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Genomic Variation of SARS-CoV-2

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 7675

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Dr. Carlos Flores

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Guest Editor

1. Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain
2. Genomics Division, Instituto Tecnológico y de Energías Renovables, 38600 Santa Cruz de Tenerife, Spain
Interests: COVID-19; sepsis; ARDS; genomic surveillance; complex respiratory traits

Special Issue Information

Dear Colleagues,

The SARS-CoV-2 pandemic has evidenced the challenges in establishing and maintaining resources that allow us to be able to face emerging viral zoonoses rapidly and efficiently around the globe. Genomic surveillance, leveraging applications of next-generation sequencing, is emerging as a central requirement to achieve effective actions to mitigate and control transmission. In parallel, the threat has encouraged local, national, and international collaborative networks to deeply dissect COVID-19 pathogenesis, risk factors, and outcomes from different angles based on genetic, immunological, molecular, and cellular studies. These networks have assembled complementary solutions, resources, and knowledge in order to detect distinctive health events quickly and to link them with the public health system as the pandemic evolves.

This Special Issue welcomes the submission of original research articles, short communications, and comprehensive reviews describing developments for effective COVID-19 diagnosis, surveillance, and preparedness against outbreaks, fundamental studies at molecular and cellular levels, methods that could offer novel approximations to detect spreading variants and innovative analytic solutions for viral genome variation in general, strategies to effectively mitigate and contain outbreaks, and transmission dynamics in notable settings.

Dr. Carlos Flores
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

diagnosis
variants of concern
technological improvements
surveillance
viral sequencing
phylogenetics
outbreaks
preparedness
One Health
transmission dynamics
next-generation sequencing

Published Papers (4 papers)

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Research

17 pages, 1941 KiB

Open AccessArticle

Enhancing SARS-CoV-2 Surveillance through Regular Genomic Sequencing in Spain: The RELECOV Network

by Sonia Vázquez-Morón, María Iglesias-Caballero, José Antonio Lepe, Federico Garcia, Santiago Melón, José M. Marimon, Darío García de Viedma, Maria Dolores Folgueira, Juan Carlos Galán, Carla López-Causapé, Rafael Benito-Ruesca, Julia Alcoba-Florez, Fernando Gonzalez Candelas, María de Toro, Miguel Fajardo, Carmen Ezpeleta, Fernando Lázaro, Sonia Pérez Castro, Isabel Cuesta, Angel Zaballos, Francisco Pozo, Inmaculada Casas and on behalf of RELECOV Network Members Show full author list Hide full author list

Int. J. Mol. Sci. 2023, 24(10), 8573; https://doi.org/10.3390/ijms24108573 - 10 May 2023

Cited by 1 | Viewed by 2255

Abstract

Millions of SARS-CoV-2 whole genome sequences have been generated to date. However, good quality data and adequate surveillance systems are required to contribute to meaningful surveillance in public health. In this context, the network of Spanish laboratories for coronavirus (RELECOV) was created with the main goal of promoting actions to speed up the detection, analyses, and evaluation of SARS-CoV-2 at a national level, partially structured and financed by an ECDC-HERA-Incubator action (ECDC/GRANT/2021/024). A SARS-CoV-2 sequencing quality control assessment (QCA) was developed to evaluate the network’s technical capacity. QCA full panel results showed a lower hit rate for lineage assignment compared to that obtained for variants. Genomic data comprising 48,578 viral genomes were studied and evaluated to monitor SARS-CoV-2. The developed network actions showed a 36% increase in sharing viral sequences. In addition, analysis of lineage/sublineage-defining mutations to track the virus showed characteristic mutation profiles for the Delta and Omicron variants. Further, phylogenetic analyses strongly correlated with different variant clusters, obtaining a robust reference tree. The RELECOV network has made it possible to improve and enhance the genomic surveillance of SARS-CoV-2 in Spain. It has provided and evaluated genomic tools for viral genome monitoring and characterization that make it possible to increase knowledge efficiently and quickly, promoting the genomic surveillance of SARS-CoV-2 in Spain. Full article

(This article belongs to the Special Issue Genomic Variation of SARS-CoV-2)

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20 pages, 4535 KiB

Open AccessArticle

In Silico Design of New Dual Inhibitors of SARS-CoV-2 M^PRO through Ligand- and Structure-Based Methods

by Alessia Bono, Antonino Lauria, Gabriele La Monica, Federica Alamia, Francesco Mingoia and Annamaria Martorana

Int. J. Mol. Sci. 2023, 24(9), 8377; https://doi.org/10.3390/ijms24098377 - 06 May 2023

