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Microorganisms
Special Issues
The Evolution of SARS-CoV-2: Molecular Properties, Virulence and Epidemiology
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The Evolution of SARS-CoV-2: Molecular Properties, Virulence and Epidemiology

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

Deadline for manuscript submissions: closed (31 May 2025) | Viewed by 9840

Special Issue Editor

Dr. Barbara Camilloni

E-Mail Website
Guest Editor
Department of Medicine and Surgery, Microbiology and Clinical Microbiology, Santa Maria Della Misericordia” Hospital, University of Perugia, 06129 Perugia, Italy
Interests: clinical microbiology; SARS-CoV-2; molecular epidemiology; infection; diagnosis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The world is grappling with the unprecedented COVID-19 pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As the virus continues to spread globally, understanding its evolution and epidemiology is critical to developing effective strategies to control its transmission, protect vulnerable populations, and mitigate its impact on public health.

The field of epidemiology plays a vital role in studying the patterns, determinants, and dynamics of infectious diseases within populations. By studying the epidemiology of SARS-CoV-2 infection, we can gain insights into various aspects of the pandemic, such as the evolution of the virus, disease transmission, risk factors, clinical outcomes, and the effectiveness of interventions.

This Special Issue aims to connect researchers, scientists, and health professionals, and thus encourage them to share their research and contribute to our collective understanding of the epidemiological characteristics of SARS-CoV-2.

Within the "One Health" concept, we invite researchers from various disciplines to contribute original research articles and comprehensive reviews to this Special Issue. Through rigorous peer-review, we aim to publish high-quality articles that significantly contribute to advancing our knowledge of SARS-CoV-2 infection. Together, let us strive towards an enhanced understanding of this virus, paving the way for evidence-based strategies able to mitigate its impact on public health.

Dr. Barbara Camilloni
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
  • molecular epidemiology
  • epidemiology infection
  • transmission
  • monitoring
  • diagnosis

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Published Papers (5 papers)

