Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2
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 d...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-11-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/11/2744 |
| _version_ | 1797458309731581952 |
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| author | 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 Svetoslav Nanev Slavov |
| author_facet | 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 Svetoslav Nanev Slavov |
| author_sort | Gabriel Montenegro de Campos |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T16:35:13Z |
| format | Article |
| id | doaj.art-7017b0d40a104290858447fcc81eb256 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T16:35:13Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-7017b0d40a104290858447fcc81eb2562023-11-24T14:57:07ZengMDPI AGMicroorganisms2076-26072023-11-011111274410.3390/microorganisms11112744Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2Gabriel Montenegro de Campos0Debora Glenda Lima de La-Roque1Alex Ranieri Jerônimo Lima2Victória Simionatto Zucherato3Eneas de Carvalho4Loyze Paola Oliveira de Lima5Pedro de Queiroz Cattony Neto6Murilo Marconi dos Santos7Massimo Ciccozzi8Marta Giovanetti9Rodrigo Haddad10Luiz Carlos Júnior Alcantara11Maria Carolina Elias12Sandra Coccuzzo Sampaio13Dimas Tadeu Covas14Simone Kashima15Svetoslav Nanev Slavov16Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, BrazilBlood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, BrazilCenter for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, BrazilBlood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, BrazilCenter for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, BrazilCenter for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, BrazilCenter for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, BrazilCenter for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, BrazilUnit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, ItalyInstututo Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, BrazilCampus Ceilândia, University of Brasília, Federal District of Brazil, Brasília 70910-900, BrazilInstututo Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, BrazilCenter for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, BrazilCenter for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, BrazilCenter for Scientific Development (CDC), Butantan Institute, São Paulo 05503-900, BrazilBlood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, BrazilBlood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14050-190, BrazilThe 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.https://www.mdpi.com/2076-2607/11/11/2744viral metagenomicsacute infectionrespiratory virusesenterovirusesrespiratory syncytial virusnext-generation sequencing |
| spellingShingle | 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 Svetoslav Nanev Slavov Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2 Microorganisms viral metagenomics acute infection respiratory viruses enteroviruses respiratory syncytial virus next-generation sequencing |
| title | Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2 |
| title_full | Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2 |
| title_fullStr | Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2 |
| title_full_unstemmed | Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2 |
| title_short | Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2 |
| title_sort | exploring viral metagenomics in pediatric patients with acute respiratory infections unveiling pathogens beyond sars cov 2 |
| topic | viral metagenomics acute infection respiratory viruses enteroviruses respiratory syncytial virus next-generation sequencing |
| url | https://www.mdpi.com/2076-2607/11/11/2744 |
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