The emergence and evolution of SARS-CoV-2 variants, such as Delta and Omicron, pose significant challenges to pandemic management. This study evaluated the effectiveness of reverse-transcription polymerase chain reaction (RT-PCR) and whole-genome sequencing (WGS) in detecting and characterizing SARS-CoV-2 variants using 624 samples collected [...] Read more.
The emergence and evolution of SARS-CoV-2 variants, such as Delta and Omicron, pose significant challenges to pandemic management. This study evaluated the effectiveness of reverse-transcription polymerase chain reaction (RT-PCR) and whole-genome sequencing (WGS) in detecting and characterizing SARS-CoV-2 variants using 624 samples collected in South Korea from mid-2021 to mid-2022. Two RT-PCR genotyping assays demonstrated a high concordance rate (90.4%) in identifying the Delta variant during its dominance. In contrast, WGS revealed extensive genetic diversity among Omicron sub-lineages, identifying 29 distinct sub-lineages, including two South Korea-specific variants (BA.1.1.5 and BA.2.3.8). Clustering analysis of WGS data highlighted distinct groupings of BA.1, BA.2, and BA.5 sub-lineages, with overlap in shared mutations suggesting evolutionary convergence. Sub-lineage diversity expanded during rapid transmission phases and subsequently consolidated as dominant lineages emerged. These findings highlight the complementary strengths of RT-PCR and WGS and underscore the importance of integrating these methodologies for effective variant monitoring and public health response. Full article
(This article belongs to the Special Issue New Knowledge in the Study of Coronaviruses: Towards One Health and Whole Genome Sequencing Approaches, 2nd Edition)
10 pages, 255 KiB  
Article
How Trustworthy Are the Genomic Sequences of SARS-CoV-2 in GenBank?
by Xuhua Xia
Microorganisms 2024, 12(11), 2187; https://doi.org/10.3390/microorganisms12112187 - 30 Oct 2024
Viewed by 1190
Abstract
Well-annotated gene and genomic sequences serve as a foundation for making inferences in molecular biology and evolution and can directly impact public health. The first SARS-CoV-2 genome was submitted to the GenBank database hosted by the U.S. National Center for Biotechnology Information and [...] Read more.
Well-annotated gene and genomic sequences serve as a foundation for making inferences in molecular biology and evolution and can directly impact public health. The first SARS-CoV-2 genome was submitted to the GenBank database hosted by the U.S. National Center for Biotechnology Information and used to develop the two successful vaccines. Conserved protein domains are often chosen as targets for developing antiviral medicines or vaccines. Mutation and substitution patterns provide crucial information not only on functional motifs and genome/protein interactions but also for characterizing phylogenetic relationships among viral strains. These patterns, together with the collection time of viral samples, serve as the basis for addressing the question of when and where the host-switching event occurred. Unfortunately, viral genomic sequences submitted to GenBank undergo little quality control, and critical information in the annotation is frequently changed without being recorded. Researchers often have no choice but to hold blind faith in the authenticity of the sequences. There have been reports of incorrect genome annotation but no report that casts doubt on the genomic sequences themselves because it seems theoretically impossible to identify genomic sequences that may not be authentic. This paper takes an innovative approach to show that some SARS-CoV-2 genomes submitted to GenBank cannot possibly be authentic. Specifically, some SARS-CoV-2 genomic sequences deposited in GenBank with collection times in 2023 and 2024, isolated from saliva, nasopharyngeal, sewage, and stool, are identical to the reference genome of SARS-CoV-2 (NC_045512). The probability of such occurrence is effectively 0. I also compile SARS-CoV-2 genomes with changed sample collection times. One may be led astray in bioinformatic analysis without being aware of errors in sequences and sequence annotation. Full article
(This article belongs to the Special Issue New Knowledge in the Study of Coronaviruses: Towards One Health and Whole Genome Sequencing Approaches, 2nd Edition)
16 pages, 3108 KiB  
Article
An Analysis of Combined Molecular Weight and Hydrophobicity Similarity between the Amino Acid Sequences of Spike Protein Receptor Binding Domains of Betacoronaviruses and Functionally Similar Sequences from Other Virus Families
by Jamie D. Dixson, Lavanya Vumma and Rajeev K. Azad
Microorganisms 2024, 12(10), 2021; https://doi.org/10.3390/microorganisms12102021 - 5 Oct 2024
Viewed by 1181
Abstract
Recently, we proposed a new method, based on protein profiles derived from physicochemical dynamic time warping (PCDTW), to functionally/structurally classify coronavirus spike protein receptor binding domains (RBD). Our method, as used herein, uses waveforms derived from two physicochemical properties of amino acids (molecular [...] Read more.
