Marta Ibañez-Lligoña, Sergi Colomer-Castell, Alejandra González-Sánchez, Josep Gregori, Carolina Campos, Damir Garcia-Cehic, Cristina Andrés, Maria Piñana, Tomàs Pumarola, Francisco Rodríguez-Frias, Andrés Antón, Josep Quer, Institut Català de la Salut, [Ibañez-Lligoña M, Colomer-Castell S, Campos C, Quer J] Grup de Recerca de Malalties Hepàtiques, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei d’Hepatologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain. Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain. [González-Sánchez A, Andrés C, Piñana M] Servei de Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. [Gregori J] Grup de Recerca de Malalties Hepàtiques, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei d’Hepatologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Garcia-Cehic D] Grup de Recerca de Malalties Hepàtiques, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei d’Hepatologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain. [Pumarola T, Antón A] Servei de Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Departament de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain. [Rodríguez-Frias F] Grup de Recerca de Malalties Hepàtiques, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei d’Hepatologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain. Department of Basic Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus
Diagnostic tools; Metagenomics; Viruses Herramientas diagnosticas; Metagenómica; Virus Eines diagnòstiques; Metagenòmica; Virus 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. This study was partially supported by Pla Estratègic de Recerca i Innovació en Salut (PERIS)—Direcció General de Recerca i Innovació en Salut (DGRIS), Catalan Health Ministry, Generalitat de Catalunya; the Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0003) from the European Regional Development Fund (ERDF); Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business, grant number IDI-20200297; grants PI19/00301 and PI22/00258 from Instituto de Salud Carlos III, cofinanced by the European Regional Development Fund (ERDF); and Gilead’s biomedical research project GLD21/00006. S.C-C is a recipient of a predoctoral fellowship, FPU, from Ministerio de Universidades (FPU21/04150).