Cited by 2 | Viewed by 1314

Abstract

The viral main protease is one of the most attractive targets among all key enzymes involved in the life cycle of SARS-CoV-2. Considering its mechanism of action, both the catalytic and dimerization regions could represent crucial sites for modulating its activity. Dual-binding the SARS-CoV-2 main protease inhibitors could arrest the replication process of the virus by simultaneously preventing dimerization and proteolytic activity. To this aim, in the present work, we identified two series’ of small molecules with a significant affinity for SARS-CoV-2 M^PRO, by a hybrid virtual screening protocol, combining ligand- and structure-based approaches with multivariate statistical analysis. The Biotarget Predictor Tool was used to filter a large in-house structural database and select a set of benzo[b]thiophene and benzo[b]furan derivatives. ADME properties were investigated, and induced fit docking studies were performed to confirm the DRUDIT prediction. Principal component analysis and docking protocol at the SARS-CoV-2 M^PRO dimerization site enable the identification of compounds 1b,c,i,l and 2i,l as promising drug molecules, showing favorable dual binding site affinity on SARS-CoV-2 M^PRO. Full article

(This article belongs to the Special Issue Genomic Variation of SARS-CoV-2)

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18 pages, 2271 KiB

Open AccessArticle

Quasispecies Analysis of SARS-CoV-2 of 15 Different Lineages during the First Year of the Pandemic Prompts Scratching under the Surface of Consensus Genome Sequences

by Wahiba Bader, Jeremy Delerce, Sarah Aherfi, Bernard La Scola and Philippe Colson

Int. J. Mol. Sci. 2022, 23(24), 15658; https://doi.org/10.3390/ijms232415658 - 10 Dec 2022

Cited by 3 | Viewed by 1535

Abstract

The tremendous majority of SARS-CoV-2 genomic data so far neglected intra-host genetic diversity. Here, we studied SARS-CoV-2 quasispecies based on data generated by next-generation sequencing (NGS) of complete genomes. SARS-CoV-2 raw NGS data had been generated for nasopharyngeal samples collected between March 2020 and February 2021 by the Illumina technology on a MiSeq instrument, without prior PCR amplification. To analyze viral quasispecies, we designed and implemented an in-house Excel file (“QuasiS”) that can characterize intra-sample nucleotide diversity along the genomes using data of the mapping of NGS reads. We compared intra-sample genetic diversity and global genetic diversity available from Nextstrain. Hierarchical clustering of all samples based on the intra-sample genetic diversity was performed and visualized with the Morpheus web application. NGS mapping data from 110 SARS-CoV-2-positive respiratory samples characterized by a mean depth of 169 NGS reads/nucleotide position and for which consensus genomes that had been obtained were classified into 15 viral lineages were analyzed. Mean intra-sample nucleotide diversity was 0.21 ± 0.65%, and 5357 positions (17.9%) exhibited significant (>4%) diversity, in ≥2 genomes for 1730 (5.8%) of them. ORF10, spike, and N genes had the highest number of positions exhibiting diversity (0.56%, 0.34%, and 0.24%, respectively). Nine hot spots of intra-sample diversity were identified in the SARS-CoV-2 NSP6, NSP12, ORF8, and N genes. Hierarchical clustering delineated a set of six genomes of different lineages characterized by 920 positions exhibiting intra-sample diversity. In addition, 118 nucleotide positions (0.4%) exhibited diversity at both intra- and inter-patient levels. Overall, the present study illustrates that the SARS-CoV-2 consensus genome sequences are only an incomplete and imperfect representation of the entire viral population infecting a patient, and that quasispecies analysis may allow deciphering more accurately the viral evolutionary pathways. Full article

(This article belongs to the Special Issue Genomic Variation of SARS-CoV-2)

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17 pages, 1515 KiB

Open AccessArticle

A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations

by Jacobo Pardo-Seco, Xabier Bello, Alberto Gómez-Carballa, Federico Martinón-Torres, José Ignacio Muñoz-Barús and Antonio Salas

Int. J. Mol. Sci. 2022, 23(21), 12899; https://doi.org/10.3390/ijms232112899 - 25 Oct 2022

Cited by 1 | Viewed by 1798

Abstract

Establishing the timeframe when a particular virus was circulating in a population could be useful in several areas of biomedical research, including microbiology and legal medicine. Using simulations, we demonstrate that the circulation timeframe of an unknown SARS-CoV-2 genome in a population (hereafter, estimated time of a queried genome [QG]; t_E-QG) can be easily predicted using a phylogenetic model based on a robust reference genome database of the virus, and information on their sampling dates. We evaluate several phylogeny-based approaches, including modeling evolutionary (substitution) rates of the SARS-CoV-2 genome (~10⁻³ substitutions/nucleotide/year) and the mutational (substitutions) differences separating the QGs from the reference genomes (RGs) in the database. Owing to the mutational characteristics of the virus, the present Viral Molecular Clock Dating (VMCD) method covers timeframes going backwards from about a month in the past. The method has very low errors associated to the t_E-QG estimates and narrow intervals of t_E-QG, both ranging from a few days to a few weeks regardless of the mathematical model used. The SARS-CoV-2 model represents a proof of concept that can be extrapolated to any other microorganism, provided that a robust genome sequence database is available. Besides obvious applications in epidemiology and microbiology investigations, there are several contexts in forensic casework where estimating t_E-QG could be useful, including estimation of the postmortem intervals (PMI) and the dating of samples stored in hospital settings. Full article

(This article belongs to the Special Issue Genomic Variation of SARS-CoV-2)

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