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Microorganisms
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Advances in Viral Metagenomics
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Advances in Viral Metagenomics

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

Deadline for manuscript submissions: 31 May 2025 | Viewed by 12614

Special Issue Editor

Dr. Antonio Charlys Da Costa

E-Mail Website
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 Issue Information

Dear Colleagues,

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:

  • 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
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. 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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Published Papers (7 papers)

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13 pages, 1337 KiB  
Article
Viral Metagenomics in Patients Who Underwent Allogeneic Hematopoietic Stem Cell Transplantation (HSCT): A Brazilian Experience
by Gabriel Montenegro de Campos, Thalita Cristina de Mello Costa, Roberta Maraninchi Silveira, Ian Nunes Valença, Rafael dos Santos Bezerra, Luiz Guilherme Darrigo Junior, Ana Carolina de Jesus Vieira, Camila Campos Mesquita, Patrícia da Silva Laurindo, Renato Guerino Cunha, Simone Kashima, Dimas Tadeu Covas, Belinda Pinto Simões, Sandra Coccuzzo Sampaio, Maria Carolina Elias, Marta Giovanetti and Svetoslav Nanev Slavov
Microorganisms 2024, 12(12), 2557; https://doi.org/10.3390/microorganisms12122557 - 12 Dec 2024
Viewed by 671
Abstract
Viral infections are one of the most important causes of morbidity and mortality among patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT). Immunosuppression may lead to the reactivation of latent viruses or the acquisition of new infections, resulting in severe clinical outcomes. The [...] Read more.
Viral infections are one of the most important causes of morbidity and mortality among patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT). Immunosuppression may lead to the reactivation of latent viruses or the acquisition of new infections, resulting in severe clinical outcomes. The early detection of viral reactivations is crucial for effective patient management and post-transplant care. In this study, we employed next-generation metagenomics to assess changes in viral abundance and detect clinically significant viruses in allogeneic HSCT patients. A total of 20 patients from the Transplant Unit of the University Hospital of the Faculty of Medicine of Ribeirão Preto, University of São Paulo were included, with plasma samples collected at three time points: D + 0 (pre-transplantation), D + 30 (30 days post-transplantation), and D + 100 (~100 days post-transplantation). A higher presence of clinically relevant viruses, such as the cytomegalovirus (CMV), the Epstein-Barr virus (EBV) and adenoviruses, were predominantly detected at D + 30. The diversity of commensal viruses, primarily anelloviruses, increased gradually, with the highest abundance and variability detected at D + 100. Viruses with clinical importance for HSCT, including CMV, adenovirus and EBV, were confirmed and characterized at the molecular level, showing generally high cycle threshold values. Our findings demonstrate a rise in anellovirus abundance following allogeneic HSCT, with the highest levels observed at D + 100. Notably, D + 30 was identified as a critical time point for the reactivation of clinically significant viruses. This study underscores the potential of metagenomics in the identification of clinically relevant viruses and highlights the importance of monitoring latent viruses in immunocompromised populations, including allogeneic HSCT patients. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics)
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15 pages, 3942 KiB  
Article
Identification of Viruses in Molossus Bats from the Brazilian Amazon: A Descriptive Metagenomic Analysis
by Lucas Rafael Santana Pinheiro, Érika Dayane Leal Rodrigues, Francisco Amilton dos Santos Paiva, Ana Cecília Ribeiro Cruz, Daniele Barbosa de Almeida Medeiros, Alexandre do Rosário Casseb, Sandro Patroca da Silva and Livia Medeiros Neves Casseb
Microorganisms 2024, 12(3), 593; https://doi.org/10.3390/microorganisms12030593 - 16 Mar 2024
Viewed by 1634
Abstract
Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from [...] Read more.
Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from 58 bats were divided into 13 pools for RNA isolation and sequencing followed by bioinformatic analysis. The Retroviridae family showed the highest abundance of viral reads. Although no complete genome could be recovered, the Paramyxoviridae and Dicistroviridae families showed the formation of contigs with satisfactory identity and size characteristics for further analysis. One contig of the Paramyxoviridae family was characterized as belonging to the genus Morbillivirus, being grouped most closely phylogenetically to Porcine morbillivirus. The contig related to the Dicistroviridae family was identified within the Cripavirus genus, with 94%, 91%, and 42% amino acid identity with Culex dicistrovirus 2, Rhopalosiphum padi, and Aphid lethal paralysis, respectively. The presence of viruses in bats needs constant updating since the study was able to identify viral sequences related to families or genera still poorly described in the literature in association with bats. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics)
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14 pages, 506 KiB  
Article
Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats
by Roseane da Silva Couto, Endrya do Socorro Foro Ramos, Wandercleyson Uchôa Abreu, Luis Reginaldo Ribeiro Rodrigues, Luis Fernando Marinho, Vanessa dos Santos Morais, Fabiola Villanova, Ramendra Pati Pandey, Xutao Deng, Eric Delwart, Antonio Charlys da Costa and Elcio Leal
Microorganisms 2024, 12(1), 206; https://doi.org/10.3390/microorganisms12010206 - 19 Jan 2024
Cited by 1 | Viewed by 1886
Abstract
The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in [...] Read more.
The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics)
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18 pages, 4055 KiB  
Article
Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome
by Adriana Soria-Villalba, Nicole Pesantes, Nuria Jiménez-Hernández, Javier Pons, Andrés Moya and Vicente Pérez-Brocal
Microorganisms 2024, 12(1), 162; https://doi.org/10.3390/microorganisms12010162 - 13 Jan 2024
Cited by 1 | Viewed by 1969
Abstract
Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches [...] Read more.
Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics)
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13 pages, 863 KiB  
Article
Pegivirus Detection in Cerebrospinal Fluid from Patients with Central Nervous System Infections of Unknown Etiology in Brazil by Viral Metagenomics
by Rita de Cássia Compagnoli Carmona, Audrey Cilli, Antonio Charlys da Costa, Fabricio Caldeira Reis, Élcio Leal, Fabiana Cristina Pereira dos Santos, Bráulio Caetano Machado, Cristina Santiago Lopes, Ana Maria Sardinha Afonso and Maria do Carmo Sampaio Tavares Timenetsky
Microorganisms 2024, 12(1), 19; https://doi.org/10.3390/microorganisms12010019 - 22 Dec 2023
Viewed by 1609
Abstract
Metagenomic next-generation sequencing (mNGS) methodology serves as an excellent supplement in cases where diagnosis is challenging to establish through conventional laboratory tests, and its usage is increasingly prevalent. Examining the causes of infectious diseases in the central nervous system (CNS) is vital for [...] Read more.
Metagenomic next-generation sequencing (mNGS) methodology serves as an excellent supplement in cases where diagnosis is challenging to establish through conventional laboratory tests, and its usage is increasingly prevalent. Examining the causes of infectious diseases in the central nervous system (CNS) is vital for understanding their spread, managing outbreaks, and effective patient care. In a study conducted in the state of São Paulo, Brazil, cerebrospinal fluid (CSF) samples from 500 patients with CNS diseases of indeterminate etiology, collected between 2017 and 2021, were analyzed. Employing a mNGS approach, we obtained the complete coding sequence of Pegivirus hominis (HPgV) genotype 2 in a sample from a patient with encephalitis (named IAL-425/BRA/SP/2019); no other pathogen was detected. Subsequently, to determine the extent of this virus’s presence, both polymerase chain reaction (PCR) and/or real-time PCR assays were utilized on the entire collection. The presence of the virus was identified in 4.0% of the samples analyzed. This research constitutes the first report of HPgV detection in CSF samples in South America. Analysis of the IAL-425 genome (9107 nt) revealed a 90% nucleotide identity with HPgV strains from various countries. Evolutionary analyses suggest that HPgV is both endemic and extensively distributed. The direct involvement of HPgV in CNS infections in these patients remains uncertain. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics)
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13 pages, 3075 KiB  
Article
