Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2

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de Campos, Gabriel Montenegro ; Lima de La-Roque, Debora Glenda ; Jeronimo Lima, Alex Ranieri ; Zucherato, Victoria Simionatto ; de Carvalho, Eneas ; Oliveira de Lima, Loyze Paola ; Cattony Neto, Pedro de Queiroz ; dos Santos, Murilo Marconi ; Ciccozzi, Massimo ; Giovanetti, Marta ; Haddad, Rodrigo ; Junior Alcantara, Luiz Carlos ; Elias, Maria Carolina ; Sampaio, Sandra Coccuzzo ; Covas, Dimas Tadeu ; Kashima, Simone ; Slavov, Svetoslav Nanev

• Document type: Journal article
• Source: MICROORGANISMS; v. 11, n. 11, p. 10-pg., 2023-11-01.

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 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. (AU)

• FAPESP's process: 22/00910-6 - Development and application of bioinformatic pipelines for metagenomic analysis of clinical samples
• Grantee: Gabriel Montenegro de Campos
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• FAPESP's process: 17/23205-8 - Evaluation of the impact of emerging and reemerging viruses in the field of hemotherapy and stem cell transplantation by multiple-research approach
• Grantee: Svetoslav Nanev Slavov
• Support Opportunities: Research Grants - Young Investigators Grants
• FAPESP's process: 21/11944-6 - Continuous improvement of vaccines: Center for Viral Surveillance and Serological Assessment (CeVIVAS)
• Grantee: Sandra Coccuzzo Sampaio Vessoni
• Support Opportunities: Research Grants - Science Centers for Development
• FAPESP's process: 18/15826-5 - Evaluation of the impact of emerging and reemerging viruses in the field of hemotherapy and stem-cell transplantation by multiple-research approach
• Grantee: Svetoslav Nanev Slavov
• Support Opportunities: Scholarships in Brazil - Young Researchers
• FAPESP's process: 21/09446-8 - Application of portable minion sequencing technology for viral metagenomics analysis
• Grantee: Victória Simionatto Zucherato
• Support Opportunities: Scholarships in Brazil - Master