Recently, we proposed a new method, based on protein profiles derived from physicochemical dynamic time warping (PCDTW), to functionally/structurally classify coronavirus spike protein receptor binding domains (RBD). Our method, as used herein, uses waveforms derived from two physicochemical properties of amino acids (molecular weight and hydrophobicity (MWHP)) and is designed to reach into the twilight zone of homology, and therefore, has the potential to reveal structural/functional relationships and potentially homologous relationships over greater evolutionary time spans than standard primary sequence alignment-based techniques. One potential application of our method is inferring deep evolutionary relationships such as those between the RBD of the spike protein of betacoronaviruses and functionally similar proteins found in other families of viruses, a task that is extremely difficult, if not impossible, using standard multiple alignment-based techniques. Here, we applied PCDTW to compare members of four divergent families of viruses to betacoronaviruses in terms of MWHP physicochemical similarity of their RBDs. We hypothesized that some members of the families Arteriviridae, Astroviridae, Reoviridae (both from the genera rotavirus and orthoreovirus considered separately), and Toroviridae would show greater physicochemical similarity to betacoronaviruses in protein regions similar to the RBD of the betacoronavirus spike protein than they do to other members of their respective taxonomic groups. This was confirmed to varying degrees in each of our analyses. Three arteriviruses (the glycoprotein-2 sequences) clustered more closely with ACE2-binding betacoronaviruses than to other arteriviruses, and a clade of 33 toroviruses was found embedded within a clade of non-ACE2-binding betacoronaviruses, indicating potentially shared structure/function of RBDs between betacoronaviruses and members of other virus clades. Full article
(This article belongs to the Special Issue New Knowledge in the Study of Coronaviruses: Towards One Health and Whole Genome Sequencing Approaches, 2nd Edition)
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14 pages, 3344 KiB  
Article
SARS-CoV-2 Genotyping Highlights the Challenges in Spike Protein Drift Independent of Other Essential Proteins
by Jeremy W. Prokop, Sheryl Alberta, Martin Witteveen-Lane, Samantha Pell, Hosam A. Farag, Disha Bhargava, Robert M. Vaughan, Austin Frisch, Jacob Bauss, Humza Bhatti, Sanjana Arora, Charitha Subrahmanya, David Pearson, Austin Goodyke, Mason Westgate, Taylor W. Cook, Jackson T. Mitchell, Jacob Zieba, Matthew D. Sims, Adam Underwood, Habiba Hassouna, Surender Rajasekaran, Maximiliano A. Tamae Kakazu, Dave Chesla, Rosemary Olivero and Adam J. Caulfieldadd Show full author list remove Hide full author list
Microorganisms 2024, 12(9), 1863; https://doi.org/10.3390/microorganisms12091863 - 9 Sep 2024
Viewed by 1458
Abstract
As of 2024, SARS-CoV-2 continues to propagate and drift as an endemic virus, impacting healthcare for years. The largest sequencing initiative for any species was initiated to combat the virus, tracking changes over time at a full virus base-pair resolution. The SARS-CoV-2 sequencing [...] Read more.
