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Analysis of institutional authors

Somovilla, PilarAuthorEsteban, JaimeAuthorFernandez-Roblas, RicardoAuthorGadea, IgnacioAuthor

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October 7, 2024
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Article

SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation?

Publicated to:Frontiers in Microbiology. 15 1358258- - 2024-03-14 15(), DOI: 10.3389/fmicb.2024.1358258

Authors: Martinez-Gonzalez, Brenda; Soria, Maria Eugenia; Minguez, Pablo; Lorenzo-Redondo, Ramon; Salar-Vidal, Llanos; Lopez-Garcia, Alberto; Esteban-Munoz, Mario; Duran-Pastor, Antoni; Somovilla, Pilar; Garcia-Crespo, Carlos; de avila, Ana Isabel; Gomez, Jordi; Esteban, Jaime; Fernandez-Roblas, Ricardo; Gadea, Ignacio; Domingo, Esteban; Perales, Celia

Affiliations

CSIC, Ctr Nacl Biotecnol CNB CSIC, Dept Mol & Cell Biol, Campus Cantoblanco, Madrid, Spain - Author
Ctr Biol Mol Severo Ochoa CSIC UAM, Campus Cantoblanco, Madrid, Spain - Author
Ctr Biomed Res Infect Dis Network CIBERINFEC, Madrid, Spain - Author
Fdn Jimenez Diaz Univ Hosp, Hlth Res Inst IIS FJD, Madrid, Spain - Author
Inst Parasitol & Biomed Lopez Neyra CSIC, Parque Tecnol Ciencias Salud, Granada, Spain - Author
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid, Spain - Author
Northwestern Univ, Ctr Pathogen Genom & Microbial Evolut, Feinberg Sch Med, Div Infect Dis, Chicago, IL USA - Author
Univ Autonoma Madrid IIS FJD, Fdn Jimenez Diaz Univ Hosp, Inst Invest Sanitaria, Bioinformat Unit,UAM, Madrid, Spain - Author
Univ Autonoma Madrid IIS FJD, Fdn Jimenez Diaz Univ Hosp, Inst Invest Sanitaria, Dept Genet & Genom,UAM, Madrid, Spain - Author
Univ Autonoma Madrid IIS FJD, Fdn Jimenez Diaz Univ Hosp, UAM, Dept Clin Microbiol,Inst Invest Sanitaria, Madrid, Spain - Author
Univ Autonoma Madrid, Dept Biol Mol, Campus Cantoblanco, Madrid, Spain - Author
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Abstract

Introduction SARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade.Methods Here we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra.Results In 6 out of 11 SARS-CoV-2 isolates from COVID-19 patients, the mutant spectrum of the spike (S)-coding region included two or more amino acids or deletions, that correspond to discordant viral clades. A similar observation is reported for laboratory populations of SARS-CoV-2 USA-WA1/2020, following a cell culture infection in the presence of remdesivir, ribavirin or their combinations. Moreover, some of the clade-discordant genome residues are found in the same haplotype within an amplicon.Discussion We evaluate possible interpretations of these findings, and reviewed precedents for rapid selection of genomes with multiple mutations in RNA viruses. These considerations suggest that intra-host evolution may be sufficient to generate minority sequences which are closely related to sequences typical of other clades. The results provide a model for the origin of variants of concern during epidemic spreadin particular Omicron lineagesthat does not require prolonged infection, involvement of immunocompromised individuals, or participation of intermediate, non-human hosts.

Keywords

Clade-discordant residuesCovid-19OriginRna virusUltra-deep sequencingVariant of concerVariant of concernViral emergenceViral quasispecies

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Frontiers in Microbiology due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2024 there are still no calculated indicators, but in 2023, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Microbiology.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2025-07-20:

  • Google Scholar: 1

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-20:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 3.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 4 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 1.35.
  • The number of mentions on the social network X (formerly Twitter): 3 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://repositorio.uam.es/handle/10486/718222

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: United States of America.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Martinez-Gonzalez, Brenda) and Last Author (Perales, Celia).

the authors responsible for correspondence tasks have been Domingo, Esteban and Perales, Celia.