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Viruses
Special Issues
Intra-patient Viral Evolution
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Intra-patient Viral Evolution

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: 30 August 2024 | Viewed by 1110

Special Issue Editors

Dr. Adam A. Capoferri

E-Mail Website
Guest Editor
Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
Interests: HIV translational research; HIV persistence; intra-patient viral genetics; single-cell viral genetics and expression; co-evolution of viruses by another virus and/or host factor
Dr. Mary Kearney

E-Mail Website
Guest Editor
Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
Interests: HIV translational research; HIV persistence; intra-patient viral genetics; single-cell viral genetics and expression; clonal expansion of HIV-infected cells
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viruses can persist in latent or replicating forms for weeks to years and even lifetimes in infected hosts. Viral persistence is facilitated by intra-patient viral evolution driven by many selective pressures, including adaptation to a new host, immunologic evasion and escape, tissue and cell tropism, and drug resistance, to name a few. Understanding intra-host viral evolution has revealed mechanisms for viral persistence and pathogenesis and contributed to the development of antivirals and preventive and therapeutic vaccines. In this Special Issue, Intra-patient Viral Evolution, we aim to provide original research and review articles describing how viruses including HIV, SARS-CoV-2, Ebolavirus, HCV, HTLV, and more evolve in the host and how these evolutionary patterns can be used to understand their persistence and pathogenesis and reveal new targets for the development of new treatments and curative strategies.

We are pleased to invite you to submit an original research article or a review paper on or related to intra-patient viral evolution.

We look forward to receiving your contributions.

Dr. Adam A. Capoferri
Dr. Mary Kearney
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. Viruses 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 2600 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

  • intra-patient viral evolution
  • drug resistance
  • immune escape
  • co-evolution
  • virus persistence
  • virus evolution

Published Papers (1 paper)

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Research

13 pages, 1195 KiB  
Article
Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis
by Dominique Fournelle, Fatima Mostefai, Elsa Brunet-Ratnasingham, Raphaël Poujol, Jean-Christophe Grenier, José Héctor Gálvez, Amélie Pagliuzza, Inès Levade, Sandrine Moreira, Mehdi Benlarbi, Guillaume Beaudoin-Bussières, Gabrielle Gendron-Lepage, Catherine Bourassa, Alexandra Tauzin, Simon Grandjean Lapierre, Nicolas Chomont, Andrés Finzi, Daniel E. Kaufmann, Morgan Craig and Julie G. Hussin
Viruses 2024, 16(3), 342; https://doi.org/10.3390/v16030342 - 23 Feb 2024
Viewed by 860
Abstract
Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein’s receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in [...] Read more.
Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein’s receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we present the case of an immunosuppressed patient that developed distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. These mutations were acquired without the patient being treated with mAbs nor convalescent sera and without them developing a detectable immune response to the virus. We also provide additional evidence for a viral reservoir based on intra-host phylogenetics, which led to a viral substrain that evolved elsewhere in the patient’s body, colonizing their upper respiratory tract (URT). The presence of SARS-CoV-2 viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable, and potential explanations for long-COVID cases. Full article
(This article belongs to the Special Issue Intra-patient Viral Evolution)
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