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PERSPECTIVE article

Front. Trop. Dis
Sec. Major Tropical Diseases
Volume 5 - 2024 | doi: 10.3389/fitd.2024.1512606
This article is part of the Research Topic Recent Advances In “Omics” Of Tropical Diseases View all 5 articles

Beyond surveillance: Leveraging the Potential of Next Generation Sequencing In Clinical Virology

Provisionally accepted
Paula C. Aulicino Paula C. Aulicino 1,2*Jason T. Kimata Jason T. Kimata 3
  • 1 Area of Specialized Laboratories, Garrahan Hospital, Buenos Aires, Argentina
  • 2 National Scientific and Technical Research Council (CONICET), Buenos Aires, Buenos Aires, Argentina
  • 3 Baylor College of Medicine, Houston, Texas, United States

The final, formatted version of the article will be published soon.

    The COVID-19 pandemic demonstrated the strength of massive sequencing or next generation sequencing (NGS) techniques in viral genomic characterization. Millions of complete SARS-CoV-2 genomes were sequenced in almost real time. Laboratories around the world dedicated to the molecular diagnosis of infectious diseases were equipped with cutting-edge technologies for deep sequencing, coupled with strengthening or development of previously limited bioinformatics capacities. Almost 5 years have passed from the initiation of the COVID pandemic, and, opposed to what could be envisioned as an opportunity for viral genomics to expand, this has essentially scaled back in most clinical settings. Most of NGS equipment and capacities in many regions of the world have been repurposed for the study of cancer driver mutations, microbiome-related diseases, and pharmacogenomics, as the most important applications in health. Although financial constraints can limit their implementation, technical, regulatory, medical and data management factors are also part of the equation that will or will not make NGS a real game changer for advancing healthcare and guiding clinical decisions related to viral infections.Next generation sequencing and metagenomics is an important tool for diagnosing viral infections and managing treatment.

    Keywords: Clinical Virology, NGS, Genomics, Deep sequencing, Viral genomics

    Received: 17 Oct 2024; Accepted: 28 Oct 2024.

    Copyright: © 2024 Aulicino and Kimata. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Paula C. Aulicino, Area of Specialized Laboratories, Garrahan Hospital, Buenos Aires, Argentina

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.