Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses
Ibañez-Lligoña, Marta (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Colomer-Castell, Sergi (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
González-Sánchez, Alejandra (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Gregori i Font, Josep (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Campos, Carolina (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Garcia-Cehic, D (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas)
Andrés, Cristina (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Piñana, Maria (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Pumarola Suñé, Tomàs (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Rodríguez Frías, Francisco (Universitat Internacional de Catalunya)
Antón, Andrés (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Quer, Josep 1963- (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)

Data:	2023
Resum:	Epidemics and pandemics have occurred since the beginning of time, resulting in millions of deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism, antigenicity, and susceptibility to antiviral drugs, vaccines, and the host immune response. The best strategy to face the emergence of new infectious genomes is prompt identification. However, currently available diagnostic tests are often limited for detecting new agents. High-throughput next-generation sequencing technologies based on metagenomics may be the solution to detect new infectious genomes and properly diagnose certain diseases. Metagenomic techniques enable the identification and characterization of disease-causing agents, but they require a large amount of genetic material and involve complex bioinformatic analyses. A wide variety of analytical tools can be used in the quality control and pre-processing of metagenomic data, filtering of untargeted sequences, assembly and quality control of reads, and taxonomic profiling of sequences to identify new viruses and ones that have been sequenced and uploaded to dedicated databases. Although there have been huge advances in the field of metagenomics, there is still a lack of consensus about which of the various approaches should be used for specific data analysis tasks. In this review, we provide some background on the study of viral infections, describe the contribution of metagenomics to this field, and place special emphasis on the bioinformatic tools (with their capabilities and limitations) available for use in metagenomic analyses of viral pathogens.
Ajuts:	Ministerio de Economía y Competitividad RD16/0016/0003 Instituto de Salud Carlos III PI19/00301 Instituto de Salud Carlos III PI22/00258 Ministerio de Economía y Competitividad IDI-20200297
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	NGS ; Deep-sequencing ; Viruses ; Metagenomics ; Zoonosis ; Diagnostic tools
Publicat a:	Viruses, Vol. 15, Issue 2 (February 2023) , art. 587, ISSN 1999-4915

DOI: 10.3390/v15020587
PMID: 36851800

15 p, 348.7 KB

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