As of 2024, SARS-CoV-2 continues to propagate and drift as an endemic virus, impacting healthcare for years. The largest sequencing initiative for any species was initiated to combat the virus, tracking changes over time at a full virus base-pair resolution. The SARS-CoV-2 sequencing represents a unique opportunity to understand selective pressures and viral evolution but requires cross-disciplinary approaches from epidemiology to functional protein biology. Within this work, we integrate a two-year genotyping window with structural biology to explore the selective pressures of SARS-CoV-2 on protein insights. Although genotype and the Spike (Surface Glycoprotein) protein continue to drift, most SARS-CoV-2 proteins have had few amino acid alterations. Within Spike, the high drift rate of amino acids involved in antibody evasion also corresponds to changes within the ACE2 binding pocket that have undergone multiple changes that maintain functional binding. The genotyping suggests selective pressure for receptor specificity that could also confer changes in viral risk. Mapping of amino acid changes to the structures of the SARS-CoV-2 co-transcriptional complex (nsp7-nsp14), nsp3 (papain-like protease), and nsp5 (cysteine protease) proteins suggest they remain critical factors for drug development that will be sustainable, unlike those strategies targeting Spike. Full article
(This article belongs to the Special Issue New Knowledge in the Study of Coronaviruses: Towards One Health and Whole Genome Sequencing Approaches, 2nd Edition)
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17 pages, 1606 KiB  
Article
Efficacy of a Multistrain Synbiotic Treatment in Acute and Post-Acute COVID-19 Patients: A Double-Blind, Placebo-Controlled Randomized Trial
by Maria Letizia Giancola, Andrea Fontana, Concetta Panebianco, Antonio Mazzarelli, Alessia Beccacece, Patrizia De Marco, Giovanna Cocomazzi, Chiara De Giuli, Germana Grassi, Carla Fontana, Giorgio Maria Baldini, Viviana Contu, Massimiliano Copetti, Francesco Perri, Emanuele Nicastri and Valerio Pazienza
Microorganisms 2024, 12(7), 1443; https://doi.org/10.3390/microorganisms12071443 - 16 Jul 2024
Viewed by 1596
Abstract
Background and Aims: Several studies reported the effect of COVID-19 on inducing gut dysbiosis, which is also correlated with disease severity. This study aims to investigate the effect of a nutraceutical formula on the shift of microbiota profiles and, secondly, on the clinical–pathological [...] Read more.
Background and Aims: Several studies reported the effect of COVID-19 on inducing gut dysbiosis, which is also correlated with disease severity. This study aims to investigate the effect of a nutraceutical formula on the shift of microbiota profiles and, secondly, on the clinical–pathological parameters of acute and post-acute COVID-19 patients. Methods: In this randomised, double-blind, placebo-controlled trial conducted at National Institute for Infectious diseases (INMI) Lazzaro Spallanzani (Italy), 52 patients were randomly assigned (1:1) to receive a multistrain synbiotic formula (Kebirah®) or placebo orally for 35 days at COVID-19 diagnosis. Health professionals, investigators, and patients were masked to group assignments. The V3–V4 hypervariable region of 16S rRNA gene sequencing was employed to study the gut microbiota composition in the two groups. Results: Supplementation with Kebirah® prevented the decrease in the Shannon diversity index of gut microbiota, which was instead observed in patients receiving the placebo. In addition, decreases in lymphocyte count and haemoglobin levels were observed only in the placebo group and not in the treated group, which was also characterised by an amelioration of the gut microbial profile, with an enrichment in beneficial bacteria and a preservation of species diversity. Conclusions: Our data suggest that modulating the gut microbiota in acute disease through administration of a specific symbiotic formula could be a useful strategy in the frame of SARS-CoV-2 infections. Full article
(This article belongs to the Special Issue New Knowledge in the Study of Coronaviruses: Towards One Health and Whole Genome Sequencing Approaches, 2nd Edition)
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