Advances in Viral Metagenomics, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Virology".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 2123

Editors


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Guest Editor
Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
Interests: viral genetic diversity; viral metagenomics; new viruses; genomics
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
1. Department of Infectious Diseases and Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
2. Medical Research Laboratory LIM 52, Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
Interests: virology; human herpesviruses; infectious diseases; molecular biology; immunology; public health; viral shedding; genetic polymorphisms; tropical medicine; HIV/AIDS

E-Mail Website
Guest Editor
1. Department of Infectious Diseases and Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
2. Medical Research Laboratory LIM 52, Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
Interests: HIV; hepatitis C; coinfection; viral hepatitis; AIDS

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Advances in Viral Metagenomics”.

Viral metagenomics, a powerful and rapidly evolving field, has revolutionized our understanding of the viral world and its impact on diverse ecosystems, including human health, agriculture, and the environment. By employing high-throughput sequencing technologies and bioinformatics tools, viral metagenomics enables the comprehensive study of viral communities and their genetic diversity without the need for isolation and cultivation. This Special Issue aims to highlight the latest advances in viral metagenomics, exploring its applications, methodologies, and contributions to unravel the complexity of viral populations and their interactions with hosts.

This Special Issue invites original research articles, reviews, and perspectives that encompass a wide range of topics related to advances in viral metagenomics, including, but not limited to, the following:

  • Innovative methodologies and bioinformatics approaches in viral metagenomics;
  • Viral diversity and dynamics in different environments, including oceans, soils, and the human microbiome;
  • Viral discovery and characterization using metagenomic approaches;
  • Viral–host interactions and co-evolutionary dynamics revealed by metagenomics;
  • The role of viral metagenomics in studying emerging and zoonotic viral diseases;
  • Applications of viral metagenomics in environmental monitoring and surveillance;
  • Viral metagenomics in agricultural systems and plant virome studies;
  • Metagenomic approaches for studying viral communities in the human virome and their implications for health and disease.

We aim to foster a deeper understanding of viral metagenomics and its far-reaching implications. Contributions from researchers and experts in the field will further propel the field forward, unraveling the hidden diversity and functions of viruses in various ecosystems. We welcome researchers, virologists, bioinformaticians, and scientists from related disciplines to contribute their valuable work to this Special Issue, facilitating knowledge exchange and stimulating further advancements in viral metagenomics.

Dr. Antonio Charlys Da Costa
Dr. Tania Regina Tozetto Mendoza
Dr. Maria Cássia Mendes-Correa
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms 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 2700 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

  • virus
  • metagenomics
  • virosphere
  • virome
  • viral diversity
  • viral evolution

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Related Special Issue

Published Papers (2 papers)

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Research

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21 pages, 3512 KB  
Article
Highly Divergent Partiti-like and Narna-like Viral RNA Sequences Detected in Pintomyia fischeri from São Paulo, Brazil: An Exploratory Metatranscriptomic Report
by Vera Lucia Fonseca de Camargo-Neves, Antonio Charlys da Costa, Tatiana Maia de Oliveira Gonçalves, Lilian de Oliveira Guimarães, Roseane da Silva Couto, Marcos Anciete-Santos, Ramendra Pati Pandey, Vanessa Christe Helfstein, Karin Kirchgatter and Elcio Leal
Microorganisms 2026, 14(8), 1723; https://doi.org/10.3390/microorganisms14081723 - 5 Aug 2026
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Abstract
This study investigated the RNA virome associated with the phlebotomine sand fly Pintomyia fischeri using a metatranscriptomic approach applied to the Meta29 library, composed of 21 specimens collected at the São Paulo Zoo, Brazil. Read-based taxonomic analysis revealed a diverse viral community composed [...] Read more.
This study investigated the RNA virome associated with the phlebotomine sand fly Pintomyia fischeri using a metatranscriptomic approach applied to the Meta29 library, composed of 21 specimens collected at the São Paulo Zoo, Brazil. Read-based taxonomic analysis revealed a diverse viral community composed of viruses associated with the families Iflaviridae, Narnaviridae, Partitiviridae, Reoviridae, Solemoviridae, Tombusviridae, Totiviridae, and Tymoviridae, in addition to highly abundant unclassified RNA viruses related to the ShiM 2016 group. Assembly and annotation analyses enabled the characterization of four viral RNA genomes associated with the families Partitiviridae (PfPartitiV-1a-SP, PfPartitiV-1b-SP, and PfPartitiV-2-SP) and Narnaviridae (PfNarnaV-1-SP). Sequence comparisons revealed low amino acid identity relative to currently available reference viral sequences, supporting the classification of these sequences as highly divergent and potentially novel viral lineages. Structural modeling of the RNA-dependent RNA polymerase (RdRp) proteins identified the viral polymerase-specific catalytic motifs A, B, and C. Phylogenetic analyses further supported the evolutionary divergence of the identified viruses relative to currently described taxa. Overall, these findings expand current knowledge of viral RNA diversity associated with Neotropical sand flies and highlight the value of metatranscriptomic approaches for the detection and characterization of previously undescribed viruses associated with medically important insect vectors. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics, 2nd Edition)
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Review

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21 pages, 1056 KB  
Review
The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites—A Narrative Review
by Rebecca Feletti, Antonio Mori, Amina Zaffagnini, Concetta Castilletti and Elena Pomari
Microorganisms 2026, 14(5), 969; https://doi.org/10.3390/microorganisms14050969 - 25 Apr 2026
Cited by 1 | Viewed by 1374
Abstract
The human virome, comprising eukaryotic viruses, bacteriophages, and viral genetic material, is a dynamic component of the microbiome with growing relevance in infectious diseases. This narrative review is structured to: (i) summarize the general composition of the human virome and methodological challenges, including [...] Read more.
The human virome, comprising eukaryotic viruses, bacteriophages, and viral genetic material, is a dynamic component of the microbiome with growing relevance in infectious diseases. This narrative review is structured to: (i) summarize the general composition of the human virome and methodological challenges, including the fraction of unclassified viral “dark matter”; (ii) describe virome alterations in chronic infections; and (iii) explore site-specific virome dynamics across respiratory, intestinal, and genito-urinary tracts in both chronic and acute infections. In chronic viral infections such as HIV, HBV, HCV, and HPV, a recurrent feature is the expansion of Anelloviridae—particularly torque teno virus—reflecting impaired immune surveillance rather than direct pathogenicity, suggesting their potential as surrogate biomarkers of immune competence. Evidence on virome changes in chronic bacterial and parasitic infections remains limited, highlighting a critical knowledge gap. Acute infections are associated with compartment-specific shifts in eukaryotic viruses and bacteriophage communities, often paralleling changes in bacterial populations and inflammatory responses, with implications for disease severity. Despite advances in metagenomic approaches, a substantial proportion of viral sequences remains unclassified, limiting functional interpretation. Nevertheless, virome profiling provides an ecosystem-level perspective, offering insights beyond single-pathogen detection and supporting emerging applications in diagnostics, immune monitoring, prognosis, and infectious disease surveillance. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics, 2nd Edition)
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