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Research

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19 pages, 4368 KiB  
Article
A Genomic Surveillance Circuit for Emerging Viral Pathogens
by Carlos S. Casimiro-Soriguer, Maria Lara, Andrea Aguado, Carlos Loucera, Francisco M. Ortuño, Nicola Lorusso, Jose M. Navarro-Marí, Sara Sanbonmatsu-Gámez, Pedro Camacho-Martinez, Laura Merino-Diaz, Adolfo de Salazar, Ana Fuentes, The Andalusian COVID-19 Sequencing Initiative, Jose A. Lepe, Federico García, Joaquín Dopazo and Javier Perez-Florido
Microorganisms 2025, 13(4), 912; https://doi.org/10.3390/microorganisms13040912 - 16 Apr 2025
Viewed by 662
Abstract
Genomic surveillance has been crucial in monitoring the evolution and spread of SARS-CoV-2. In Andalusia (Spain), a coordinated genomic surveillance circuit was established to systematically sequence and analyze viral genomes across the region. This initiative organizes sample collection through 27 hospitals, which act [...] Read more.
Genomic surveillance has been crucial in monitoring the evolution and spread of SARS-CoV-2. In Andalusia (Spain), a coordinated genomic surveillance circuit was established to systematically sequence and analyze viral genomes across the region. This initiative organizes sample collection through 27 hospitals, which act as regional hubs within their respective health districts. Sequencing is performed at three reference laboratories, with downstream data analysis and reporting centralized at a bioinformatics platform. From 2021 to 2025, over 42,500 SARS-CoV-2 genomes were sequenced, enabling the identification of major variants and their evolutionary dynamics. The circuit tracked the transition from Alpha and Delta to successive Omicron waves, including both recombinant and non-recombinant clades. The integration of genomic and epidemiological data facilitated rapid variant detection, outbreak investigation, and public health decision making. This surveillance framework at a regional granularity demonstrates the feasibility of large-scale sequencing within a decentralized healthcare system and has expanded to monitor other pathogens, reinforcing its value for epidemic preparedness. Continued investment in genomic surveillance is critical for tracking viral evolution, guiding interventions, and mitigating future public health threats. Full article
(This article belongs to the Special Issue The Evolution of SARS-CoV-2: Molecular Properties, Virulence and Epidemiology)
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15 pages, 9261 KiB  
Article
SARS-CoV-2 Molecular Evolution: A Focus on Omicron Variants in Umbria, Italy
by Giulia Bicchieraro, Raffaella Ciurnelli, Alessandro Graziani, Alicia Yoke Wei Wong, Barbara Camilloni, Antonella Mencacci and Roberta Spaccapelo
Microorganisms 2024, 12(7), 1330; https://doi.org/10.3390/microorganisms12071330 - 29 Jun 2024
Cited by 1 | Viewed by 1549
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 6 million deaths worldwide, and the spread of new variants over time increased the ability of this virus to cause infection. The Omicron variant was detected for the first time in Umbria, [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 6 million deaths worldwide, and the spread of new variants over time increased the ability of this virus to cause infection. The Omicron variant was detected for the first time in Umbria, a region of central Italy, in November 2021 and it induced an unprecedented increase in the number of infection cases. Here, we analysed 3300 SARS-CoV-2 positive samples collected in Umbria between April 2022 and December 2023. We traced the molecular evolution of SARS-CoV-2 variants over time through the Next-Generation Sequencing (NGS) approach. We assessed correlation between SARS-CoV-2 infection and patients’ health status. In total, 17.3% of our samples came from patients hospitalised as a consequence of COVID-19 infection even though 81.4% of them received at least three vaccine doses. We identified only Omicron variants, and the BA.5 lineage was detected in the majority of our samples (49.2%). Omicron variants outcompeted each other through the acquisition of mutations especially in Spike glycoprotein that are fingerprints of each variant. Viral antigenic evolution confers higher immunological escape and makes a continuous improvement of vaccine formulation necessary. The continuous update of international genomic databases with sequencing results obtained by emergent pathogens is essential to manage a possible future pandemic. Full article
(This article belongs to the Special Issue The Evolution of SARS-CoV-2: Molecular Properties, Virulence and Epidemiology)
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25 pages, 4836 KiB  
Article
Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia
by Feda A. Alsuwairi, Asma N. Alsaleh, Dalia A. Obeid, Ahmed A. Al-Qahtani, Reem S. Almaghrabi, Basma M. Alahideb, Maha A. AlAbdulkareem, Madain S. Alsanea, Layla A. Alharbi, Sahar I. Althawadi, Sara A. Altamimi, Abeer N. Alshukairi and Fatimah S. Alhamlan
Microorganisms 2024, 12(3), 467; https://doi.org/10.3390/microorganisms12030467 - 26 Feb 2024
Cited by 5 | Viewed by 2781
Abstract
The genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS-CoV-2 [...] Read more.
The genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS-CoV-2 and detect the variants present in specimens from Saudi Arabia. Furthermore, we sought to analyze and characterize the amino acid changes in the various proteins of the identified SARS-CoV-2 variants. A total of 1161 samples from patients diagnosed with COVID-19 in Saudi Arabia, between 1 April 2021 and 31 July 2023, were analyzed. Whole genome sequencing was employed for variant identification and mutation analysis. The statistical analysis was performed using the Statistical Analytical Software SAS, version 9.4, and GraphPad, version 9.0. This study identified twenty-three variants and subvariants of SARS-CoV-2 within the population, with the Omicron BA.1 (21K) variant (37.0%) and the Delta (21J) variant (12%) being the most frequently detected. Notably, the Omicron subvariants exhibited a higher mean mutation rate. Amino acid mutations were observed in twelve proteins. Among these, the spike (S), ORF1a, nucleocapsid (N), and ORF1b proteins showed a higher frequency of amino acid mutations compared to other the viral proteins. The S protein exhibited the highest incidence of amino acid mutations (47.6%). Conversely, the ORF3a, ORF8, ORF7a, ORF6, and ORF7b proteins appeared more conserved, demonstrating the lowest percentage and frequency of amino acid mutations. The investigation of structural protein regions revealed the N-terminal S1 subunit of the S protein to frequently harbor mutations, while the N-terminal domain of the envelope (E) protein displayed the lowest mutation frequency. This study provides insights into the variants and genetic diversity of SARS-CoV-2, underscoring the need for further research to comprehend its genome evolution and the occurrence of mutations. These findings are pertinent to the development of testing approaches, therapeutics, and vaccine strategies. Full article
(This article belongs to the Special Issue The Evolution of SARS-CoV-2: Molecular Properties, Virulence and Epidemiology)
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Review

