| Author | Campos, Gabriel Montenegro de | |
| Author | Clemente, Luan Gaspar | |
| Author | Lima, Alex Ranieri Jerônimo | |
| Author | Cella, Eleonora | |
| Author | Fonseca, Vagner | |
| Author | Ximenez, João Paulo Bianchi | |
| Author | Nishiyama Junior, Milton Yutaka | |
| Author | Carvalho, Enéas de | |
| Author | Sampaio, Sandra Coccuzzo | |
| Author | Giovanetti, Marta | |
| Author | Elias, Maria Carolina | |
| Author | Slavov, Svetoslav Nanev | |
| Access date | 2025-04-30T17:54:18Z | |
| Available date | 2025-04-30T17:54:18Z | |
| Document date | 2025 | |
| Citation | DE CAMPOS, Gabriel Montenegro et al. Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples. Virology Journal, v. 22, n. 1, 88, 2025. | en_US |
| ISSN | 1743-422X | en_US |
| URI | https://www.arca.fiocruz.br/handle/icict/70047 | |
| Language | eng | en_US |
| Publisher | BioMed Central | en_US |
| Rights | open access | en_US |
| Title | Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples. | en_US |
| Type | Article | en_US |
| DOI | 10.1186/s12985-025-02708-8 | |
| Abstract | Background: Viral metagenomics has expanded significantly in recent years due to advancements in next-generation sequencing, establishing it as the leading method for identifying emerging viruses. A crucial step in metagenomics is taxonomic classification, where sequence data is assigned to specific taxa, thereby enabling the characterization of species composition within a sample. Various taxonomic classifiers have been developed in recent years, each employing distinct classification approaches that produce varying results and abundance profiles, even when analyzing the same sample.
Methods: In this study, we propose using the identification of Torque Teno Viruses (TTVs), from the Anelloviridae family, as indicators to evaluate the performance of four short-read-based metagenomic classifiers: Kraken2, Kaiju, CLARK and DIAMOND, when evaluating human plasma samples.
Results: Our results show that each classifier assigns TTV species at different abundance levels, potentially influencing the interpretation of diversity within samples. Specifically, nucleotide-based classifiers tend to detect a broader range of TTV species, indicating higher sensitivity, while amino acid-based classifiers like DIAMOND and CLARK display lower abundance indices. Interestingly, despite employing different algorithms and data types (protein-based vs. nucleotide-based), Kaiju and Kraken2 performed similarly.
Conclusion: Our study underscores the critical impact of classifier selection on diversity indices in metagenomic analyses. Kaiju effectively assigned a wide variety of TTV species, demonstrating it did not require a high volume of reads to capture diversity. Nucleotide-based classifiers like CLARK and Kraken2 showed superior sensitivity, which is valuable for detecting emerging or rare viruses. At the same time, protein-based approaches such as DIAMOND and Kaiju proved robust for identifying known species with low variability. | en_US |
| Affilliation | Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Programa de Pós-graduação em Oncologia Clínica, Células-Tronco e Terapia Celular. Ribeirão Preto, SP, Brasil. | en_US |
| Affilliation | Universidade de São Paulo. Escola Superior de Agricultura Luiz de Queiroz. Departamento de Zootecnia. Piracicaba, SP, Brasil. | en_US |
| Affilliation | Centro de Vigilância Viral e Avaliação Sorológica. São Paulo, SP, Brasil. | en_US |
| Affilliation | Burnett School of Medical Sciences. College of Medicine. University of Central Florida. Orlando, FL, USA. | en_US |
| Affilliation | Universidade Estadual da Bahia. Departamento de Ciências Exatas e Terra. Salvador, BA, Brasil. / Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa. | en_US |
| Affilliation | Universidade de São Paulo. Faculdade de Ciências Farmacêuticas de Ribeirão Preto. Departamento de Análises Clínicas, Toxicológicas e Bromatológicas. Ribeirão Preto, SP, Brasil. | en_US |
| Affilliation | Instituto Butantan. Laboratório de Toxinologia Aplicada. São Paulo, SP, Brasil. | en_US |
| Affilliation | Instituto Butantan. Laboratório de Bacteriologia. São Paulo, SP, Brasil. | en_US |
| Affilliation | Centro de Vigilância Viral e Avaliação Sorológica. São Paulo, SP, Brasil. | en_US |
| Affilliation | Department of Science and Technologies for Sustainable Development and One Health. Università Campus Bio-Medico di Roma. Rome, Italy. / Fundação Oswaldo Cruz. Instituto Rene Rachou. Belo Horizonte, MG, Brasil. | en_US |
| Affilliation | Centro de Vigilância Viral e Avaliação Sorológica. São Paulo, SP, Brasil. | en_US |
| Affilliation | Instituto Butantan. Centro de Vigilância Viral e Avaliação Sorológica. São Paulo, SP, Brasil. | en_US |
| Subject | Abundance | en_US |
| Subject | Metagenomics | en_US |
| Subject | TTV | en_US |
| Subject | Taxonomic classifiers | en_US |
| Subject | Torque teno viruses | en_US |