Unlocking the Viral Universe: Metagenomic Analysis of Bat Samples Using Next-Generation Sequencing
by German V. Roev, Nadezhda I. Borisova, Nadezhda V. Chistyakova, Matvey R. Agletdinov, Vasily G. Akimkin and Kamil Khafizov
Microorganisms 2023, 11(10), 2532; https://doi.org/10.3390/microorganisms11102532 - 10 Oct 2023
Cited by 2 | Viewed by 2081
Abstract
Next-generation sequencing technologies have revolutionized the field of virology by enabling the reading of complete viral genomes, extensive metagenomic studies, and the identification of novel viral pathogens. Although metagenomic sequencing has the advantage of not requiring specific probes or primers, it faces significant [...] Read more.
Next-generation sequencing technologies have revolutionized the field of virology by enabling the reading of complete viral genomes, extensive metagenomic studies, and the identification of novel viral pathogens. Although metagenomic sequencing has the advantage of not requiring specific probes or primers, it faces significant challenges in analyzing data and identifying novel viruses. Traditional bioinformatics tools for sequence identification mainly depend on homology-based strategies, which may not allow the detection of a virus significantly different from known variants due to the extensive genetic diversity and rapid evolution of viruses. In this work, we performed metagenomic analysis of bat feces from different Russian cities and identified a wide range of viral pathogens. We then selected sequences with minimal homology to a known picornavirus and used “Switching Mechanism at the 5′ end of RNA Template” technology to obtain a longer genome fragment, allowing for more reliable identification. This study emphasizes the importance of integrating advanced computational methods with experimental strategies for identifying unknown viruses to better understand the viral universe. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics)
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10 pages, 2286 KiB  
Brief Report
Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2
by Gabriel Montenegro de Campos, Debora Glenda Lima de La-Roque, Alex Ranieri Jerônimo Lima, Victória Simionatto Zucherato, Eneas de Carvalho, Loyze Paola Oliveira de Lima, Pedro de Queiroz Cattony Neto, Murilo Marconi dos Santos, Massimo Ciccozzi, Marta Giovanetti, Rodrigo Haddad, Luiz Carlos Júnior Alcantara, Maria Carolina Elias, Sandra Coccuzzo Sampaio, Dimas Tadeu Covas, Simone Kashima and Svetoslav Nanev Slavov
Microorganisms 2023, 11(11), 2744; https://doi.org/10.3390/microorganisms11112744 - 10 Nov 2023
Viewed by 1811
Abstract
The emergence of SARS-CoV-2 and the subsequent pandemic have prompted extensive diagnostic and clinical efforts to mitigate viral spread. However, these strategies have largely overlooked the presence of other respiratory viruses. Acute respiratory diseases in pediatric patients can be caused by a diverse [...] Read more.
The emergence of SARS-CoV-2 and the subsequent pandemic have prompted extensive diagnostic and clinical efforts to mitigate viral spread. However, these strategies have largely overlooked the presence of other respiratory viruses. Acute respiratory diseases in pediatric patients can be caused by a diverse range of viral agents, and metagenomics represents a powerful tool for their characterization. This study aimed to investigate the viral abundance in pediatric patients with acute respiratory symptoms who tested negative for SARS-CoV-2 during the Omicron pandemic wave. To achieve this, viral metagenomics and next-generation sequencing were employed on 96 nasopharyngeal swab samples, which were organized into 12 pools, with each pool consisting of eight individual samples. Metagenomic analysis revealed that the most prevalent viruses associated with acute disease in pediatric patients were respiratory syncytial virus (detected in all pools) and enteroviruses, which are known to cause significant morbidity and mortality in children. Additionally, clinically significant viruses such as mumps orthorubulavirus, human metapneumovirus, influenza A, and a wide array of human herpesviruses (1, 3–7) were identified. These findings highlight the extensive potential of viral metagenomics in identifying viruses other than SARS-CoV-2 that contribute to acute infections in children. Consequently, this methodology should garner clinical attention in terms of differential diagnosis and the development of public policies to address such conditions in the global pediatric population. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics)
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