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Special Issue "Genetic Variability and Molecular Evolution of SARS-CoV-2"

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

Deadline for manuscript submissions: 20 December 2023 | Viewed by 482

Special Issue Editors

Department of Biomedical Sciences, University of Sassari, Sassari, Italy
Interests: genetics; population genetics; bioinformatics; biostatistics; population genomics; phylogenetics/phylogenomics; population dynamics; molecular dating; molecular epidemiology; SARS-CoV-2; pandemic; epidemic
Special Issues, Collections and Topics in MDPI journals
Unit of Statistics, Faculty of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
Interests: epidemiology; statistics; molecular evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The proposed Special Issue, titled "Genetic Variability and Molecular Evolution of SARS-CoV-2," aims to collate significant scientific contributions made by leading international experts in the molecular evolution of SARS-CoV-2. Due to its unique biological characteristics, SARS-CoV-2 has exhibited a high propensity for molecular changes and adaptation. Consequently, numerous variants, subvariants, and recombinants of SARS-CoV-2 have emerged since the beginning of the pandemic. Several molecular surveys have been conducted and published over the years, revealing varying expansion capabilities and molecular characteristics among lineages. However, all studies emphasize the necessity for continuous and uninterrupted genome-based surveillance. This approach would provide the most comprehensive understanding of the current predominant lineage’s genomic composition. Indeed, constant monitoring is crucial for identifying and predicting significant changes in genomic composition, enabling the development of appropriate action plans.

Dr. Fabio Scarpa
Prof. Dr. Massimo Ciccozzi
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. 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.


  • SARS-CoV-2 phylogenomics
  • genetics
  • molecular epidemiology

Published Papers (1 paper)

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Integrative Genome-Based Survey of the SARS-CoV-2 Omicron XBB.1.16 Variant
Int. J. Mol. Sci. 2023, 24(17), 13573; https://doi.org/10.3390/ijms241713573 - 01 Sep 2023
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The XBB.1.16 SARS-CoV-2 variant, also known as Arcturus, is a recent descendant lineage of the recombinant XBB (nicknamed Gryphon). Compared to its direct progenitor, XBB.1, XBB.1.16 carries additional spike mutations in key antigenic sites, potentially conferring an ability to evade the [...] Read more.
The XBB.1.16 SARS-CoV-2 variant, also known as Arcturus, is a recent descendant lineage of the recombinant XBB (nicknamed Gryphon). Compared to its direct progenitor, XBB.1, XBB.1.16 carries additional spike mutations in key antigenic sites, potentially conferring an ability to evade the immune response compared to other circulating lineages. In this context, we conducted a comprehensive genome-based survey to gain a detailed understanding of the evolution and potential dangers of the XBB.1.16 variant, which became dominant in late June. Genetic data indicates that the XBB.1.16 variant exhibits an evolutionary background with limited diversification, unlike dangerous lineages known for rapid changes. The evolutionary rate of XBB.1.16, which amounts to 3.95 × 10−4 subs/site/year, is slightly slower than that of its direct progenitors, XBB and XBB.1.5, which have been circulating for several months. A Bayesian Skyline Plot reconstruction suggests that the peak of genetic variability was reached in early May 2023, and currently, it is in a plateau phase with a viral population size similar to the levels observed in early March. Structural analyses indicate that, overall, the XBB.1.16 variant does not possess structural characteristics markedly different from those of the parent lineages, and the theoretical affinity for ACE2 does not seem to change among the compared variants. In conclusion, the genetic and structural analyses of SARS-CoV-2 XBB.1.16 do not provide evidence of its exceptional danger or high expansion capability. Detected differences with previous lineages are probably due to genetic drift, which allows the virus constant adaptability to the host, but they are not necessarily connected to a greater danger. Nevertheless, continuous genome-based monitoring is essential for a better understanding of its descendants and other lineages. Full article
(This article belongs to the Special Issue Genetic Variability and Molecular Evolution of SARS-CoV-2)
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