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16 pages, 371 KiB  
Review
The Intersection of SARS-CoV-2 and Diabetes
by Jacob H. Nichols, Amber M. Smith and Colleen B. Jonsson
Microorganisms 2025, 13(6), 1390; https://doi.org/10.3390/microorganisms13061390 - 14 Jun 2025
Viewed by 698
Abstract
The interplay between comorbidities and viral infections is a critical factor that influences disease severity and outcomes. Diabetes Mellitus (DM) is one such comorbidity that significantly elevates the risk of severe viral infection from coronaviruses, namely, SARS-CoV-2. DM is characterized by either a [...] Read more.
The interplay between comorbidities and viral infections is a critical factor that influences disease severity and outcomes. Diabetes Mellitus (DM) is one such comorbidity that significantly elevates the risk of severe viral infection from coronaviruses, namely, SARS-CoV-2. DM is characterized by either a lack of insulin production (type 1 diabetes) or insulin resistance (type 2 diabetes), both of which contribute to a state of hyperglycemia, or high blood sugar. Hyperglycemia significantly promotes chronic inflammation, metabolic dysfunction, and immune dysregulation, which put diabetics at an elevated risk of critical health outcomes. Additionally, diabetes is hypothesized to amplify viral titers during infection by promoting the expression of the viral entry receptor ACE2 and providing a favorable cellular energy environment for viral replication. This review focuses on explaining the mechanisms that link diabetics with more severe COVID-19 disease and exploring some of the mechanisms that contribute to the phenomenon where COVID-19 can promote new-onset diabetes. By highlighting the interconnections between diabetes and COVID-19, this review aims to emphasize the implications that the SARS-CoV-2 outbreak has had on metabolic health. Full article
(This article belongs to the Special Issue The Evolution of SARS-CoV-2: Molecular Properties, Virulence and Epidemiology)
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Other

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8 pages, 1402 KiB  
Brief Report
Outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 in a Rural Community Hospital during Omicron Predominance
by Amar Krishna, Julie Tutt, Mehr Grewal, Sheila Bragdon and Suzanne Moreshead
Microorganisms 2024, 12(4), 686; https://doi.org/10.3390/microorganisms12040686 - 28 Mar 2024
Viewed by 1754
Abstract
Healthcare-associated infections due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has increased since the discovery of the Omicron variant. We describe a SARS-CoV-2 outbreak in the medicine–surgery unit of a rural community hospital at the time of high community transmission of Omicron [...] Read more.
Healthcare-associated infections due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has increased since the discovery of the Omicron variant. We describe a SARS-CoV-2 outbreak in the medicine–surgery unit of a rural community hospital at the time of high community transmission of Omicron variant in our county. The outbreak occurred in the medicine–surgery unit of an 89-bed rural community hospital in northern Maine. The characteristics of the patients and healthcare workers (HCWs) affected by the outbreak are described. Patient and HCW data collected as part of the outbreak investigation were used in this report. The outbreak control measures implemented are also described. A total of 24 people tested positive for SARS-CoV-2 including 11 patients and 13 HCWs. A total of 12 of the 24 (50%) persons were symptomatic, and rhinorrhea was the most common symptom noted (8/12, 67%). None of the symptomatic persons had gastrointestinal symptoms or symptoms of a loss of sense of smell or taste. All HCWs were vaccinated and 8 of the 11 patients were vaccinated. Outbreak control measures in the affected unit included implementation of full PPE (N95 respirators, eye protection, gowns and gloves) during all patient care, serial testing of employees and patients in the affected unit, cohorting positive patients, closing visitation and thorough environmental cleaning including use of ultraviolet (UV) light disinfection. This outbreak exemplifies the high transmissibility of the Omicron variant of SARS-CoV-2. The outbreak occurred despite a well-established infection control program. We noted that serial testing, use of N95 respirators during all patient care and UV disinfection were some of the measures that could be successful in outbreak control. Full article
(This article belongs to the Special Issue The Evolution of SARS-CoV-2: Molecular Properties, Virulence and Epidemiology)
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